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.

The course is taght with lectures, student presentations of research papers, and computer exercises. The computer exercises and the presentation of a research paper is mandatory.

Basic classes in chemistry and mathematics för K och BIO.

You will perform the computer lab exercises on your personal laptop. Please make sure to have one available or contact the course responsible if you do not have access to a computer.

You need to install either Anaconda or Miniconda (not both) on your computer for the exercises. 

https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html

https://docs.anaconda.com/free/anaconda/install/index.html

For building molecules we will use Avogadro which can be downloaded from the link below. 

https://avogadro.cc/

More information will be given at the first lectures.

Students at KTH with a permanent disability can get support during studies from Funka:

Funka - compensatory support for students with disabilities

A, B, C, D, E, FX, F

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

Laboratory Work ( LAB1 )

Written exam ( TEN1 )

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

• 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.