分子模拟实验课程建设的探索与实践

doi:10.3866/PKU.DXHX201901035

Abstract

Abstract:

We put forward the idea of building a molecular simulation experiment course. After two-year teaching practice, we write the experiment textbook which not only covers the classic experimental projects, but also includes the frontier hot issues, and open exploration experiment. This article summarizes the teaching requirements, basic content, assessment methods, the initial achievements made so far and the prospects for the future.

Key words: Molecular simulation experiment, Structural chemistry, Computational chemistry, Curriculum construction

Heng ZHANG,Ying MA,Gang LIU,Dongju ZHANG,Qisheng SONG,Shiling YUAN. Exploration and Practice on Construction of Molecular Simulation Experiment Course[J].University Chemistry, 2019, 34(9): 26-31.

Figures/Tables 3

References 13

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理论基础	具体内容
1.绪论	分子模拟的概念、发展历史
2.统计力学基础	统计力学基本原理、粒子动力学
3.力场	势函数、简正模式、简单体系的分子力场、势能函数的具体形式、常见的力场、联合原子和约化处理、粗粒力场、多体势、水分子力场、选择力场
4.能量最小化	势能面、势函数的极小值、非导数求极值法、导数求极值法、一级导数求极值法、二级导数求极值法、方法的选择和收敛性判据、过渡态结构与反应路径、溶剂化效应
5.模拟中的基本原理	短程相互作用、长程相互作用、模拟过程
6. Monte Carlo模拟	Monte Carlo模拟中的配分函数、Monte Carlo原理、基本Monte Carlo模拟、不同系综中的Monte Carlo模拟
7.分子动力学模拟	积分运动等式、Verlet预测方法、Gear预测校正方法、分子体系中的积分方法、不同系综中的分子动力学、相关函数
8.介观模拟	耗散粒子动力学模拟、介观动力学模拟
9.量子化学方法	Schrödinger方程、电子相关和后HF方法、密度泛函理论、基函数(基组)的选择、半经验分子轨道方法

实验项目	具体内容
1.分子模型的创建与优化	分子模型的绘制、分子构型优化、复杂分子结构的创建
2.分子轨道的计算和分析	分子轨道等值面图、总电子密度图、静电势图、电荷分布图、分子表面
3.势能面计算	键的断裂、分子间的弱相互作用、分子构象搜索、化学反应势能面扫描、对比氢键和卤键势能面
4.化学反应模拟	计算化学反应的自由能、优化搜索过渡态
5.分子光谱计算	红外和拉曼光谱、紫外-可见光谱、X射线衍射光谱
6.分子动力学模拟	乙醇水溶液体系的模拟
7. Monte Carlo模拟	表面吸附行为：吸附等温线、吸附构型、吸附动力学
8.聚集行为的介观模拟	表面活性剂在溶液中的聚集行为、嵌段共聚物的相行为
9.粗粒化模拟	生物膜的搭建及粗粒化

姓名	题目
赵留鹏	两种^{[2, 2]}环仿类化合物催化活性的对比研究
刘盈秋	通过氮吸附的钯修饰石墨烯去除卤代污染物TBBPA的分子机制
李永豪	Micheal加成反应机理的研究
李萌萌	Beckman重排反应机理的研究
张帅	碳纳米管对氢气吸附性能的模拟
赵巾钦	[Fe-Fe]氢化酶催化过程中催化剂电子云密度的计算
李庆存	不同的R基对S_N1反应可能性的影响

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Exploration and Practice on Construction of Molecular Simulation Experiment Course

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