DFT method and AIM analysis of noncovalent stacking interactions between DNA bases and some aromatic drug fragments

DFT and the atoms in molecule (AIM) analysis were employed to investigate the π-π stacking interactions between some popular drug fragments (DF) including indole (I), benzothiophene (Bt) benzofuran (Bf) and guanine (G), adenine (A), A-thymine (AT), G-cytosine (GC) base pairs were optimized at the M062X/6-311++G(d,p) level of theory. The result shows that the IG1 (see the notation below) and IA6 has the maximum interaction energy in all of the two G-based and A-based conformers; and order of the adsorption strength is IG1 BtG6 BfG1 for G-based complexes and IA6 BtA6 BfG6, for A-based complexes. Furthermore, our results show that stacking interaction leads to an increase and decrease of hydrogen bond length that involved in the nucleic base-drug fragment interactions. DFT calculated interaction energies for all present conformers, were found to be in a good agreement with the bond critical points data from AIM analysis.