Understanding and rationalizing chemical reactions, their mechanism, and the relation between molecular structure and function is key to today's science. It is a difficult task for experiments alone and computational methods are often used to complement experiment.

This course covers basic theory and practical application of computational methods and programs widely used in chemistry and molecular physics, for example density functional theory, semi-empirical calculations, molecular dynamics, MM/PBSA and free-energy perturbation.  An additional learning outcome is how to employ the programs in connection with local high-performance (HPC) computing facilities. The course's main focus is on the practical aspects and the methods are introduced through computational exercises, starting with gas-phase reaction for simple molecules. Gradually, we will move to larger systems, calculating thermochemical properties for organic reactions, amino acids solvated in water, as well as optical and magnetic spectroscopy for organic and inorganic molecules (including bio-inorganic systems). Moving the yet larger systems, we will investigate folding of small polypeptides, as well as DNA stability.  We will also set up and run molecular dynamics simulations for protein, calculating binding free energies for drug candidates with end-point methods and solvation free energies by free-energy perturbation.

Schedule

One class per week, Thursdays (1 h Lecture and 3 h exercise classes). The course runs for 10 weeks, starting in week 2 (12th January) until week 11 (16th March).

Course responsible

Ulf Ryde

Teachers

Ulf Ryde, Petter Persson and Erik Hedegård

Registration

Registration deadline is the 16th December 2022 (firm)

Please us the registration page to register for the course