Crystal structure refinement with SHELXL

Crystal packing in three related disaccharides: precursors to heparan sulfate oligosaccharides

The three title compounds form part of a set of important precursor dissacharides which lead to novel therapeutics, in particular for Alzheimer's disease. All three crystallize as poorly diffracting crystals with one independent mol-ecule in the asymmetric unit. Two of them are isostructural: 4-meth-oxy-phenyl 4-O-[6-O-acetyl-2-azido-3-O-benzyl-2-de-oxy-4-O-(9-fluor-en-yl-methyl-oxycarbon-yl)-α-d-gluco-pyranos-yl]-2-O-benzoyl-3-O-benzyl-6-O-chloro-acetyl-α-l-ido-pyran-oside, C59H56ClN3O16, (I), the ido-relative of a reported gluco-disaccharide [Gainsford et al., 2013 ▶). Acta Cryst. C69, 679-682] and 4-meth-oxy-phenyl 4-O-[6-O-acetyl-2-azido-3-O-benzyl-2-de-oxy-4-O-(9-fluorenyl-methyl-oxycarbon-yl)-α-d-gluco-pyranos-yl]-2-O-benzoyl-3-O-benzyl-6-O-meth-oxy-acetyl-α-l-ido-pyran-oside, C60H59N3O17, (II). Both exhibit similar conformational disorder of pendant groups. The third compound 4-meth-oxy-phenyl 4-O-[6-O-acetyl-2-azido-3,4-di-O-benzyl-2-de-oxy-α-d-gluco-pyranos-yl]-2-O-benzoyl-3-O-benzyl-6-O-meth-oxy-oacetyl-β-d-gluco-pyran-oside, C52H55N3O15, (III), illustrates that a slightly larger set of weak inter-molecular inter-actions can result in a less disordered mol-ecular arrangement. The mol-ecules are bound by weak C-H⋯O(ether) hydrogen bonds in (I) and (II), augmented by C-H⋯π inter-actions in (III). The absolute configurations were determined, although at varying levels of significance from the limited observed data.

Crystal structure of 4-(tri-methyl-germ-yl)benzoic acid

The title compound, [Ge(CH3)3(C7H5O2)], was obtained as a by-product in the synthesis of the corresponding aldehyde. Two slightly different mol-ecules are present in the asymmetric unit. In both mol-ecules, the geometry of the aromatic ring plane is distorted by varying intensities. Additionally, the Ge atoms deviate from the mean aromatic ring planes. Whereas the distance of the Ge atom to the ring plane is only 0.101 (4) Å in the first mol-ecule, this distance is increased to 0.210 (4) Å in the second. In the crystal structure, centrosymmetric O-H⋯O hydrogen-bonded dimers are formed. The title compound is isostructural with the Si analogue [Haberecht et al. (2004 ▶). Acta Cryst. E60, o329-0330].

Crystal structure of aqua-[(E)-N'-(5-bromo-2-oxido-benzyl-idene-κO)benzohydrazidato-κ(2) O,N']dioxidomolybdenum(VI) di-methyl-formamide monosolvate

The title compound, [Mo(C14H9BrN2O2)O2(H2O)]·C3H7NO, has a distorted octa-hedral geometry around the Mo atom, with the two terminal oxide groups lying cis to each other. The two aromatic rings present in the mol-ecule are almost coplanar, forming a dihedral angle of 1.4 (2)°. The five-membered ring involving the metal atom is puckered, with an amplitude Q = 0.358 (2) Å and ϕ = 204.1 (6)°. In the crystal, pairs of inversion-related mol-ecules are linked by O-H⋯N hydrogen bonds. An O-H⋯O hydrogen bond connects the water ligand to the di-methyl-formamide solvent mol-ecule. The crystal packing also features π-π [centroid-centroid distance of 3.688 (2) Å] and C-H⋯O inter-actions.

Crystal structure of N,N'-[(thio-phene-2,5-di-yl)bis-(methanylyl-idene)]di-p-toluidine

The title compound, C20H18N2S, was synthesized by the condensation reaction between p-tolu-idine and thio-phene-2,5-dicarboxaldehye in refluxing toluene with p-toluene-sulfonic acid added as catalyst. The mol-ecule lies on a twofold rotation axis and adopts an E orientation with respect to the azomethine bonds. The dihedral angle between the unqiue benzene ring and the least-squares plane [maximum deviation = 0.0145 (14) Å] containing the azomethine and thio-phene groups is 32.31 (6)°.

Crystal structure of 4-amino-2,6-di-chloro-phenol

The title compound, C6H5Cl2NO, has a single planar mol-ecule in the asymmetric unit with the non-H atoms possessing a mean deviation from planarity of 0.020 Å. In the crystal, O-H⋯N hydrogen bonds lead to the formation of infinite chains along [101] which are further linked by N-H⋯O hydrogen bonds, forming (010) sheets.

Crystal structure of 4-chloro-2-{(E)-[(3,4-di-methyl-phen-yl)imino]-meth-yl}phenol

In the title compound, C15H14ClNO, which is isostructural with its bromo analogue [Tahir et al. (2012 ▶). Acta Cryst., E68, o2730], the dihedral angle between the planes of the aromatic rings is 2.71 (7)° and an intra-molecular O-H⋯N hydrogen bond closes an S(6) ring. In the crystal, extremely weak C-H⋯π inter-actions link the mol-ecules into a three-dimensional network.

