对包含极化力场信息的粗粒化模型的理论研究

Because of the high complexity of soft matters, many traditional methods and strategies stemed from quantum mechanics and equilibrium statistical mechanics can not be adopted to those systems. So we must develop mescoscopic methods to do this. As well known that the efficiency of molecular simulations is controled by the molecular force field. However, the first and second periods of force field cannot discribe the electrostatic polarizable phenomena in that the electrostatic potential model with the fixed center of atom and the invariable charge of point are used to build the molecular force field. For there widely exist the polarizable phenomena in soft matters, we must introduce the polarizable force field into the coarse-grained models in order to simulate the quantities of those systems. In the current research, we will investigate three kinds of soft matters, such as the organic molecular liquids, the mixed systems of hetadeca-alkyl and naphthalenealkyl, and peptides of (Ala)n (n=9,13,17), respectively, within the framework of the coarse-grained model combining the Gay-Berne and electrostaic multipole expansion potentials. For this purpose, the first step is to build coarse-grained force field for atom clusters, hetadeca-alkyl, three kinds of naphthalenealkyl as well as alanine. Next, to select rationally conformational groups, and then we obtained the coarse-grained parameters, namely GB parameters and EMP ones. With GB-EMP parameters, we will carry out coarse-grained molecular simulations for the aforementioned systems. Besides that, we will make comparsion between the results with this model and those from all-atom model, i.e. AMOEBA all-atom model. The aims of this research are to study the efficiency of the current coarse-grained model, and the roles of the polarizable force field.

软物质体系具有高度的复杂性，故传统的量子力学和平衡态统计物理方法难以直接应用，必需发展各种介观模拟方法。用经典力学进行分子模拟的准确性由力场的质量决定，而传统力场由于采用了固定原子中心固定点电荷的原因，所以无法细致地描述静电极化现象。鉴于在软物质体系中静电极化现象的普遍存在，为了更加准确地描述体系性质，就需在介观模型中引入极化力场。本项目基于考虑了极化力场信息的粗粒化模型对三类软物质体系，即有机分子液体、烷基萘和正十六烷的共混物和丙氨酸饱和多肽链进行粗粒化分子动力学模拟。为此，我们首先应创建针对某些官能团、正十六烷、三种烷基萘和丙氨酸的粗粒化力场，然后合理选取模拟体系的构象集，最后通过数值拟合和量化计算得到了相应体系的粗粒化参数，最后进行对由粗粒化模拟得到的结果与由全原子模型到的结果相比较以期检验目前粗粒化模型的效率，并从多个视角获知极化力场的作用。

软物质体系具有高度的复杂性，故传统的量子力学和平衡态统计物理方法难以直接应用，必需发展各种介观模拟方法。用经典力学进行分子模拟的准确性由力场的质量决定，而传统力场由于采用了固定原子中心固定点电荷的原因，所以无法细致地描述静电极化现象。鉴于在软物质体系中静电极化现象的普遍存在，为了更加准确地描述体系性质，就需在介观模型中引入极化力场。一方面，基于考虑极化力场信息的粗粒化模型对有机分子液体和丙氨酸饱和多肽链进行粗粒化分子动力学模拟。为此，我们首先创建针对某些官能团和丙氨酸的粗粒化力场，然后合理选取模拟体系的构象集，通过数值拟合和量化计算得到了相应体系的粗粒化参数，最后进行对由粗粒化模拟得到的结果与由全原子模型到的结果相比较以期检验目前粗粒化模型的效率，并从多个视角获知极化力场的作用。另一方面，为了研究团簇分子解离反应中存在的非谐振效应，我们首先优化了甲醛、乙基、苯基等分子和自由基的构型，然后计算了其谐振和非谐振频率及单点能，再根据RRKM理论，计算出在不同温度或能量下分子解离反应正则系综和微正则系综的速率常数,速率常数与实验数据符合的非常好。最后通过分析各个反应中存在的非谐振效应可知，在正则系统中，反应的非谐振效应比较小，而在微正则系统中，则反之。