The course is designed to give student in chemistry and related subjects an introduction to the theory for modeling, and use of modeling as a tool in chemical research. Considerable emphasis will be placed on practical use of modeling and an understanding of the methods which extends beyond purely operational skills. The aim is to give the students the sufficient background to independently evaluate choice of methods and reliability of results in molecular modeling.

Computational methods based on molecular mechanics, statistical mechanics and informatics are introduced with the focus on molecular systems. The methodologies include force fields, molecular dynamics and Monte Carlo simulations, energy minimizations and conformational analysis, solvation models periodic systems.

• Contextualize and define the discipline of Molecular Modeling.
• Define the foundations and theoretical calculations in molecular mechanics.
• Understand and apply the methods of optimization of molecular models: minimization and molecular dynamics.
• Understand Monte Carlo and Molecular Dynamics simulations of molecular systems.
• Appreciate the wide variety of molecular simulation methods that have been developed, and learn to choose an appropriate method for a desired mechanism.
• Understand how microscopic properties such as atomic velocities are related to macroscopic material properties such as temperature, diffusivity etc.
• Assess articles from the scientific literature that utilize molecular simulations critically.