Crystal structure of catena-poly[[chlorido-(4,4'-dimethyl-2,2'-bi-pyridine-κ(2) N,N')copper(II)]-μ-chlorido]

The title compound, [CuCl2(C12H12N2)] n , was obtained via a DMSO-mediated dehydration of Cu(4,4'-dimethyl-2,2'-bi-pyridine)-copper(II)·0.25H2O. The central Cu(II) atom is coordinated in a distorted trigonal-bipyramidal geometry by two N atoms of a chelating 4,4'-dimethyl-2,2'-bi-pyridine ligand [average Cu-N = 2.03 (3) Å] and three Cl atoms, one terminal with a short Cu-Cl bond of 2.2506 (10) Å, and two symmetry-equivalent and bridging bonds. The bridging Cl atom links the Cu(II) ions into chains parallel to [001] via one medium and one long Cu-Cl bond [2.3320 (10) and 2.5623 (9) Å]. The structure displays both inter- and intra-molecular C-H⋯Cl hydrogen bonding.

Crystal structure of 3β-acet-oxy-androsta-5,16-dien-17-yl tri-fluoro-methane-sulfon-ate

The title compound, C22H29F3O5S [systematic name: (3S,8R,9S,10R,13S,14S)-10,13-dimethyl-17-(tri-fluoro-methylsulfon-yloxy)-2,3,4,7,8,9,10,11,12,13,14,15-dodeca-hydro-1H-cyclo-penta-[a]phenanthren-3-yl acetate], contains a fused four-ring steroidal system. Rings A and C adopt a chair conformation, while rings B and D adopt half-chair and envelope (with the fused CH atom as the flap) conformations, respectively. In the crystal, weak inter-molecular C-H⋯O inter-actions link the mol-ecules into layers parallel to the ab plane.

Crystal structure of 1,13,14-tri-aza-dibenz[a,j]anthracene 1,1,2,2-tetra-chloro-ethane monosolvate

The asymmetric unit of the title compound, C19H11N3·C2H2Cl4, consists of one half-mol-ecule of 1,13,14-tri-aza-dibenz[a,j]anthracene (dibenzo[c,h]-1.9,10-anthyridine, dbanth) and one half of 1,1,2,2-tetra-chloro-ethane (TCE), both of which are located on a crystallographic twofold rotation axis. The dihedral angle between the planes of the terminal benzene rings in dbanth is 3.59 (7)° owing to the steric repulsion between the H atoms in the two benzo groups and the H atom in the central pyridine ring of the anthridine skeleton. In the crystal, π-π inter-actions between pyridine rings [centroid-centroid distances = 3.568 (2) and 3.594 (2) Å] link the dbanth mol-ecules to form a one-dimensional columnar structure along the c axis. The dbanth and TCE mol-ecules are connected through weak bifurcated C-H⋯(N,N) hydrogen bonds.

Crystal structure of 4-meth-oxy-phenyl 2-oxo-2H-chromene-3-carboxyl-ate

In the title compound, C17H12O5, the dihedral angle between the planes of the coumarin ring system (r.m.s. deviation = 0.015 Å) and the benzene ring is 48.04 (10)°. The central CO2 group subtends a dihedral angle of 27.15 (11)° with the coumarin ring system and 74.86 (13)° with the benzene ring. In the crystal, mol-ecules are linked by C-H⋯O inter-actions, which generate a three-dimensional network. Very weak C-H⋯π inter-actions are also observed.

Crystal structure of di-benzyl-dimethyl-silane

In the title compound, C16H20Si, a geometry different from an ideal tetra-hedron can be observed at the Si atom. The bonds from Si to the benzylic C atoms [Si-C = 1.884 (1) and 1.883 (1) Å] are slightly elongated compared to the Si-Cmeth-yl bonds [Si-C = 1.856 (1) and 1.853 (1) Å]. The Cbenz-yl-Si-Cbenz-yl bond angle [C-Si-C = 107.60 (6)°] is decreased from the ideal tetra-hedral angle by 1.9°. These distortions can be explained easily by Bent's rule. In the crystal, mol-ecules inter-act only by van der Waals forces.

Crystal structure of 1-[(6-chloro-pyridin-3-yl)sulfon-yl]-1,2,3,4-tetra-hydro-quinoline

The tetra-hydro-pyridine ring of the quinoline system in the title compound, C14H13ClN2O2S, adopts a half-chair conformation with the bond-angle sum at the N atom being 350.0°. The dihedral angle between the least-squares planes of the two aromatic rings is 50.13 (11)°. In the crystal, inversion dimers linked by pairs of C-H⋯O hydrogen bonds generate R 2 (2)(10) loops. Additional inter-molecular C-H⋯O hydrogen bonds generate C(7) chains along [100].

Crystal structure of (4Z)-4-[(2E)-3-(4-chloro-phen-yl)-1-hy-droxy-prop-2-en-1-yl-idene]-5-methyl-2-phenyl-1H-pyrazol-5(4H)-one

In the the asymmetric unit of the title compound, C19H15ClN2O2, there are two symmetry-independent mol-ecules, which adopt similar conformations. The largest difference is observed in the dihedral angles between the phenyl and the pyrazole fragments [17.00 (12) and 23.42 (10)°]. A strong intra-molecular O-H⋯O hydrogen bond with the S (6) motif is observed in both mol-ecules. Pairs of π-π stacking inter-actions between the phenyl groups [centroid-centroid distances = 3.6627 (13) and 3.7156 (14) Å] assemble the mol-ecules into two types of centrosymmetric dimers. Weak C-H⋯O inter-actions connect mol-ecules into chains along the b axis.

