Synthesis, characterization and molecular docking studies of new indol(1-3-yl)pyrimidine derivatives: Insights into their role in DNA interaction.

This study reports the synthesis of new indol(1-3-yl) pyrimidine derivatives using various substituted indole-3-carbaldehydes, urea and malononitrile in the presence of ammonium chloride. The resulting compounds were characterized using analytical and spectroscopic methods. The molecular docking study exhibits that among the synthesized compounds, have great binding ability toward B-DNA.

2-[1-(4--Butyl-phen-yl)-4,5-diphenyl-1-imid-azol-2-yl]-4,6-di-chloro-phenol.

In the title compound, CHClNO, the 4,6-di-chloro-phenol and the imidazole rings are almost coplanar, with a dihedral angle of 8.89 (6)° between them and an intra-molecular O-H⋯N hydrogen bond occurs between the rings. The dihedral angles subtended by the -butyl-phenyl ring and the two phenyl rings with the imidazole ring are 85.

(2-Hy-droxy-phen-yl)(4,2':4',4''-terpyridin-6'-yl)methanone.

The title compound, CHNO, can be described as a ketone with a phenol substituent and a terpyridine ligand coordinated to the carbonyl group. The three six-membered rings of the terpyridine ligand are not coplanar. The dihedral angles between the mean planes of the central ring and the external pyridine ligands are 22.

6-Methyl-4-{[4-(tri-methyl-sil-yl)-1-1,2,3-triazol-1-yl]meth-yl}-2-chromen-2-one.

In the title compound, CHNOSi, the dihedral angle between the coumarin ring system (r.m.s.

4-Amino-6-(piperidin-1-yl)pyrimidine-5-carbo-nitrile.

In the title compound, CHN, 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 (7) ring.

4-Chloro-2-[1-(4-ethyl-phen-yl)-4,5-diphenyl-1-imidazol-2-yl]phenol.

In the title compound, CHClNO, the 5-chloro-phenol ring and the imidazole ring are nearly coplanar, with a dihedral angle of 15.76 (9)° between them. The ethyl-phenyl ring and the two phenyl rings subtend angles of 71.

Crystal structure of ethyl 5-[3-(di-methyl-amino)-acrylo-yl]-2-{[(di-methyl-amino)-methyl-idene]-amino}-4-methylthio-phene-3-carb-oxy-late.

In the title compound, C16H23N3O3S, the dihedral angles between the thio-phene ring and the almost planar di-methyl-amino-methyl-ene-amino (r.m.s.

Crystal structure of methyl 4-(2-fluoro-phenyl)-6-methyl-2-sulfanylidene-1,2,3,4-tetra-hydro-pyrimidine-5-carb-oxy-late.

In the title compound, C13H13FN2O2S, the pyrimidine ring adopts a twist-boat conformation with the MeCN and methine-C atoms displaced by 0.0938 (6) and 0.2739 (3) Å, respectively, from the mean plane through the other four atoms of the ring.

Crystal structure of 2-acetyl-5-(3,4-di-meth-oxy-phen-yl)-6-eth-oxy-carbonyl-3,7-dimethyl-5H-thia-zolo[3,2-a]pyrimidin-8-ium chloride.

The title mol-ecular salt, C21H25N2O5S(+)·Cl(-), crystallizes with two ion pairs in the asymmetric unit. The cations have similar conformations (r.m.

Crystal structure of ethyl 5-acetyl-2-{[(di-methyl-amino)-methyl-idene]amino}-4-methyl-thio-phene-3-carboxyl-ate.

In the title thio-phene derivative, C13H18N2O3S, the dihedral angles between the thio-phene ring and the [(di-methyl-amino)-methyl-idene]amino side chain (r.m.s.

Crystal structure of ethyl 4-(2-fluoro-phen-yl)-6-methyl-2-sulfanyl-idene-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

The title compound, C14H15FN2O2S, crystallizes with two mol-ecules in the asymmetric unit. In each mol-ecule, the pyrimidine ring adopts a sofa conformation with the sp (3)-hybridized C atom forming the flap and the fluoro-substituted ring in an axial position. In the crystal, mol-ecules are linked via N-H⋯S hydrogen bonds, forming chains of R 2 (2)(8) rings along [100].

Crystal structure of ethyl 2-acetyl-3,7-dimethyl-5-(thio-phen-2-yl)-5H-thia-zolo[3,2-a]pyrimidine-6-carboxyl-ate.

In the title compound, C17H18N2O3S2, the pyrimidine ring adopts a shallow sofa conformation, with the C atom bearing the axially-oriented thio-phene ring as the flap [deviation = 0.439 (3) Å]. The plane of the thio-phene ring lies almost normal to the pyrimidine ring, making a dihedral angle of 79.

Crystal structure of 2-(4-chloro-3-fluoro-phen-yl)-1H-benzimidazole.

In the title compound, C13H8ClFN2, the dihedral angle between the plane of the benzimidazole ring system (r.m.s.

Crystal structure of ethyl 2-cyano-3-[(1-eth-oxy-ethyl-idene)amino]-5-(3-meth-oxy-phen-yl)-7-methyl-5H-1,3-thia-zolo[3,2-a]pyrimidine-6-carboxyl-ate.

