Interaction of cations with 2′‐deoxythymidine nucleoside and analysis of the nature and strength of cation bonds

Abstract

Binding of Mg2+, Ca2+, Zn2+, and Cu+ metal ions with 2′‐deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6‐311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri‐coordinated η (O2, O4′, O5′). Among the four types of cations, Zn2+ cation exhibited the most tendency to interact with the dT. Cations via their interaction with dT can affect the N‐glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules was also applied to determine the nature of interactions. It was shown that in dT–Mg2+ and dT–Ca2+ complexes, the bonds are electrostatic (closed‐shell) interactions, although they are partially covalent and partially electrostatic interactions in dT–Zn2+ and dT–Cu+ complexes. Copyright © 2011 John Wiley & Sons, Ltd.