Crystal structure of 3-methyl-5-tri-methyl-silyl-1H-pyrazole

The title compound, C7H14N2Si, crystallizes in a tetra-gonal space group and exists as an N-H⋯N hydrogen-bonded tetra-mer, formed around the crystallographic fourfold rotoinversion axis. The mol-ecular identity is clearly the 5-tri-methyl-silyl-3-methyl-1H-pyrazole tautomer and the structure is isomorphous with that of 5-tert-butyl-3-methyl-1H-pyrazole [Foces-Foces & Trofimenko (2001 ▶). Acta Cryst. E57, o32-o34].

A sterically congested cis-stilbene and its phosphonium salt precursor

Triphenyl(2,4,5-trimethoxybenzyl)phosphonium chloride is formed in solvent-free form by the reaction under anhydrous conditions between triphenylphosphane and 2,4,5-trimethoxybenzyl chloride, but when it is crystallized from a mixture of ethyl acetate and chloroform in the presence of air it forms a stoichiometric monohydrate, C28H28O3P(+)·Cl(-)·H2O, (I). The reactions between the anhydrous phosphonium salt and alkoxy-substituted benzaldehydes, using Wittig reactions in the presence of potassium tert-butoxide, provide a series of multiply substituted stilbenes, most of which were assigned the Z configuration on the basis of their NMR spectra. However, no such deduction could be made for the symmetrically substituted (Z)-2,2',4,4',5,5'-hexamethoxystilbene, C20H24O6, (II). Compound (II) does in fact have the Z configuration and the molecular geometry provides evidence for steric congestion around the central double bond; in particular, the central alkene fragment is nonplanar, with a C-C=C-C torsion angle of 7.8 (4)°. In hydrated salt (I), the chloride anions and water molecules are linked by O-H···Cl hydrogen bonds to form C2(1)(4) chains; each cation is linked by C-H···O hydrogen bonds to two different chains, so forming a sheet structure. There are no direction-specific intermolecular interactions in the structure of (II).

Crystal structures of (1,4,7,10-tetra-aza-cyclo-dodecane-κ(4) N)bis-(tri-cyano-methanido-κN)nickel and (1,4,7,10-tetra-aza-cyclo-dodecane-κ(4) N)(tri-cyano-methanido-κN)copper tri-cyano-methanide

The structures of two mononuclear transition-metal complexes with tri-cyano-methanide (tcm(-)) and 1,4,7,10-tetra-aza-cyclo-dodecane (cyclen) ligands, [Ni(C4N3)2(C8H20N4)], (I), and [Cu(C4N3)(C8H20N4)](C4N3), (II), are reported. In the neutral complex (I), the nickel cation is coordinated by one cyclen ligand and two monodentate N-bound tcm(-) anions in a distorted octa-hedral geometry. The tcm(-) ligands are mutually cis. The Cu(II) atom in (II) displays a distorted tetra-gonal-pyramidal geometry, with the four N-donor atoms of the cyclen ligand in the equatorial plane, and one tcm(-) anion bound through a single N atom in an axial site, forming a monocation. The second tcm(-) molecule acts as a counter-ion not directly coordinating to the copper cation. In both (I) and (II), extensive series of N-H⋯N and C-H⋯N hydrogen bonds generate three-dimensional network structures.

The structure of the first stable monosubstituted sulfur diimide

The title compound, 4-(4-methylphenyl)-1,3-diaza-2,4-dithiabuta-1,2-diene, C7H8N2S2, was the first example of a stable monosubstituted sulfur diimide to be documented [Jones (1988). PhD thesis, Imperial College, University of London, England]. Although a partial description of this structure was published previously, the full details are presented here. This allows a detailed comparison against the only other example of this system published to date, highlighting differences in bonding, conformation and packing.

Crystal structures of five (2-chloro-quinolin-3-yl)methyl ethers: supra-molecular assembly in one and two dimensions mediated by hydrogen bonding and π-π stacking

In the mol-ecules of the title compounds, methyl 5-bromo-2-[(2-chloro-quinolin-3-yl)meth-oxy]benzoate, C18H13BrClNO3, (I), methyl 5-bromo-2-[(2-chloro-6-methyl-quinolin-3-yl)meth-oxy]benzoate, C19H15BrClNO3, (II), methyl 2-[(2-chloro-6-methyl-quinolin-3-yl)meth-oxy]benzoate, C19H16ClNO3, (III), which crystallizes with Z' = 4 in space group P212121, and 2-chloro-3-[(naphthalen-1-yl-oxy)meth-yl]quinoline, C20H14ClNO, (IV), the non-H atoms are nearly coplanar, but in {5-[(2-chloro-quinolin-3-yl)meth-oxy]-4-(hy-droxy-meth-yl)-6-methyl-pyridin-3-yl}methanol, C18H17ClN2O3, (V), the planes of the quinoline unit and of the unfused pyridine ring are almost parallel, although not coplanar. The mol-ecules of (I) are linked by two independent π-π stacking inter-actions to form chains, but there are no hydrogen bonds present in the structure. In (II), the mol-ecules are weakly linked into chains by a single type of π-π stacking inter-action. In (III), three of the four independent mol-ecules are linked by π-π stacking inter-actions but the other mol-ecule does not participate in such inter-actions. Weak C-H⋯O hydrogen bonds link the mol-ecules into three types of chains, two of which contain just one type of independent mol-ecule while the third type of chain contains two types of mol-ecule. The mol-ecules of (IV) are linked into chains by a C-H⋯π(arene) hydrogen bond, but π-π stacking inter-actions are absent. In (V), there is an intra-molecular O-H⋯O hydrogen bond, and mol-ecules are linked into sheets by a combination of O-H⋯N hydrogen bonds and π-π stacking inter-actions.

