《Theoretical and Computational Chemistry》course for graduates

Credit: 2;  Class hours: 32.  Lecturer: Prof. Zhirong Liu.

Aims:

    Molecular mechanics (also known as force field method) adopts classical mechanics to describe the properties of molecular system, and combines computer techniques to determine molecular conformation, energy and other thermodynamic and dynamic properties. It is widely used in computational chemistry, computational biology, materials science and other fields. This course mainly introduces principles and applications of molecular mechanics, so that students can master the background knowledge needed to read and understand the contents related to molecular simulation in the literature, and also provides a basic training for those who are interested in molecular simulation research.

    Shortly, the purpose of the course is to prepare students to read and interpret the molecular modeling literature and to apply molecular modeling in their research.

References:

1. Andrew R. Leach, Molecular modeling: principles and applications, 2nd ed. (Pearson Education, Harlow, 2001).

2. Luhua Lai, Protein structure prediction and molecular design. (Peking University Press, Beijing, 1993).

3. Minbo Chen, Computational chemistry: from theoretical chemistry to molecular modelling. (Science Press in China, Beijing 2009).

4. Jonathan M. Goodman, Chemical applications of molecular modeling, The royal society of chemistry, Cambridge, 1998.

Outlines:

* Introduction to molecular mechanics

* Force field: formula and parameterization

* Energy minimization

* Conformation analysis

* Molecular dynamics

* Monte Carlo simulations

* Automatic construction of molecular conformation: from 2D to 3D

* Solvation model

* Free energy

* Molecular docking

* QM/MM

* Applications in drug design