Theoretical Study of Polaron Formation in Poly(G)−Poly(C) Cations

Abstract

Polaron formation in poly(G)-poly(C) cations is investigated with density functional theory (DFT) and molecular mechanics (MM) employing a two-layer ONIOM method. In these calculations, the high layer, composed of all complementary base pairs, is treated by a DFT method, while the low layer, which includes the sugar-phosphate backbone, counterions and water molecules, is described by the AMBER force field. The high layer is the model system in which the charge transfer takes place. According to our calculations, three or four guanines move in a paddle-like fashion when an electron is removed from the neutral model system. In the cation model system, about 80% of the charge is delocalized onto the guanine residues, and the remaining charge is delocalized onto the cytosine residues. This happens because guanine has a lower ionization potential (IP) than cytosine. The counterions and water molecules in the low layer are important in the geometry optimization. The optimized geometry of the model system is closer to the standard B-form structure when counterions and water molecules are included than when they are omitted. Comparison of the optimized neutral and cationic model systems reveals a polaron in poly(G)-poly(C) cations extending from the first to the third guanine. It is demonstrated that the position of counterions and the number of surrounding water molecules can affect polaron formation.