DFT study and topological analysis of the bonding in DNA Hoogsteen-type base pairs

Abstract

The purpose of our work is to characterize and present a theoretical comparative study of a variety of compounds based on DNA base pairs linked with some transition metal ions in gas phase: C–M–G (Cytosine–metal–Guanine) where [Formula: see text](I), Zn(II), Cd(II) and A–M–T (Adenine–metal–Thyminate) where [Formula: see text](II), Ru(I), Ni(I), Y(II), Zn(I), Cd(I), Cu(II). Geometry optimization and frequency calculations were carried out at DFT/ZORA/BLYP-D/TZ2P level. M–N and M–O bonds were investigated with the quantum chemical topology (QCT): Quantum theory of atoms in molecules (QTAIM) and electron localization functions (ELF). The hydrogen bonds: N10–H[Formula: see text]O7 for A–M–T complexes and N7–H[Formula: see text]O10 for C–M–T ones were visualized and discussed, QTAIM and ELF prove the existence of O7–H[Formula: see text]N10 hydrogen bond for some A–M–T systems, since the bond critical point (BCP) of N7–H having [Formula: see text], so it has a covalent character confirming the existence of a tautomer process of these complexes. Bonding energy [Formula: see text], Pauli repulsion [Formula: see text], electrostatic [Formula: see text], and orbital [Formula: see text] interactions were represented and compared together. Hirschfeld’s charges showed the existence of charge transfer process in the bridge moieties. It seems that, in contrast to natural base pairs that are stabilized by hydrogen bonding, Hoogsteen-type base pairs are held together by coordinative bond with metal ions.