(9E)-9-benzylidene-2-methylsulfanyl-5-phenyl-6,7,8,9-tetrahydropyrimido[4,5-b]quinolin-4(3H)-one: a hydrogen-bonded R2(2)(8) dimer.

In the molecule of the title compound, C25H21N3OS, which was prepared by mild oxidation of the corresponding 5,6,7,8,9,10-hexahydro analogue, the fused carbocyclic ring adopts an envelope conformation. Pairs of molecules are linked into cyclic centrosymmetric dimers by pairs of inversion-related N-H···O hydrogen bonds.

(E)-3-tert-butyl-4-(4-chlorobenzyl)-N-(4-chlorobenzylidene)-1-phenyl-1H-pyrazol-5-amine: sheets built from π-stacked hydrogen-bonded dimers.

The title compound, C27H25Cl2N3, is an unexpected but high-yield product from the microwave-mediated reaction between 3-tert-butyl-N-4-chlorobenzyl-1-phenyl-1H-pyrazol-5-amine and 4-chlorobenzaldehyde. Inversion-related pairs of molecules are linked by C-H···π(arene) hydrogen bonds to form cyclic centrosymmetric dimers, and dimers of this type are linked into sheets by two independent π-π stacking interactions.

5,5'-Methylenebis[6-amino-3-methyl-2-methylsulfanylpyrimidin-4(3H)-one]: an unusual molecular geometry within a hydrogen-bonded molecular ribbon.

The molecules of the title compound, C13H18N6O2S2, lie across twofold rotation axes in the space group C2/c. Although the pyrimidine ring is effectively planar, the bridging methylene C atom is displaced from the plane of the pyrimidine ring by 0.213 (2) Å, while the C-C-C angle at the bridging C atom is 120.3 (2)°. The molecule contains two symmetry-related N-H···O hydrogen bonds, generating S(8) motifs, and intermoecular N-H···O hydrogen bonds link the molecules into a ribbon of edge-fused rings.

3,3'-[(1RS,3SR)-2-oxocyclohexane-1,3-diyl]bis[(3RS,3'SR)-3-hydroxyindolin-2-one] dihydrate: organic layers of R2(2)(8), R2(2)(16) and R6(6)(40) rings linked by tetrameric water aggregates.

The organic component of the title compound, C22H20N2O5·2H2O, exhibits approximate but noncrystallographic mirror symmetry. The molecules of the organic component are linked by a combination of one O-H...O hydrogen bond and two N-H···O hydrogen bonds to form sheets containing R2(2)(8), R2(2)(16) and R6(6)(40) rings. These sheets are linked into a continuous three-dimensional framework structure by cyclic centrosymmetric R4(2)(8) water tetramers. Comparisons are made with some simpler analogues.

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

In the title compound, C31H29N3O2, the reduced pyridine ring adopts a conformation intermediate between the envelope and half-chair forms. The aryl rings of the benzyl and phenyl substituents are nearly parallel and overlap, indicative of an intramolecular π-π stacking interaction. A combination of two C-H∙∙∙O hydrogen bonds and one C-H∙∙∙N hydrogen bond links the molecules into a bilayer having tert-butyl groups on both faces.

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

In the molecules of both methyl (1RS,3SR,3aRS,6aSR)-1-methyl-3-(3-methyl-1-phenyl-1H-pyrazol-4-yl)-4,6-dioxo-5-phenyloctahydropyrrolo[3,4-c]pyrrole-1-carboxylate, C25H24N4O4, (I), and methyl (1RS,3SR,3aRS,6aSR)-5-(4-chlorophenyl)-1-methyl-3-(3-methyl-1-phenyl-1H-pyrazol-4-yl)-4,6-dioxooctahydropyrrolo[3,4-c]pyrrole-1-carboxylate, C25H23ClN4O4, (II), the two rings of the pyrrolopyrrole fragment are both nonplanar, with conformations close to half-chair forms. The overall conformations of the molecules of (I) and (II) are very similar, apart from the orientation of the ester function. The molecules of (I) are linked into sheets by a combination of an N-H∙∙∙π(pyrrole) hydrogen bond and three independent C-H∙∙∙O hydrogen bonds. The molecules of (II) are also linked into sheets, which are generated by a combination of an N-H∙∙∙N hydrogen bond and two independent C-H∙∙∙O hydrogen bonds, weakly augmented by a C-H∙∙∙π(arene) hydrogen bond.

