Nucleobase Pair–Metal Dimer/Dinuclear Metal Cation Interaction: A Theoretical Study

Abstract

Nucleobase pair–metal dimer/dinuclear metal cation interactions play an important role in biological applications because of their highly symmetrical structures and high stabilities. In this work, we have selected five adenine–adenine hydrogen bonding, adenine–thymine (AT), adenine–uracil, adenine–adenine stacking pairs, and Watson–Crick AT stacking pairs and studied their interaction with the coinage metal dimer M 2 and M 2 2+ metal cations, where M = Ag, Au, and Cu. Quantum chemical calculations have been carried out with density functional theory (DFT) and time-dependent DFT (TDDFT) methods. Electronic structures were analyzed by the partial density of states method. During interactions, we find that M–M distances are shorter than the sum of van der Waals radii of the corresponding two homocoinage metal atoms, which show the existence of significant metallophilic interactions. Results indicated that nucleobase–M 2 2+ complexes are stronger as compared to nucleobase–M 2 complexes. Also, the replacement of the hydrogen bond by the dinuclear metal cation-coordinated bond forms more stable alternative metallo-DNA sequences in AAST base pairs. TDDFT calculations reveal that nucleobase–Cu 2 complexes and nucleobase–Ag 2 2+ /Au 2 2+ complexes can be used for fluorescent markers and logic gate applications. Atom-in-molecules analysis predicted the noncovalent interaction in these complexes.