In the title compound, C22H24N4O4S, the central pyrimidine ring adopts a sofa conformation with the ring-junction N atom displaced by 0.2358 (6) Å from the mean plane of the remaining ring atoms. The 3-meth-oxy-phenyl ring, at the chiral C atom opposite the other N atom, is positioned axially and is inclined to the thia-zolo-pyrimidine ring with a dihedral angle of 83.

Crystal structure of 4-azido-methyl-6-isopropyl-2H-chromen-2-one.

In the title mol-ecule, C13H13N3O2, the benzo-pyran ring system is essentially planar, with a maximum deviation of 0.017 (1) Å. In the crystal, weak C-H⋯O hydrogen bonds link mol-ecules into ladders along [010].

Crystal structure of ethyl 6-(2-fluoro-phen-yl)-4-hy-droxy-2-sulfanyl-idene-4-tri-fluoro-meth-yl-1,3-diazinane-5-carboxyl-ate.

In the title compound, C14H14F4N2O3S, the central di-hydro-pyrimidine ring adopts a sofa conformation with the C atom bearing the 2-fluoro-benzene ring displaced by 0.596 (3) Å from the other five atoms. The 2-fluoro-benzene ring is positioned axially and bis-ects the pyrimidine ring with a dihedral angle of 70.

Crystal structure of ethyl 2-(2-fluoro-benzyl-idene)-5-(4-fluoro-phen-yl)-7-methyl-3-oxo-2,3-di-hydro-5H-1,3-thia-zolo[3,2-a]pyrimidine-6-carb-oxy-late.

In the title mol-ecule, C23H18F2N2O3S, the 4-fluoro-substituted and 2-fluoro-substituted benzene rings form dihedral angles of 88.16 (8) and 23.1 (1)°, respectively, with the thia-zole ring.

Crystal structure of 1-(2,4-di-methyl-phen-yl)-2-(4-tri-methyl-silyl-1H-1,2,3-triazol-1-yl)ethanone.

The asymmetric unit of the title compound, C15H21N3OSi, contains two mol-ecules with similar conformations (r.m.s.

Crystal structure of 2-acetyl-5-(3-methoxyphenyl)-3,7-dimethyl-5H-1,3-thiazolo[3,2-a]pyrimidine-6-carboxylate.

In the title mol-ecule, C20H22N2O4S, the pyrimidine ring is in a flattened half-chair conformation and the 3-meth-oxyphenyl substituent is in an axial arrangement. The thia-zole ring forms a dihedral angle of 81.3 (1)° with the benzene ring.

Crystal structure of ethyl 5-(3-fluoro-phen-yl)-2-[(4-fluoro-phen-yl)methyl-idene]-7-methyl-3-oxo-2H,3H,5H-[1,3]thia-zolo[3,2-a]pyrimidine-6-carboxyl-ate.

In the title mol-ecule, C23H18F2N2O3S, the pyrimidine ring is in a half-chair conformation and the 3-fluoro-phenyl group is in the axial position. The thia-zole ring (r.m.

2-[4-(Tri-fluoro-meth-yl)phen-yl]-1H-benzimidazole.

In the title compound, C14H9F3N2, the mean planes of the benzimidazole ring system and the tri-fluoro-methyl-substituted benzene ring form a dihedral angle of 30.1 (1)°. In the crystal, mol-ecules are linked by N-H⋯N hydrogen bonds into chains along [010].

Methyl 4-(4-hy-droxy-phen-yl)-6-methyl-2-sulfanyl-idene-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

In the title mol-ecule, C13H14N2O3S, the di-hydro-pyrimidine ring is in a flattened sofa conformation, with the methine C atom forming the flap. The dihedral angle between the mean plane of the five essentially planar atoms of the di-hydro-pyrimidine ring [maximum deviation = 0.056 (4) Å] and the benzene ring is 89.

2-(3,4-Di-fluoro-phen-yl)-1H-benzimidazole.

In the title mol-ecule, C13H8F2N2, the dihedral angle between the benzimidazole ring system and the di-fluoro-substituted benzene ring is 30.0 (1)°. In the crystal, mol-ecules are linked by N-H⋯N hydrogen bonds, forming chains along [010].

Methyl 5-(4-acet-oxy-phen-yl)-2-(2-bromo-benzyl-idine)-7-methyl-3-oxo-2,3-di-hydro-5H-1,3-thia-zolo[3,2-a]pyrimidine-6-carboxyl-ate.

In the title mol-ecule, C24H19BrN2O5S, the pyrimidine ring is in a flattened half-chair conformation and the 4-acet-oxy-phenyl group is substituted axially to this ring. The thia-zole ring is essentially planar [with a maximum deviation of 0.012 (2) Å for the N atom] and forms dihedral angles of 17.

6-Chloro-3-[(di-methyl-amino)-methyl-idene]thio-chroman-4-one.

The asymmetric unit of the title compound, C12H12ClNOS, contains three independent mol-ecules, with the thio-chroman ring adopting a sofa conformation in each one. The crystal structure features C-H⋯O inter-actions; one of the O atoms accepts three such bonds. Together, the hydrogen bonds give rise to a molecular tape propagating in [010].