Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada.
J Phys Chem B. 2011 Mar 31;115(12):3136-45. doi: 10.1021/jp108818u. Epub 2011 Mar 9.
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.
聚（G）-聚（C）阳离子中极化子的形成采用密度泛函理论（DFT）和分子力学（MM），利用两层 ONIOM 方法进行研究。在这些计算中，由所有互补碱基对组成的高层采用 DFT 方法处理，而包括糖-磷酸骨架、反离子和水分子的低层则由 AMBER 力场描述。高层是发生电荷转移的模型体系。根据我们的计算，当从中性模型体系中除去一个电子时，三个或四个鸟嘌呤以桨式方式移动。在阳离子模型体系中，约 80%的电荷离域到鸟嘌呤残基上，其余的电荷离域到胞嘧啶残基上。这是因为鸟嘌呤的电离势（IP）低于胞嘧啶。低层中的反离子和水分子在几何优化中很重要。当包括反离子和水分子时，模型体系的优化几何形状更接近标准 B 型结构，而当省略它们时则更接近。比较优化的中性和阳离子模型体系揭示了聚（G）-聚（C）阳离子中的极化子从第一个鸟嘌呤延伸到第三个鸟嘌呤。结果表明，反离子的位置和周围水分子的数量可以影响极化子的形成。