Crystal structures of five 1-alkyl-4-aryl-1,2,4-triazol-1-ium halide salts

The asymmetric units for the salts 4-(4-fluoro-phen-yl)-1-isopropyl-1,2,4-triazol-1-ium iodide, C11H13FN3 (+)·I(-), (1), 1-isopropyl-4-(4-methyl-phen-yl)-1,2,4-triazol-1-ium iodide, C12H16N3 (+)·I(-), (2), 1-isopropyl-4-phenyl-1,2,4-triazol-1-ium iodide, C11H14N3 (+)·I(-), (3), and 1-methyl-4-phenyl-1,2,4-triazol-1-ium iodide, C9H10N3 (+)·I(-), (4), contain one cation and one iodide ion, whereas in 1-benzyl-4-phenyl-1,2,4-triazol-1-ium bromide monohydrate, C15H14N3 (+)·Br(-)·H2O, (5), there is an additional single water mol-ecule. There is a predominant C-H⋯X(halide) inter-action for all salts, resulting in a two-dimensional extended sheet network between the triazolium cation and the halide ions. For salts with para-substitution on the aryl ring, there is an additional π-anion inter-action between a triazolium carbon and iodide displayed by the layers. For salts without the para-substitution on the aryl ring, the π-π inter-actions are between the triazolium and aryl rings. The melting points of these salts agree with the predicted substituent inductive effects.

Crystal structure of an unknown solvate of bis-(tetra-n-butyl-ammonium) [N,N'-(4-tri-fluoro-methyl-1,2-phenyl-ene)bis-(oxamato)-κ(4) O,N,N',O']nickelate(II)

In the title compound, [N(C4H9)4]2[Ni(C11H3F3N2O6)] or [N(n-Bu)4]2[Ni(topbo)] [n-Bu = n-butyl and topbo = 4-tri-fluoro-methyl-1,2-phenyl-enebis(oxamate)], the Ni(2+) cation is coordinated by two deprotonated amido N atoms and two carboxyl-ate O atoms, setting up a slightly distorted square-planar coordination environment. The [Ni(topbo](2-) anion lies on a twofold rotation axis. Due to an incompatibility with the point-group symmetry of the complete mol-ecule, orientational disorder of the CF3 group is observed. The tetra-hedral ammonium cations and the anion are linked by weak inter-molecular C-H⋯O and C-H⋯F hydrogen-bonding inter-actions into a three-dimensional network. A region of electron density was treated with the SQUEEZE procedure in PLATON [Spek (2015). Acta Cryst. C71, 9-18] following unsuccessful attempts to model it as plausible solvent mol-ecule(s). The given chemical formula and other crystal data do not take into account the unknown solvent mol-ecule.

Crystal structure of (E)-4-ethyl-2-(4-meth-oxy-benzyl-idene)-3,4-di-hydro-naphthalen-1(2H)-one

In the title compound, C20H20O2, the exocyclic C=C double bond has an E conformation. The ethyl substituent on the cyclo-hexa-none ring is in an axial orientation. The cyclo-hexa-none ring adopts a screw-boat conformation, with the methyl-ene C atom and the C atom bearing the 4-meth-oxy-benzyl-idene group displaced from the other atoms by 0.812 (1) and 0.334 (1) Å, respectively. The dihedral angle between the planes of the benzene rings is 42.20 (8)°. In the crystal, no directional inter-actions beyond van der Waals contacts are observed.

The exopolyhedral ligand orientation (ELO) in 3-(nitrato-κO)-3,3-bis(triphenylphosphane-κP)-3-rhoda-1,2-dicarba-closo-dodecaborane(11) dichloromethane 2.2-solvate

In the title compound, [Rh(C2H11B9)(NO3)(C18H15P)2]·2.2CH2Cl2, studied as a 2.2-solvate of what was assumed to be dichloromethane, the nitrate ligand liesciswith respect to both cage C atoms. Accordingly, the compound displays a pronounced preferred exopolyhedral ligand orientation (ELO) which is traced to both the greatertransinfluence of the cage B over the cage C atoms and the greatertransinfluence of the triphenylphosphane ligands over the nitrate ligand. The overall molecular architecture therefore agrees with that of a number of similar 3-L-3,3-L′2-3,1,2-closo-MC2B9H11species in the literature.

Isolation of 3-amino-4-nitro-benzyl acetate: evidence of an undisclosed impurity in 5-amino-2-nitro-benzoic acid

Yellow crystals of the title compound 3-amino-4-nitro-benzyl acetate, C9H10N2O4, were isolated from the reaction of acetic anhydride with (5-amino-2-nitro-phen-yl)methanol, prepared from reduction of commerically available 5-amino-2-nitro-benzoic acid with borane-THF. The mol-ecule is essentially planar (r.m.s. deviation = 0.028 Å). The mol-ecules are linked by inter-molecular N-H⋯O hydrogen-bonding inter-actions between the carbonyl and amine groups, forming a zigzag chain along the b-axis direction lying in a plane parallel to (-102). The chains are stacked along the c axis by π-π inter-actions [centroid-centroid distances = 3.6240 (3) and 3.5855 (4) Å]. A strong intra-molecular N-H⋯O hydrogen-bonding inter-action is observed between the nitro group and the amine group [2.660 (2) Å].

