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

ABSTRACT: 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).

SUBMITTER: Mohamed-Ezzat RA

PROVIDER: S-EPMC8100259 | biostudies-literature |

REPOSITORIES: biostudies-literature

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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.

Project description: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.

| S-EPMC4644996 | 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

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

Ethyl 1,6-dimethyl-2-oxo-4-(quinolin-4-yl)-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

Project description:In the title compound, C(18)H(19)N(3)O(3), the tetra-hydro-pyrimidone ring adopts a distorted boat conformation. In the crystal structure, inter-molecular N-H⋯O hydrogen bonds link the mol-ecules into centrosymmetric dimers, which are further linked via inter-molecular C-H⋯π inter-actions. In addition, an intra-molecular C-H⋯O hydrogen bond occurs.

| S-EPMC3006892 | 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-Amino-6-(piperidin-1-yl)pyrimidine-5-carbo-nitrile.

Project description:In the title compound, C10H13N5, the piperidine ring adopts a chair conformation with the exocyclic N-C bond in an axial orientation, and the dihedral angle between the mean planes of piperidine and pyrimidine rings is 49.57 (11)°. A short intra-molecular C-H⋯N contact generates an S(7) ring. In the crystal, N-H⋯N hydrogen bonds link the mol-ecules into (100) sheets and a weak aromatic π-π stacking inter-action is observed [centroid-centroid separation = 3.5559 (11) Å] between inversion-related pyrimidine rings.

| S-EPMC9462203 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of (<i>Z</i>)-2-amino-4-(2,6-di-chloro-phen-yl)-5-(1-hy-droxy-ethyl-idene)-6-oxo-1-phenyl-1,4,5,6-tetra-hydro-pyridine-3-carbo-nitrile.

Project description:The mol-ecular conformation of the title compound, C20H15Cl2N3O2, is stabilized by an intra-molecular O-H⋯O hydrogen bond, forming an S(6) ring motif. The central pyridine ring is almost planar [maximum deviation = 0.074 (3) Å]. It subtends dihedral angles of 86.10 (15) and 87.17 (14)°, respectively, with the phenyl and di-chloro-phenyl rings, which are at an angle of 21.28 (15)° to each other. The =C(-OH)CH3 group is coplanar. In the crystal, mol-ecules are linked by inter-molecular N-H⋯N and C-H⋯N hydrogen bonds, and N-H⋯π and C-H⋯π inter-actions, forming a three-dimensional network. The most important contributions to the crystal packing are from H⋯H (33.1%), C⋯H/H⋯C (22.5%), Cl⋯H/H⋯Cl (14.1%), O⋯H/H⋯O (11.9%) and N⋯H/H⋯N (9.7%) inter-actions.

| S-EPMC8423002 | biostudies-literature

Ethyl 6-methyl-2-sulfanyl-idene-4-[4-(trifluoro-meth-yl)phen-yl]-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

Project description:The title compound, C(15)H(15)F(3)N(2)O(2)S, adopts a conformation with an intra-molecular C-H?? inter-action. The dihedral angles between the planes of the 4-(trifluoro-meth-yl)phenyl and ester groups with the plane of the six-membered tetra-hydro-pyrimidine ring are 81.8?(1) and 16.0?(1)°, respectively. In the crystal structure, inter-molecular N-H?S hydrogen bonds link pairs of mol-ecules into dimers and N-H?O inter-actions generate hydrogen-bonded mol-ecular chains along the crystallographic a axis.

| S-EPMC3152077 | 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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