The new water-soluble derivative of pyrazino[2,3-f][1,10] phenanthroline has been synthesized and characterized by conductivity measurement, elemental analysis, FT-IR, 1H NMR, 13C NMR spectroscopic studies, as well as single crystal x-ray crystallography. Theoretical calculations have been performed using the density functional theory (DFT) in order to confirm the structure and understand the electronic structure of the synthesized compound. The DNA binding properties of the compound were investigated by absorption spectroscopy, melting temperature and viscosity measurements. The intrinsic binding constant, Kb, was determined as 7.84 103 M1 at 298 K. Thermodynamic parameters showed that the binding interaction is enthalpy-favored. All of the experimental results indicated that the binding mode of interaction between this compound and CT-DNA is groove binding. Furthermore, molecular modeling studies was done to confirm the binding mode.