Crystal structure of 2,2-dimethyl-N-(5-methyl-pyridin-2-yl)propanamide

There are two mol-ecules in the asymmetric unit of the title compound, C11H16N2O. The pyridine rings and amide groups overlap almost perfectly (r.m.s. overlay fit = 0.053 Å), but the tertiary butyl groups have different orientations: in one mol-ecule, one of the methyl C atoms is syn to the amide O atom [O-C-C-C = -0.8 (3)°] and in the other the equivalent torsion angle is 31.0 (2)°. In the crystal, the two independent mol-ecules are linked by a pair of N-H⋯N hydrogen bonds in the form of an R 2 (2)(8) loop to form a dimer. A C-H⋯O inter-action connects the dimers into [100] chains.

Crystal structure of (4Z)-4-[(2E)-1-hydroxy-3-(naphthalen-2-yl)prop-2-en-1-yl-idene]-3-methyl-1-phenyl-1H-pyrazol-5(4H)-one

In the title compound, C23H18N2O2, the pyrazole ring subtends dihedral angles of 2.01 (13) and 1.55 (10)° with the pendant benzene ring and the naphthalene ring system, respectively. The mol-ecule is almost planar (r.m.s. deviation for the 27 non-H atoms = 0.025 Å) and intra-molecular O-H⋯O and C-H⋯O hydrogen bonds both close S(6) loops. In the crystal, very weak aromatic π-π stacking inter-actions between the benzene and the pyrazole rings, with centroid-centroid distances of 3.8913 (14) and 3.9285 (15) Å, are observed.

Crystal structure of (4E)-4-(8-meth-oxy-2H-chromen-2-yl-idene)-3-methyl-1-phenyl-1H-pyrazol-5(4H)-one

In the title compound, C20H16N2O3, the phenyl substituent attached to the pyrazole ring makes a dihedral angle of 4.87 (7)° with the rest of the mol-ecule. In the crystal, mol-ecules are connected into inversion dimers of the R 2 (2)(14) type by pairs of C-H⋯O inter-actions. π-π inter-actions exist between the benzene and pyrazole rings at a distance of 3.701 (1) Å. Similarly, π-π inter-actions are present at a centroid-centroid distance of 3.601 (1) Å between the oxygen-containing heterocyclic ring and meth-oxy substituted aromatic ring of a neighbouring mol-ecule. Additional C-H⋯π and C=O⋯π inter-actions are also observed.

Crystal structure of tetra-aqua-bis(3,5-di-amino-4H-1,2,4-triazol-1-ium)cobalt(II) bis-[bis-(pyridine-2,6-di-carboxyl-ato)cobaltate(II)] dihydrate

The asymmetric unit of the title compound, [Co(C2H6N5)2(H2O)4][Co(C7H3NO4)2]2·2H2O, features 1.5 Co(II) ions (one anionic complex and one half cationic complex) and one water mol-ecule. In the cationic complex, the Co(II) atom is located on an inversion centre and is coordinated by two triazolium cations and four water mol-ecules, adopting an octa-hedral geometry where the N atoms of the two triazolium cations occupy the axial positions and the O atoms of the four water mol-ecules the equatorial positions. The two triazole ligands are parallel offset (with a distance of 1.38 Å between their planes). In the anionic complex, the Co(II) ion is six-coordinated by two N and four O atoms of the two pyridine-2,6-di-carboxyl-ate anions, exhibiting a slightly distorted octa-hedral coordination geometry in which the mean plane of the two pyridine-2,6-di-carboxyl-ate anions are almost perpendicular to each other, making a dihedral angle of 85.87 (2)°. In the crystal, mol-ecules are linked into a three-dimensional network via C-H⋯O, C-H⋯N, O-H⋯O and N-H⋯O hydrogen bonds.

Crystal structure of (4Z)-4-[(2E)-3-(2-chloro-phen-yl)-1-hy-droxy-prop-2-en-1-yl-idene]-3-methyl-1-phenyl-1H-pyrazol-5(4H)-one

In the title compound, C19H15ClN2O2, the pyrazole ring is almost planar (r.m.s. deviation = 0.002 Å) and subtends dihedral angles of 5.31 (16) and 1.86 (16)° with the phenyl and chloro-benzene rings, respectively. An intra-molecular O-H⋯O hydrogen bond closes an S(6) ring and a short C-H⋯O contact is also observed. In the crystal, mol-ecules are linked by weak C-H⋯O inter-actions to generate (001) sheets. Weak aromatic π-π inter-actions between the chloro-benzene and pyrazole rings, with a centroid-centroid distance of 3.7956 (17) Å are also observed.

Redetermined crystal structure of β-dl-me-thio-nine at 320 K

The structure of β-dl-me-thio-nine, C5H11NO2S, in the space group C2/c, is here confirmed to be fully ordered all the way up to the phase transition at approximately 326 K, where displacive sliding of mol-ecular bilayers gives the disordered P21/c α form [data at 340 K; Görbitz (2014). Acta Cryst. E70, 341-343]. The geometry of hydrogen bonds in LD-LD hydrogen-bonding patterns [Görbitz et al. (2009). Acta Cryst. B65, 393-400] at the hydro-philic core of each mol-ecular bilayer are virtually unperturbed by the phase shift, but the C-C-S-C torsion angle of the side chain changes from trans at 320 K to gauche+ for the major conformation at 340 K.