A hydrogen-bonded tetramer in (2RS,4SR)-7-bromo-2-(2-methylphenyl)-2,3,4,5-tetrahydro-1H-naphtho[1,2-b]azepin-4-ol and a three-dimensional hydrogen-bonded framework in (2RS,4SR)-2-(3-methylthiophen-2-yl)-2,3,4,5-tetrahydro-1H-naphtho[1,2-b]azepin-4-ol.

(2RS,4SR)-7-Bromo-2-(2-methylphenyl)-2,3,4,5-tetrahydro-1H-naphtho[1,2-b]azepin-4-ol, C21H20BrNO, (I), and (2RS,4SR)-2-(3-methylthiophen-2-yl)-2,3,4,5-tetrahydro-1H-naphtho[1,2-b]azepin-4-ol, C19H19NOS, (II), both crystallize with Z' = 2 in the space groups P2(1)/c and Cc, respectively; compound (II) crystallizes as a nonmerohedral twin, with twin fractions 0.183 (2) and 0.817 (2). The molecules of (I) are linked by O-H···O and O-H···N hydrogen bonds to form a cyclic centrosymmetric R4(4)(16) tetramer. The molecules of (II) are linked by O-H···O hydrogen bonds to form a C2(2)(4) chain and these chains are weakly linked by a single C-H···π(thienyl) interaction to form a three-dimensional array. Comparisons are made with some related compounds.

Three closely related thienyl-substituted 1,4-epoxynaphtho[1,2-b]azepines: hydrogen-bonded assembly in one, two and three dimensions.

(2R,4S)-2-(3-Methylthiophen-2-yl)-2,3,4,5-tetrahydro-1,4-epoxynaphtho[1,2-b]azepine, C19H17NOS, (I), crystallizes with a single enantiomer in each crystal, whereas its geometrical isomer (2RS,4SR)-2-(5-methylthiophen-2-yl)-2,3,4,5-tetrahydro-1,4-epoxy-naphtho[1,2-b]azepine, (II), and (2RS,4SR)-2-(5-bromothiophen-2-yl)-2,3,4,5-tetrahydro-1,4-epoxynaphtho[1,2-b]azepine, C18H14BrNOS, (III), both crystallize as racemic mixtures. A combination of one C-H...O hydrogen bond and two C-H...π(arene) hydrogen bonds links the molecules of (I) into a three-dimensional framework; the molecules of (II) are linked into a C(4)C(4)[R2(2)(7)] chain of rings by a combination of C-H...N and C-H...O hydrogen bonds; and in (III), where Z' = 2, a combination of four C-H...π(arene) hydrogen bonds and two C-H...π(thienyl) hydrogen bonds links the molecules into complex sheets. Comparisons are made with the assembly patterns in some aryl-substituted 1,4-epoxynaphtho[1,2-b]azepines.

Four related esters: two 4-(aroylhydrazinyl)-3-nitrobenzoates and two 3-aryl-1,2,4-benzotriazine-6-carboxylates.

