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Crystal structure of (E)-2-amino-4-methyl-sulfanyl-6-oxo-1-{[(thiophen-2-yl)-methyl-idene]-amino}-1,6-di-hydro-pyrimidine-5-carbo-nitrile.

ABSTRACT: The title compound, C11H9N5OS2, a 1-thio-phen-2-yl-methyl-ene-amino-pyrimidine derivative, displays an essentially planar C-NH2 group. The conformation across the N=C bond linking the pyrimidine and thienyl groups is E. The pyrimidine and thienyl ring systems subtend an inter-planar angle of 42.72 (5)°. In the crystal, mol-ecules are linked by N-H⋯Nnitrile and N-H⋯O=C hydrogen bonds, forming chains parallel to the b axis.

SUBMITTER: Elgemeie GH

PROVIDER: S-EPMC4644996 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Crystal structures of (<i>E</i>)-2-amino-4-methyl-sulfanyl-6-oxo-1-(1-phenyl-ethyl-idene-amino)-1,6-di-hydro-pyrimidine-5-carbo-nitrile and (<i>E</i>)-2-amino-4-methyl-sulfanyl-6-oxo-1-[1-(pyridin-2-yl)ethyl-idene-amino]-1,6-di-hydro-pyrimidine-5-carbo-nitrile.

Project description:The title compounds 3a, C14H13N5OS, and 3b, C13H12N6OS, both show an E configuration about the N=C bond and a planar NH2 group. The mol-ecules, which only differ in the presence of a phenyl (in 3a) or pyridyl (in 3b) substituent, are closely similar except for the different orientations of these groups. The amino hydrogen atoms form classical hydrogen bonds; in 3a the acceptors are the oxygen atom and the cyano nitro-gen atom, leading to ribbons of mol-ecules parallel to the b axis, whereas in 3b the acceptors are the oxygen atom and the pyridyl nitro-gen, leading to a layer structure perpendicular to (01).

| S-EPMC8100259 | biostudies-literature

Crystal structure of 4,6-di-amino-2-sulfanyl-idene-1,2-di-hydro-pyridine-3-carbo-nitrile.

Project description:The title compound, C6H6N4S, crystallizes with two independent mol-ecules, A and B, in the asymmetric unit. Both independent mol-ecules are almost planar [maximum deviations of 0.068?(6)?Å in mol-ecule A and 0.079?(6)?Å in mol-ecule B]. In the crystal, mol-ecules A and B are linked by N-H?S, N-H?N and C-H?S hydrogen bonds, forming a three-dimensional network.

| S-EPMC4186145 | biostudies-literature

10-Methyl-2-oxo-4-phenyl-2,11-di-hydro-pyrano[2,3-a]carbazole-3-carbo-nitrile.

Project description:In the title mol-ecule, C23H14N2O2, the atoms in the carbazole unit deviate from planarity [maximum deviation from mean plane = 0.1018 (8) Å]. The pyrrole ring makes dihedral angles of 4.44 (5), 3.84 (5), 2.18 (5) and 56.44 (5)° with the pyran, fused benzene rings and phenyl ring, respectively. In the crystal, pairs of N-H⋯O hydrogen bonds generate R 2 (2)(14) loops and a C-H⋯N inter-action is also found. Mol-ecules are further linked by a number of π-π interactions [centroid-centroid distances vary from 3.5702 (5) to 3.7068 (6) Å], forming a three-dimensional network.

| S-EPMC3684919 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of 2-(4-bromo-phen-yl)-4-methyl-6-oxo-1-phenyl-1,6-di-hydro-pyridine-3-carbo-nitrile.

Project description:In the title compound, C19H13BrN2O, the pyridine ring is essentially planar [maximum deviation = 0.024 (4) Å for the N atom] and makes dihedral angles of 74.6 (2) and 65.8 (2)°, respectively, with the phenyl and bromo-phenyl rings, which subtend a dihedral angle of 63.1 (2)°. In the crystal, mol-ecules are connected along the c-axis direction via C-Br⋯π inter-actions, generating zigzag chains parallel to the (010) plane. C-H⋯N and C-H⋯O hydrogen-bonding inter-actions further connect the mol-ecules, forming a three-dimensional network and reinforcing the mol-ecular packing. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (36.2%), C⋯H/H⋯C (21.6%), N⋯H/H⋯N (12.2%), and Br⋯H/H⋯Br (10.8%) inter-actions.

| S-EPMC9361383 | biostudies-literature

Crystal structures and Hirshfeld surface analyses of 2-amino-4-(4-bromo-phen-yl)-6-oxo-1-phenyl-1,4,5,6-tetra-hydro-pyridine-3-carbo-nitrile hemi-hydrate and 1,6-di-amino-2-oxo-4-phenyl-1,2-di-hydro-pyridine-3,5-dicarbo-nitrile.