Crystal structure of bis-[μ-bis-(di-phenyl-phosphan-yl)methane-κ(2) P:P']-μ-chlorido-chlorido-1κCl-(1-phenyl-thio-urea-2κS)disilver aceto-nitrile hemisolvate

In the dinuclear title complex, [Ag2Cl2(C7H8N2S)(C25H22P2)2]·0.5CH3CN, each Ag(I) ion displays a distorted tetra-hedral coordination geometry with two P atoms from two bis-(di-phenyl-phosphan-yl)methane (dppm) ligands, one bridging chloride ion, one terminal chloride ion and one terminal S atom from the N,N'-phenyl-thio-urea (ptu) ligand. The dppm ligands and the bridging chloride ion force the two Ag atoms into close proximity, with a short Ag⋯Ag separation of 3.2064 (2) Å. In the crystal, complex mol-ecules are linked by N-H⋯Cl hydrogen bonds forming a dimer. The dimers are linked via weak C- H⋯Cl hydrogen bonds forming a two-dimensional supra-molecular architecture in the yz plane. In addition, an intra-molecular N-H⋯Cl hydrogen bond is observed.

1-{[(E)-(4-{[(2Z)-2,3-Di-hydro-1,3-thia-zol-2-yl-idene]sulfamo-yl}phen-yl)iminium-yl]meth-yl}naphthalen-2-olate

In the title zwitterionic compound, C20H15N3O3S2, the 2-hy-droxy-naphthalene-1-carbaldehyde group A, the anilinic unit B and the 1,3-thia-zol-2(3H)-imine group C are each approximately planar with r.m.s. deviation of 0.0721, 0.0412 and 0.0125 Å, respectively. The dihedral angles between A/B, A/C and B/C are 24.70 (10), 79.97 (7) and 83.14 (6)°, respectively. There is an intra-molecular S(6) motif involving the imine N-H and the naphtho-late O atom. In the crystal, inversion-related mol-ecules form dimers as a result of N-H⋯N and N-H⋯O hydrogen bonds with R 2 (2)(8) and R 1 (2)(4) motifs, respectively. Weak π-π inter-actions between the benzene and naphthyl rings of inversion-related mol-ecules have ring centroid-centroid distances of 3.638 (2) and 4.041 (2) Å. A C-H⋯π inter-action occurs between the thia-zol ring and the benzene ring of an adjacent mol-ecule.

Crystal structure of trans-bis-(ethane-1,2-diamine-κ(2) N,N')bis-(thio-cyanato-κN)chromium(III) perchlorate from synchrotron data

The structure of the title compound, [Cr(NCS)2(C2H8N2)2]ClO4, has been determined from synchroton data. The asymmetric unit consists of one half of a centrosymmetric Cr(III) complex cation and half of a perchlorate anion with the Cl atom on a twofold rotation axis. The Cr(III) ion is coordinated by the four N atoms of two ethane-1,2-di-amine (en) ligands in the equatorial plane and two N-bound thio-cyanate (NCS(-)) anions in a trans-axial arrangement, displaying a slightly distorted octa-hedral geometry with crystallographic inversion symmetry. The Cr-N(en) bond lengths are in the range 2.053 (16)-2.09 (2) Å, while the Cr-N(thio-cyanate) bond length is 1.983 (2) Å. The five-membered en rings are disordered over two sites, with occupancy ratios of 0.522 (16):0.478 (16). Each ClO4 (-) anion is disordered over two sites with equal occupancy. The crystal structure is stabilized by inter-molecular hydrogen bonds involving the en NH2 groups as donors and perchlorate O and thio-cyanate S atoms as acceptors.

Crystal structure of benzyl-tri-phenyl-phospho-nium chloride monohydrate

The title compound, Ph3(PhCH2)P(+)·Cl(-)·H2O, was obtained unintentionally as the product of an attempted synthesis of a silver di-thio-carbamate complex using benzyl-tri-phenyl-phospho-nium as the counter-ion. The asymmetric unit consists of a phospho-nium cation and a chloride anion, and a water mol-ecule of crystallization. In the crystal, the chloride ion is linked to the water mol-ecule by an O-H⋯Cl hydrogen bond. The three units are further linked via C-H⋯Cl and C-H⋯O hydrogen bonds and C-H⋯ π inter-actions, forming a three-dimensional structure.

Crystal structure of 3-(3,4-di-methyl-anilino)-2-benzo-furan-1(3H)-one

In the title compound, C16H15NO2, the 2-benzo-furan-1(3H)-one and 3,4-di-methyl-aniline fragments are oriented with a dihedral angle of 89.12 (5)°. N-H⋯O hydrogen-bond inter-actions join mol-ecules into C(6) chains propagating along the a axis. In addition, there are π-π stacking inter-actions between the 2-benzo-furan-one benzene rings [centroid-centroid dis-tance = 3.7870 (13) Å] and C-H⋯π inter-actions between one of the methyl groups and the 3,4-di-methyl-aniline benzene ring.

