Stability of Ag-DNA nucleotide base complexes: A quantum-chemical study

DNA-metal interactions play a significant role in both biological function and DNA-based nanomaterials. In particular, DNA complexes with Ag+ ions, forming a nanowire inside the double helix, are of fundamental and practical importance. Here, we present a quantum-chemical density functional theory (DFT) study of Ag+ complexes with DNA, focusing on Ag+ binding to the N1 atom of thymine, the N1 and N7 atoms of guanine, and the N3 atom of 5-bromocytosine. The B3LYP and M06-2X functionals were employed in combination with the polarizable continuum model (PCM) and solvation model based on density (SMD). The results show that the stability of these complexes strongly depends on the nucleobase type and the position of the donor atom. Electrically neutral complexes involving Ag+ at the N3 atom of thymine and the N1 atom of guanine exhibited the highest thermodynamic stability, whereas positively charged complexes with the N1 atom of adenine were the least stable, consistent with the experimentally observed extrusion of adenine from the double helix in metallized Ag-DNA. Comparison of computational methods indicates that the B3LYP functional combined with the SMD solvation model provides the most reliable description of Ag+–nucleobase complexes. These findings are essential for understanding the structural features of metallized Ag-DNA and its potential as a nanomaterial.