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BB2280 Molecular Modeling 7.5 credits

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For course offering

Autumn 2024 Start 28 Oct 2024 programme students

Application code


Headings with content from the Course syllabus BB2280 (Autumn 2024–) are denoted with an asterisk ( )

Content and learning outcomes

Course contents

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

Intended learning outcomes

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.

Literature and preparations

Specific prerequisites

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.

Recommended prerequisites

Basic classes in chemistry and mathematics för K och BIO.


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Examination and completion

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

Grading scale

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.

Other requirements for final grade

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

Opportunity to complete the requirements via supplementary examination

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Opportunity to raise an approved grade via renewed examination

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Ethical approach

  • 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.

Further information

Course room in Canvas

Registered students find further information about the implementation of the course in the course room in Canvas. A link to the course room can be found under the tab Studies in the Personal menu at the start of the course.

Offered by

Main field of study


Education cycle

Second cycle

Add-on studies

No information inserted

Supplementary information

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.