Crystal structure of poly[[μ-4-(hy-droxy-meth-yl)pyridine-κ(2) N:O][4-(hy-droxy-meth-yl)pyridine-κN](μ-thio-cyanato-κ(2) N:S)(thio-cyanato-κN)cadmium]

The crystal structure of the title compound, [Cd(NCS)2(C6H7NO)2] n is made up of Cd(2+) cations that are coordinated by three thio-cyanate ligands and three 4-(hy-droxy-meth-yl)pyridine ligands within distorted N4OS octa-hedra. The asymmetric unit consists of one Cd(2+) cation, two thio-cyanate anions and two 4-(hy-droxy-meth-yl)pyridine ligands in general positions. Two Cd(2+) cations are linked by two μ-1,3 N- and S-bonding thio-ycanate anions into dimers which are further linked into branched chains along [100] by two μ-1,6 N- and O-bonding 4-(hy-droxy-meth-yl)pyridine ligands. One additional N-bonded 4-(hy-droxy-meth-yl)pyridine ligand and one additional N-bonded thio-cyanate anion are only terminally bonded to the metal cation. Inter-chain O-H⋯S hydrogen bonds between the hy-droxy H atoms and one of the thio-cyanate S atoms connect the chains into a three-dimensional network.

Crystal structure of 4-amino-3-(3-methyl-5-phenyl-1H-pyrazol-1-yl)-1H-1,2,4-triazole-5(4H)-thione

In the title compound, C12H12N6S, the dihedral angles between the central pyrazole ring and the pendant triazole and benzene rings are 68.01 (4) and 59.83 (9)°, respectively. In the crystal, mol-ecules are linked by N-H⋯N and N-H⋯S hydrogen bonds, generating (10-1) sheets.

Crystal structures of coordination polymers from CaI2 and proline

Completing our reports concerning the reaction products from calcium halides and the amino acid proline, two different solids were found for the reaction of l- and dl-proline with CaI2. The enanti-opure amino acid yields the one-dimensional coordination polymer catena-poly[[aqua-μ3-l-proline-tetra-μ2-l-proline-dicalcium] tetra-iodide 1.7-hydrate], {[Ca2(C5H9NO2)5(H2O)]I4·1.7H2O} n , (1), with two independent Ca(2+) cations in characteristic seven- and eightfold coordination. Five symmetry-independent zwitterionic l-proline mol-ecules bridge the metal sites into a cationic polymer. Racemic proline forms with Ca(2+) cations heterochiral chains of the one-dimensional polymer catena-poly[[di-aquadi-μ2-dl-proline-calcium] diiodide], {[Ca(C5H9NO2)2(H2O)2]I2} n , (2). The centrosymmetric structure is built by one Ca(2+) cation that is bridged towards its symmetry equivalents by two zwitterionic proline mol-ecules. In both structures, the iodide ions remain non-coordinating and hydrogen bonds are formed between these counter-anions, the amino groups, coordinating and co-crystallized water mol-ecules. While the overall composition of (1) and (2) is in line with other structures from calcium halides and amino acids, the diversity of the carboxyl-ate coordination geometry is quite surprising.

Crystal structure of μ-cyanido-1:2κ(2) N:C-dicyanido-1κC,2κC-bis-(quinolin-8-amine-1κ(2) N,N')-2-silver(I)-1-silver(II): rare occurrence of a mixed-valence Ag(I,II) compound

The title dinuclear complex, [Ag2(CN)3(C9H8N2)2], may be considered as an Ag(II) compound with the corresponding metal site coordinated by two bidentate quinolin-8-amine mol-ecules, one cyanide group and one dicyanidoargentate(I) anion, [Ag(CN)2](-). Since this latter ligand contains an Ag(I) atom, the complex should be a class 1 or class 2 mixed-valence compound, according to the Robin-Day classification. The Ag(II) atom is six-coordinated in a highly distorted octa-hedral geometry, while the Ag(I) atom displays the expected linear geometry. In the crystal, the amino groups of the quinolin-8-amine ligands form N-H⋯N hydrogen bonds with the N atoms of the non-bridging cyanide ligands, forming a two-dimensional network parallel to (102). The terminal cyanide ligands are not engaged in polymeric bonds and the title compound is an authentic mol-ecular complex. The title mol-ecule is thus a rare example of a stable Ag(I,II) complex, and the first mixed-valence Ag(I,II) mol-ecular complex characterized by X-ray diffraction.

Crystal structure of penta-potassium di-hydrogen nona-vanadato(V)platinate(IV) nona-hydrate

The title compound, K5[H2PtV9O28]·9H2O, containing the nona-vanado-platinate(IV) polyanion, was obtained by hydro-thermal reaction at pH = 4.2. The polyanion has approximate mm2 (C 2v ) symmetry. The two platinum-bound μ2-O atoms are protonated in the polyanion. The heteropolyanions form inversion-generated dimers, {[H2PtV9O28]2}(10-), held together by μ2-O-H⋯μ2-O and μ2-O-H⋯μ3-O hydrogen bonds. All K(+) cations are located on general positions of the space group P-1.

DSR: enhanced modelling and refinement of disordered structures with SHELXL

One of the remaining challenges in single-crystal structure refinement is the proper description of disorder in crystal structures. This paper describes a computer program that performs semi-automatic modelling of disordered moieties in SHELXL [Sheldrick (2015 ▶). Acta Cryst. C71, 3-8.]. The new program contains a database that includes molecular fragments and their corresponding stereochemical restraints, and a placement procedure to place these fragments on the desired position in the unit cell. The program is also suitable for speeding up model building of well ordered crystal structures.

Crystal structure of methyl (2Z)-3-(4-chloro-phen-yl)-2-[(3-methyl-1H-indol-1-yl)meth-yl]prop-2-enoate

In the title indole derivative, C20H18ClNO2, the chloro-phenyl ring is almost perpendicular to the indole moiety, making a dihedral angle of 87.6 (1)°. The mol-ecular packing is stabilized by C-H⋯π inter-actions, which form a C(9) chain motif along [10-1]. In addition, there are weak π-π inter-actions [centroid-centroid distance 3.851 (1) Å] between the chains, involving inversion-related chloro-phenyl rings.

