Spectroscopic characterization, crystal structure determination and interaction with DNA of novel cyano substituted benzimidazole derivative

Abstract

Novel cyano-substituted benzimidazole derivatives 3 and 4 were synthesized from 4-N,N-dimethylamino-benzaldehyde and 2-cyanomethyl-benzimidazole. 2-(1H-benzimidazol-2-yl)-3-(4-N,N-dimethylamino-phenyl)-acrylonitrile hydrochloride monohydrate 4 has been studied by 1H and 13C NMR, IR, MS, UV/Vis and fluorescence spectroscopy and confirmed by X-ray crystal structure analysis. The interaction of 4 with ct-DNA has also been investigated by fluorescence spectroscopy and melting temperature determination experiment. According to the emission spectra recorded in the absence and presence of ct-DNA at different ratios r ([compound]/[polynucleotide]), 4 showed marked decrease in the fluorescence intensity and very strong hypochromic effect. Melting temperature experiment showed weak stabilization of double helix. To determine binding mode of 4, other additional experiments are necessary. The molecules of 4 are almost planar with the dihedral angle between benzimidazole and phenyl rings of 6.99(6)°. The protonation of nitrogen atom of benzimidazole ring is followed by π-electrons delocalization in the region resulting in C–N bond distances equality [1.341(2) and 1.337(2) A]. Both NH groups of benzimidazole ring form intermolecular hydrogen bonds, one with the oxygen atom of water molecule [N···O 2.689(2) A] and the other with Cl− ion (N···Cl− 3.051(1) A). Except proton acceptor, water molecule acts as double proton donor in the formation of intermolecular hydrogen bonds with Cl− ion [O···Cl− 3.126(2) and 3.169(2) A]. In that way, infinite chains along [110] direction are formed.