| Name: |
Molecular Mechanics and Modeling Principles and Applications |
| Catalog Number: |
412034Y |
Hours/Credits: |
40/2 |
| Prerequisite(s): |
|
Physical Chemistry; Fundamentals of Computer Science |
| Course Description: |
|
Principles and applications of molecular mechanism is designed as a fundamental core course for chemists in all sub-tracks and for graduate students from other related majors as a complementary course. It provides an introduction on the theoretical background and the modern computational techniques used in molecular modeling, and will illustrate how these techniques can be applied to study physical, chemical and biological problems. Three parts are included, computational principles, methods and applications. Through learning the principles and practicing multiple types of computational software, one will be trained with the fundamental applications of molecular modeling in studying molecular structure，property and function. |
| Course Content: |
|
Chapter 1: Concepts of molecular modeling
Potential energy surfaces; Molecular surfaces.
Chapter 2: Force field models of molecular mechanics
Features of force fields and equation of energy; Many-body effects in empirical potentials and effective pair potentials; United atom force field and reduced representations, Calculating thermodynamic properties using a force field; Force field parameterization.
Chapter 3: Method and usage of conformational searching
Molecular dynamics using simple models; Molecular dynamics with continuous potentials; Setting up and running a molecular dynamics simulation; Constraint dynamics; Molecular dynamics at constant temperature and pressure; Incorporating solvent effects into molecular dynamics.
Chapter 4: Molecular dynamic simulation method
Some theoretical background to the Metropolis Monte Carlo method; Monte Carlo simulation of rigid and flexible molecules; Models used in Monte Carlo simulations of polymers; Simulating phase equilibria by Gibbs ensemble.
Chapter 5: Monte Carlo simulation method
Modeling methods; Systematic search methods; Random search methods; Genetic algorithms etc.; The role of conformational analysis in predicting the structures of peptides and proteins.
Chapter 6: Introduction of molecular modeling software
HyperChem, Pcmodel, Origin and Chemsket. |
| TextBooks: |
|
Andrew R. L., Molecular Modeling Principles and Applications, Prentice Hall, 2001. |
| Reference: |
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