Crystal structure of 5-(4-methyl-phen-yl)-3-[(E)-2-(4-methyl-phen-yl)ethen-yl]cyclo-hex-2-en-1-one

In the title compound, C22H22O, the dihedral angle between the planes of the benzene rings is 53.55 (7)°. Weak C-H⋯O inter-actions help to direct the packing, forming sheets lying parallel to (020).

Crystal structure of 4-benzamido-2-hy-droxy-benzoic acid

In the title compound, C14H11NO4, the dihedral angle between the mean planes of the aromatic rings is 3.96 (12)° and an intra-molecular O-H⋯O hydrogen bond closes an S(6) ring. A short intra-molecular C-H⋯O contact is also seen. In the crystal, carb-oxy-lic acid inversion dimers linked by pairs of O-H⋯O hydrogen bonds generate R 2 (2)(8) loops. Conversely, the N-H group does not form a hydrogen bond. Aromatic π-π inter-actions exist at a centroid-centroid distance of 3.8423 (15) Å between the benzene rings. An extremely weak C-H⋯π inter-action also is present.

Crystal structure of N-carbamo-thioyl-2-methyl-benzamide

There are two mol-ecules in the asymmetric unit of the title compound, C9H10N2OS. In one, the dihedral angle between the aromatic ring and the carbamo-thioyl group is 52.31 (7)° and in the other it is 36.16 (6)°. Each mol-ecule features an intra-molecular N-H⋯O hydrogen bond, which generates an S(6) ring and the O and S atoms have an anti disposition. In the crystal, mol-ecules are linked by N-H⋯S and N-H⋯O hydrogen bonds, generating separate [130] and [1-30] infinite chains. Weak C-H⋯O and C-H⋯S inter-actions are also observed.

Crystal structure of (E)-undec-2-enoic acid

In the mol-ecule of the title low-melting α,β-unsaturated carb-oxy-lic acid, C11H20O2, the least-squares mean line through the octyl chain forms an angle of 60.10 (13)° with the normal to plane of the acrylic acid fragment (r.m.s. deviation = 0.008 Å). In the crystal, centrosymmetrically related mol-ecules are linked by pairs of O-H⋯O hydrogen bonds into dimers, forming layers parallel to the (041) plane.

Two reversible enantiotropic phase transitions in a pentacoordinate silicon complex with an O,N,O'-tridentate valinate ligand

Dimethyl[N-(4-oxidopent-3-en-2-ylidene)valinato-κ(3)O,N,O']silicon(IV), C12H21NO3Si, (II), crystallizes in the orthorhombic space group P2₁2₁2₁. The chiral compound undergoes two sharp enantiotropic phase transitions upon cooling. The first transformation occurs at 163 K to yield a unit cell with one axis having double length. This intermediate-temperature form has the monoclinic space group P2₁. The second transition takes place at 142 K and converts the single crystal into the low-temperature form in the orthorhombic space group P2₁2₁2₁. This transition proceeds under tripling of the a axis of the high-temperature form. Both phase transitions are fully reversible and correspond to order-disorder transitions of the isopropyl group of the valine unit in the ligand backbone. The phase transitions presented here raise questions, since they do not fit into the rules of group-subgroup relationships.

A structural study of (1RS,2SR,3RS,4SR,5RS)-2,4-dibenzoyl-1,3,5-triphenylcyclohexan-1-ol chloroform hemisolvate and (1RS,2SR,3RS,4SR,5RS)-2,4-dibenzoyl-1-phenyl-3,5-bis(2-methoxyphenyl)cyclohexan-1-ol

(1RS,2SR,3RS,4SR,5RS)-2,4-Dibenzoyl-1,3,5-triphenylcyclohexan-1-ol or (4-hydroxy-2,4,6-triphenylcyclohexane-1,3-diyl)bis(phenylmethanone), C38H32O3, (1), is formed as a by-product in the NaOH-catalyzed synthesis of 1,3,5-triphenylpentane-1,5-dione from acetophenone and benzaldehyde. Single crystals of the chloroform hemisolvate, C38H32O3·0.5CHCl3, were grown from chloroform. The structure has triclinic (P1) symmetry. One diastereomer [as a pair of (1RS,2SR,3RS,4SR,5RS)-enantiomers] of (1) has been found in the crystal structure and confirmed by NMR studies. The dichoromethane hemisolvate has been reported previously [Zhang et al. (2007). Acta Cryst. E63, o4652]. (1RS,2SR,3RS,4SR,5RS)-2,4-Dibenzoyl-3,5-bis(2-methoxyphenyl)-1-phenylcyclohexan-1-ol or [4-hydroxy-2,6-bis(2-methoxyphenyl)-4-phenylcyclohexane-1,3-diyl]bis(phenylmethanone), C40H36O5, (2), is also formed as a by-product, under the same conditions, from acetophenone and 2-methoxybenzaldehyde. Crystals of (2) have been grown from chloroform. The structure has orthorhombic (Pca2₁) symmetry. A diastereomer of (2) possesses the same configuration as (1). In both structures, the cyclohexane ring adopts a chair conformation with all bulky groups (benzoyl, phenyl and 2-methoxyphenyl) in equatorial positions. The molecules of (1) and (2) both display one intramolecular O-H···O hydrogen bond.