Diaminobenzene schiff base, a novel class of DNA minor groove binder.

Molecules that target the deoxyribonucleic acid (DNA) minor groove are relatively sequence specific and they can be excellent carrier structures for cytotoxic chemotherapeutic compounds which can help to minimize side effects. Two novel isomeric derivatives of diaminobenzene Schiff base [N,N'-bis (2-hydroxy-3-methoxybenzylidene)-1,2-diaminobenzene (2MJ) and N,N'-bis(2-hydroxy-3-methoxybenzylidene)-1,3-diaminobenzene (2MH)] were analyzed for their DNA minor groove binding (MGB) ability using viscometry, UV and fluorescence spectroscopy, computational modeling and clonogenic assay. The result shows that 2MJ and 2MH are strong DNA MGBs with the latter being more potent. 2MH can form interstrand hydrogen bond linkages at its oxygens with N3 of adenines. Changing the 2-hydroxy-3-methoxybenzylidene binding position to the 1,3 location on the diaminobenzene structure (2MJ) completely removed any viable hydrogen bond formation with the DNA and caused significant decrease in binding strength and minor groove binding potency. Neither compound showed any significant cytotoxicity towards human breast, colon or liver cancer cell lines.

6,6'-Dimeth-oxy-2,2'-[p-phenyl-ene-bis(nitrilo-methyl-idyne)]diphenol chloro-form disolvate.

The title compound, C(22)H(20)N(2)O(4)·2CHCl(3), a new Schiff base compound, lies across a crystallographic inversion centre. An intra-molecular O-H⋯N hydrogen bond generates a six-membered ring, producing an S(6) ring motif. Inter-molecular bifurcated C-H⋯O hydrogen bonds involving the two O atoms of the Schiff base ligand and the H atom of the chloro-form solvent of crystallization, generate an R(2) (1)(5) ring motif. The crystal structure is stabilized by inter-molecular C-H⋯π and π-π inter-actions [centroid to centroid distance = 3.6158 (10) Å]. In the crystal structure, mol-ecules are stacked down the c axis.

2-[1-(2-Hydroxy-3-methoxybenzyl)-1H-benzimidazol-2-yl]-6-methoxyphenol monohydrate.

The asymmetric unit of the title compound, C(22)H(20)N(2)O(4)·H(2)O, comprises a substituted benzimidazole molecule and a water mol-ecule of crystallization. The dihedral angles between the benzimidazole ring system and the two outer benzene rings are 16.54 (4) and 86.13 (4)°. The dihedral angle between the two hydr-oxy-substituted benzene rings is 82.20 (5)°. In the crystal structure, inter-molecular O-H⋯O hydrogen bonds, involving the hydr-oxy groups and water mol-ecules, form R(4) (4)(8) ring motifs, and link symmetry-related mol-ecules into extended chains along the c axis. The crystal structure is further stabilized by weak inter-molecular C-H⋯O hydrogen bonds, weak C-H⋯π and π-π stacking [centroid-centroid = 3.6495 (6)-3.7130 (6) Å] inter-actions. Intra-molecular O-H⋯O and O-H⋯N inter-actions are also present.

2-[1-(2-Hydr-oxy-3-methoxy-benz-yl)-1H-benzimidazol-2-yl]-6-methoxy-phenol methanol 1.13-solvate.

In the main mol-ecule of the title compound, C(22)H(20)N(2)O(4)·1.13CH(4)O, the dihedral angles between the benzimidazole plane and the two benzene rings are 80.53 (10) and 82.76 (10)°. The solvent mol-ecules are disordered between three positions, with refined occupancies of 0.506 (13), 0.373 (13) and 0.249 (5). The crystal structure is stabilized by inter-molecular O-H⋯O, O-H⋯N and C-H⋯O hydrogen bonds. The crystal studied was a merohedral twin [BASF ratio of 0.917 (1)/0.083 (1)].

2-Amino-N-(2-hydr-oxy-3-methoxy-benzyl-idene)aniline.

In the title compound, C(14)H(14)N(2)O(2), the dihedral angle between the two benzene rings is 9.67 (10)°. Two intra-molecular O-H⋯N and N-H⋯N hydrogen bonds involving the hydr-oxy and amino groups generate S(6) and S(5) ring motifs, respectively. In the crystal structure, N-H⋯O hydrogen bonds link neighboring mol-ecules. Mol-ecules are also stacked in a head-to-tail fashion along the c axis through π-π inter-actions [centroid-centroid separation of 3.7357 (12) Å] and are further linked by weak inter-molecular C-H⋯π inter-actions, giving a zigzag arrangement along the b axis.

2-Amino-N-(2-benz-yloxy-3-methoxy-benzyl-idene)aniline.

The title compound, C(21)H(20)N(2)O(2), a Schiff base ligand, contains two independent mol-ecules (A and B) in the asymmetric unit, with similar conformations. In mol-ecule A, the central benzene ring forms dihedral angles of 30.79 (13) and 23.56 (13)°, respectively, with the amino and benzyl benzene rings, while in mol-ecule B these angles are 32.30 (13) and 13.13 (12)°. The mol-ecular structure is stabilized by intra-molecular N-H⋯N and C-H⋯O hydrogen bonds. The crystal structure is stabilized by N-H⋯N hydrogen bonds and N-H⋯π and C-H⋯π inter-actions.