Thermodynamic stability of cytosine tetramers mediated by partially reduced silver trimers: QM/MM free energy analysis

Abstract

AbstractPartially reduced silver clusters growing in a polycytosine matrix could simultaneously possess stabilizing ability and remarkable optical features. The mechanisms of this phenomenon are not fully understood so far. We examined the thermodynamic stability of a cytosine–silver associate comprising four cytosines and three silver atoms that can be considered the smallest known luminescent silver marker stabilized on DNA. Quantum and molecular mechanical representations thermodynamic integration toward the dissociation pathway of the cytosine tetramer, time‐dependent density functional theory calculations of the lowest energy excited states and quantum theory of atoms in molecules analysis of bonding showed that the reduction of two ions within the silver trimer mediating cytosine tetramer leads to the appearance of the green‐emitting silver cluster with low stabilization ability of cytosines relative to a tetramer stabilized by two silver ions.