BB2280 Molecular Modeling 7.5 credits

The course consists of both theoretical lectures and practical computer exercises. The following topics will be discussed:

• Basic quantum chemistry: Molecular orbital theory, semi-empirical methods
• Basic density functional theory (DFT)
• Molecular mechanics and molecular dynamics
• Monte Carlo methods
• Energy minimization and potential energy surfaces
• QM/MM methods
• Solvation and surrounding effects
• Theoretical methods in drug discovery: Docking, protein structure prediction, QSAR
• Simulation of chemical reactions in solution
• Modelling of enzymatic catalysis
• Field trip to pharmaceutical company

Today, computer simulations are an important tool for the study of chemical processes in such different systems as isolated molecules, fluids, polymers, solid state, and biological macromolecules, like proteins and DNA.  The enormous development of computer hard drive space means that the molecular modeling field is developing very quickly. 

The goal with this course is to provide an overview of the methods and techniques which are used within modern molecular modeling.  Basic theory will be covered and applications within chemistry, biochemistry and medicinal chemistry will be discussed.

Completed degree project 15 credits, 20 university credits (hp) in Chemistry or Chemical Engineering, as well as 20 university credits (hp) in Mathematics. Documented proficiency in English corresponding to English B/6.

Basic classes in chemistry and mathematics för K och BIO.

• TEN1 - Written exam, 6.0 credits, grading scale: A, B, C, D, E, FX, F
• LAB1 - Laboratory Work, 1.5 credits, grading scale: A, B, C, D, E, FX, F

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

If the course is discontinued, students may request to be examined during the following two academic years.

Examination (TEN1, 6,0 credits, grading scale A-F) and Lab courses (LAB1, 1,5 credits, grading scale A-F).

Mårten Ahlquist

• All members of a group are responsible for the group's work.
• In any assessment, every student shall honestly disclose any help received and sources used.
• In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.

Students are required to sign up at least two weeks in advance for examination.

The course is given provided at least seven students are admitted.