摘要
Na+-G-四链体复合物是一个明显的极化体系,其形成或解离过程中,Na+的移动路线目前还不十分明确.σπ水平的原子-键电负性均衡方法融合进分子力学(ABEEMσπ/MM)模型除原子位点外,还明确地定义了孤对电子、σ键和π键的位置,并且各位点电荷随分子环境改变而浮动,因此能更好地反映该体系的极化现象.本文应用ABEEMσπ/MM方法研究了Na+-G-四平面复合物的性质,包括它的几何构型、电荷分布和结合能等,并在MP2/6-31G(d,p)水平上做了相应的从头算,两种结果十分吻合.Na+的存在改变了G-tetrad的氢键方式.通过比较Na+各条移动路线中体系的结合能,预测G-四链体中三个Na+最有可能沿α方向依次移出.以上研究为进一步应用ABEEMσπ/MM模型进行G-四链体中离子交换通道的动力学模拟打下坚实的基础.
The Na^＋-G-quadruplex complex is a polarized system and the mobility of Na^＋ during its formation or decomposition is still unclear. The atom bond electronegativity equalization method at the σπ level fused into molecular mechanics （ABEEMσπ/MM） model clearly defines the lone-pair electron, σ bond and π bond sites in addition to the atomic sites. The partial charge fluctuation is calculated in accordance with a change in the molecular environment and so this method should account well for the polarization effect. In this paper, we discuss some properties for the Na^＋-G- tetrad complex including its geometry, charge distribution, and binding energy according to the ABEEMσπ/MM method. We also investigate these properties for the Na^＋-G-tetrad complex using the ab initio method at the MP2/6- 31G（d,p） level. The ABEEMσπ/MM results are in good agreement with the ab initio results. The presence of Na^＋ changes the hydrogen bonds in the G-tetrad. By comparing the binding energy of the system for every Na^＋ mobile path, we predict that the most probable path is that three Na^＋ ions move away individually from the G-quadruplex along the σ orientation. This study lays a solid foundation for the dynamic simulation of ion exchange channels in a G- quadruplex using the ABEEMσπ/MM model.
出处
《物理化学学报》
SCIE
CAS
CSCD
北大核心
2010年第2期478-486,共9页
Acta Physico-Chimica Sinica
基金
国家自然科学基金(20633050
20873055)
辽宁省教育厅基金(2008S133
2009T057
LNETRC0503)资助项目~~