Project description:In 2-amino-4-(4-bromo-phen-yl)-6-oxo-1-phenyl-1,4,5,6-tetra-hydro-pyridine-3-carbo-nitrile hemihydrate, C18H14BrN3O·0.5H2O, (I), pairs of mol-ecules are linked by pairs of N-H⋯N hydrogen bonds, forming dimers with an R 2 2(12) ring motif. The dimers are connected by N-H⋯Br and O-H⋯O hydrogen bonds, and C-Br⋯π inter-actions, forming layers parallel to the (010) plane. 1,6-Di-amino-2-oxo-4-phenyl-1,2-di-hydro-pyridine-3,5-dicarbo-nitrile, C13H9N5O, (II), crystallizes in the triclinic space group P with two independent mol-ecules (IIA and IIB) in the asymmetric unit. In the crystal of (II), mol-ecules IIA and IIB are linked by inter-molecular N-H⋯N and N-H⋯O hydrogen bonds into layers parallel to (001). These layers are connected along the c-axis direction by weak C-H⋯N contacts. C-H⋯π and C-N⋯π inter-actions connect adjacent mol-ecules, forming chains along the a-axis direction. In (I) and (II), the stability of the packing is ensured by van der Waals inter-actions between the layers. In (I), Hirshfeld surface analysis showed that the most important contributions to the crystal packing are from H⋯H (37.9%), C⋯H/H⋯C (18.4%), Br⋯H/H⋯Br (13.3%), N⋯H/H⋯N (11.5%) and O⋯H/H⋯O (10.0%) inter-actions, while in (II), H⋯H inter-actions are the most significant contributors to the crystal packing (27.6% for mol-ecule IIA and 23.1% for mol-ecule IIB).

| S-EPMC9361375 | biostudies-literature

4-Methyl-5-(4-nitro-benzyl-idene)-2-oxo-2,5-di-hydro-1H-pyrrole-3-carbo-nitrile.

Project description:Mol-ecules of the potential non-linear optical title compound, C13H9N3O3, form dimeric stacks of mol-ecules along the a axis cross-linked around inversion centers by N-H?O hydrogen bonds and weak (phen-yl)C-H?O inter-molecular inter-actions, forming a 'collaboration' of R 2 (2)(8) and R 2 (2)(16) ring motifs. The mol-ecules are then further linked by weak C-H?O and C-H?N inter-actions into sheets parallel to (121).

| S-EPMC3770419 | biostudies-literature

6-(2-Methyl-prop-yl)-4-oxo-2-sulfanyl-idene-1,2,3,4-tetra-hydro-pyrimidine-5-carbonitrile.

Project description:The title thio-uracil derivative, C(9)H(11)N(3)OS, exists in the thione form. The six atoms comprising the ring are almost coplanar [r.m.s. deviation = 0.015?Å] and the 2-methyl-propyl group lies approximately perpendicular to this plane [the N-C-C-C torsion angle is 72.88?(14)°]. Linear supra-molecular chains along [001] sustained by N-H?O and N-H?S hydrogen bonding feature in the crystal packing.

| S-EPMC3295462 | biostudies-literature

Crystal structure of 2-amino-4-(4-chloro-phen-yl)-1-(4-methyl-phen-yl)-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carbo-nitrile.

Project description:In the title compound, C23H20ClN3O, each of the cyclo-hexene and 1,4-di-hydro-pyridine rings of the 1,4,5,6,7,8-hexa-hydro-quinoline ring system adopts a twisted-boat conformation. The dihedral angle between the two benzene rings is 11.52 (7)°. In the crystal, mol-ecules are linked through a pair of amino-nitrile N-H⋯N hydrogen bonds, forming inversion dimers. These assemble into a three-dimensional network via C-H⋯O and C-H⋯π inter-actions.

| S-EPMC4719917 | biostudies-literature

catena-Poly[[[diaqua-bis(2-methyl-6-oxo-1,6-dihydro-3,4'-bipyridine-5-carbo-nitrile)copper(II)]-μ-sulfato] tetra-hydrate].

Project description:In the title polymer, {[Cu(SO(4))(C(12)H(9)N(3)O)(2)(H(2)O)(2)]·4H(2)O}(n), both the metal center and the sulfate anion are located on a twofold axis. The Cu(II) ion is coordinated by two pyridyl N atoms from two symmetry-related organic ligands, two O atoms from two symmetry-related water mol-ecules, and two O atoms from two symmetry-related sulfate anions, resulting in a distorted octa-hedral geometry. The sulfate anions act as μ(2)-bridges and connect metal ions, forming a one-dimensional chain along the b axis. The three-dimensional crystal structure is established through inter-molecular N-H⋯O and O-H⋯O hydrogen bonds involving the organic ligands, sulfate anions, coordinated and uncoordinated water mol-ecules, and through π-π inter-acting 2-pyridone rings, with centroid-centroid separations of ca 3.96 Å and tilt angles of ca 2.62°.

| S-EPMC2959870 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of 3-amino-1-oxo-2,6,8-triphenyl-1,2,7,8-tetra-hydro-iso-quinoline-4-carbo-nitrile.

Project description:In the title compound, C28H21N3O, the 1,2-di-hydro-pyridine ring of the 1,2,7,8-tetra-hydro-iso-quinoline ring system is planar as expected, while the cyclo-hexa-1,3-diene ring has a twist-boat conformation, with Cremer-Pople parameters Q T = 0.367 (2) A, θ = 117.3 (3)° and φ = 327.3 (4)°. The dihedral angles between the best planes through the iso-quinoline ring system and the three phenyl rings are 81.69 (12), 82.45 (11) and 47.36 (10)°. In the crystal, mol-ecules are linked via N-H⋯O and C-H⋯N hydrogen bonds, forming a three-dimensional network. Furthermore, the crystal packing is dominated by C-H⋯π bonds with a strong inter-action involving the phenyl H atoms. The role of the inter-molecular inter-actions in the crystal packing was clarified using Hirshfeld surface analysis, and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H⋯H (46.0%), C⋯H/H⋯C (35.1%) and N⋯H/H⋯N (10.5%) contacts.

| S-EPMC7869549 | biostudies-literature

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