The molecules of both methyl 4-[2-(4-chlorobenzoyl)hydrazinyl]-3-nitrobenzoate, C15H12ClN3O5, (I), and methyl 4-[2-(2-fluorobenzoyl)hydrazinyl]-3-nitrobenzoate, C15H12FN3O5, (II), contain an intramolecular N-H···O hydrogen bond, and both show electronic polarization in the nitrated aryl ring. In both compounds, molecules are linked by a combination of N-H···O and C-H···O hydrogen bonds to form sheets, which are built from R4(3)(18) rings in (I) and from R4(4)(28) rings in (II). In each of methyl 3-phenyl-1,2,4-benzotriazine-6-carboxylate, C15H11N3O2, (III), and methyl 3-(4-methylphenyl)-1,2,4-benzotriazine-6-carboxylate, C16H13N3O2, (IV), the benzotriazine unit shows naphthalene-type delocalization. There are no hydrogen bonds in the structures of compounds (III) and (IV), but in both compounds, the molecules are linked into chains by π-π stacking interactions involving the benzotriazine units. The mechanism of chain formation is the same in both (III) and (IV), and the different orientations of the two chains can be related to the approximate relationship between the unit-cell metrics for (III) and (IV).

Hydrogen-bonded dimers in 3-amino-4-anilino-1H-isochromen-1-one and a hydrogen-bonded sheet in 3-amino-4-[methyl(phenyl)amino]-1H-isochromen-1-one.

The molecules of 3-amino-4-anilino-1H-isochromen-1-one, C15H12N2O2, (I), and 3-amino-4-[methyl(phenyl)amino]-1H-isochromen-1-one, C16H14N2O2, (II), adopt very similar conformations, with the substituted amino group PhNR, where R = H in (I) and R = Me in (II), almost orthogonal to the adjacent heterocyclic ring. The molecules of (I) are linked into cyclic centrosymmetric dimers by pairs of N-H···O hydrogen bonds, while those of (II) are linked into complex sheets by a combination of one three-centre N-H···(O)2 hydrogen bond, one two-centre C-H···O hydrogen bond and two C-H···π(arene) hydrogen bonds.

Dibenzylammonium hydrogen maleate and a redetermination at 120†K of bis(dibenzylamino)methane.

In dibenzylammonium hydrogen maleate [or dibenzylammonium (2Z)-3-carboxyprop-2-enoate], C14H16N(+)·C4H3O4(-), (I), the anion contains a fairly short and nearly linear O-H···O hydrogen bond, with an O··· ·O distance of 2.4603 (16) Å, but with the H atom clearly offset from the mid-point of the O···O vector. The counter-ions in (I) are linked by two N-H···O hydrogen bonds to form C2(2)(6) chains and these chains are weakly linked into sheets by a C-H···O hydrogen bond. Bis(dibenzylamino)methane, C29H30N2, (II), crystallizes with two independent molecules lying across twofold rotation axes in the space group C2/c, and the molecules are conformationally chiral; there are no direction-specific intermolecular interactions in the crystal structure of (II).

5-Methyl-N-[2-nitro-4-(trifluoromethyl)phenyl]-1H-pyrazole-3-amine: a chain of hydrogen-bonded R(2)(2)(6) and R(2)(2)(16) rings.

The molecular skeleton of the title compound, C(11)H(9)F(3)N(4)O(2), is almost planar and exhibits a polarized (charge-separated) electronic structure in the nitroaniline portion. Molecules are linked by N-H···N and C-H···O hydrogen bonds to form a chain in which centrosymmetric R(2)(2)(6) and R(2)(2)(16) rings alternate.

A chain of π-stacked molecules in 4-(2-chlorophenyl)pyrrolo[1,2-a]quinoxaline and a hydrogen-bonded sheet in (4RS)-4-(1,3-1,3-benzodioxol-6-yl)-4,5-dihydropyrrolo[1,2-a]quinoxaline.

In the molecule of 4-(2-chlorophenyl)pyrrolo[1,2-a]quinoxaline, C17H11ClN2, (I), the bond lengths are consistent with electron delocalization in the two outer rings of the fused tricyclic system, with a localized double bond in the central ring. The molecules of (I) are linked into chains by a π-π stacking interaction. In (4RS)-4-(1,3-benzodioxol-6-yl)-4,5-dihydropyrrolo[1,2-a]quinoxaline, C18H14N2O2, (II), the central ring of the fused tricyclic system adopts a conformation intermediate between screw-boat and half-chair forms. A combination of N-H···O and C-H···π(arene) hydrogen bonds links the molecules of (II) into a sheet. Comparisons are made with related compounds.

