Structural Chemistry

, Volume 18, Issue 6, pp 943–949 | Cite as

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

  • Marijana Hranjec
  • Gordana PavlovićEmail author
  • Grace Karminski-Zamola
Original Paper


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) Å]. Both NH groups of benzimidazole ring form intermolecular hydrogen bonds, one with the oxygen atom of water molecule [N···O 2.689(2) Å] and the other with Cl ion (N···Cl 3.051(1) Å). 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) Å]. In that way, infinite chains along [110] direction are formed.


Benzimidazole derivatives Synthesis Spectroscopic characterization Crystal structure determination Interaction with ct-DNA 



The Ministry of Science and Technology of the Republic of Croatia, Zagreb (grant Nos. 119-1193079-1332 and 125-0982464-1356) supported this work.


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Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Marijana Hranjec
    • 1
  • Gordana Pavlović
    • 2
    Email author
  • Grace Karminski-Zamola
    • 1
  1. 1.Department of Organic Chemistry, Faculty of Chemical Engineering and TechnologyUniversity of ZagrebZagrebCroatia
  2. 2.Faculty of Textile Technology, Department of Applied ChemistryUniversity of ZagrebZagrebCroatia

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