(E)-2-(1,3-benzothiazol-2-yl)-3-(4-fluorophenyl)acrylonitrile: a chain of π-stacked hydrogen-bonded rings.

The title compound, C16H9FN2S, crystallizes as a nonmerohedral twin with twin rotation about the reciprocal-lattice vector [101]*. The molecules are nearly planar and the dihedral angle between the planes of the two aryl rings is only 4.4 (2)°. The molecules are linked by pairs of C-H···N hydrogen bonds to form cyclic centrosymmetric R2(2)(18) dimers, which are linked into chains by an aromatic π-π stacking interaction. Comparisons are made with some related 3-aryl-2-thienylacrylonitriles.

(Z)-5-[4-(dimethylamino)benzylidene]-2-(piperidin-1-yl)-1,3-thiazolidin-4(5H)-one.

The molecules of the title compound, C(17)H(21)N(3)OS, are characterized by a wide C-C-C angle at the methine C atom linking the aryl and thiazolidine rings, associated with a short repulsive intramolecular S...H contact between atoms in these two rings. A single piperidine-arene C-H...π hydrogen bond links pairs of molecules into centrosymmetric dimers.

Hydrogen-bonded sheet structures in methyl 4-(4-chloroanilino)-3-nitrobenzoate and methyl 1-benzyl-2-(4-chlorophenyl)-1H-benzimidazole-5-carboxylate.

In methyl 4-(4-chloroanilino)-3-nitrobenzoate, C(14)H(11)ClN(2)O(4), (I), there is an intramolecular N-H...O hydrogen bond and the intramolecular distances provide evidence for electronic polarization of the o-quinonoid type. The molecules are linked into sheets built from N-H...O, C-H...O and C-H...π(arene) hydrogen bonds, together with an aromatic π-π stacking interaction. The molecules of methyl 1-benzyl-2-(4-chlorophenyl)-1H-benzimidazole-5-carboxylate, C(22)H(17)ClN(2)O(2), (II), are also linked into sheets, this time by a combination of C-H...π(arene) hydrogen bonds and aromatic π-π stacking interactions.

Triphenylsilanol-4,4'-bipyridyl (4/1): the Z' = 4 polymorph revisited.

A fully ordered structure is reported for the polymorph of triphenylsilanol-4,4'-bipyridyl (4/1), 4C18H16OSi·C10H8N2, having Z' = 4. The asymmetric unit contains four similar but distinct five-molecule aggregates, in which the central bipyridyl unit is linked to two molecules of triphenylsilanol via O-H···N hydrogen bonds, with a further pair of triphenylsilanol molecules linked to the first pair via O-H···O hydrogen bonds. An extensive series of C-H···π(arene) hydrogen bonds links these aggregates into complex sheets. This structure is compared with a previously reported structure [Bowes, Ferguson, Lough & Glidewell (2003). Acta Cryst. B59, 277-286], which was based on an erroneous disordered structural model arising from a false direct-methods solution with reference to a strong pseudo-inversion centre.

Six closely related 4,6-disubstituted 2-amino-5-formylpyrimidines: different ring conformations, polarized electronic structures, and hydrogen-bonded assembly in zero, one, two and three dimensions.

In each of ethyl N-{2-amino-5-formyl-6-[methyl(phenyl)amino]pyrimidin-4-yl}glycinate, C(16)H(19)N(5)O(3), (I), N-{2-amino-5-formyl-6-[methyl(phenyl)amino]pyrimidin-4-yl}glycinamide, C(14)H(16)N(6)O(2), (II), and ethyl 3-amino-N-{2-amino-5-formyl-6-[methyl(phenyl)amino]pyrimidin-4-yl}propionate, C(17)H(21)N(5)O(3), (III), the pyrimidine ring is effectively planar, but in each of methyl N-{2-amino-6-[benzyl(methyl)amino]-5-formylpyrimidin-4-yl}glycinate, C(16)H(19)N(5)O(3), (IV), ethyl 3-amino-N-{2-amino-6-[benzyl(methyl)amino]-5-formylpyrimidin-4-yl}propionate, C(18)H(23)N(5)O(3), (V), and ethyl 3-amino-N-[2-amino-5-formyl-6-(piperidin-4-yl)pyrimidin-4-yl]propionate, C(15)H(23)N(5)O(3), (VI), the pyrimidine ring is folded into a boat conformation. The bond lengths in each of (I)-(VI) provide evidence for significant polarization of the electronic structure. The molecules of (I) are linked by paired N-H···N hydrogen bonds to form isolated dimeric aggregates, and those of (III) are linked by a combination of N-H···N and N-H···O hydrogen bonds into a chain of edge-fused rings. In the structure of (IV), molecules are linked into sheets by means of two hydrogen bonds, both of N-H···O type, in the structure of (V) by three hydrogen bonds, two of N-H···N type and one of C-H···O type, and in the structure of (VI) by four hydrogen bonds, all of N-H···O type. Molecules of (II) are linked into a three-dimensional framework structure by a combination of three N-H···O hydrogen bonds and one C-H···O hydrogen bond.

(E,E)-1,1'-[1,2-Bis(4-chlorophenyl)ethane-1,2-diyl]bis(phenyldiazene) revisited: threefold configurational disorder of (S,S), (R,R) and (S,R) isomers, a detailed critique.

Crystal structures described as concomitant triclinic (I) and monoclinic (II) polymorphs of meso-(E,E)-1,1'-[1,2-bis(4-chlorophenyl)ethane-1,2-diyl]bis(phenyldiazene) [Mohamed et al. (2016). Acta Cryst. C72, 57-62] have been re-investigated. The published model for II was distorted due to forcing the symmetry of space group C2/c on an incomplete structure model. It is shown here to be a likely three-component superposition of S,S and R,R enantiomers with a lesser amount of the meso form. A detailed analysis of how the improbable distortion in the published model aroused suspicion and the subsequent construction of undistorted chemically and crystallographically plausible alternatives having the symmetry of Cc and C2/c is presented. For the sake of completeness, an improved model for the triclinic P-1 structure of the meso isomer I, revised to include a minor disorder component, is also given.

Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products.

A concise and versatile synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidines has been developed, starting from 4-(1H-benzo[d]imidazol-1-yl)pyrimidines, and we report here the synthesis and spectroscopic and structural characterization of three such products, along with those of two intermediates in the reaction pathway. The intermediates 4-[2-(4-chlorophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (II), and 4-[2-(4-bromophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (III), crystallize as the isostructural monohydrates C18H15ClN5O·H2O and C18H15BrN5O·H2O, respectively, in which the components are linked into complex sheets by O-H...N and N-H...O hydrogen bonds. In the product (E)-4-methoxy-5-[(4-nitrobenzylidene)amino]-6-[2-(4-nitrophenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, which crystallizes as a 1:1 solvate with dimethyl sulfoxide, C25H18N8O5·C2H6OS, (IV), inversion-related pairs of the pyrimidine component are linked by N-H...N hydrogen bonds to form cyclic centrosymmetric R22(8) dimers to which pairs of solvent molecules are linked by N-H...O hydrogen bonds. (E)-4-Methoxy-5-[(4-methylbenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C27H24N6O, (V), crystallizes with Z' = 2 and the molecules are linked into a three-dimensional framework structure by a combination of N-H...N, C-H...N and C-H...π(arene) hydrogen bonds. The analogous product (E)-4-methoxy-5-[(4-chlorobenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C26H21ClN6O, (VI), crystallizes from dimethyl sulfoxide in two forms: one, denoted (VIa), is isostructural with (V), and the other, denoted (VIb), crystallizes with Z' = 1, but as an unknown solvate in which the pyrimidine molecules are linked by N-H...N hydrogen bonds to form a ribbon containing two types of centrosymmetric ring.