Course memo Autumn 2021
Course presentation
Headings denoted with an asterisk ( * ) is retrieved from the course syllabus version Autumn 2021
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.
Learning activities
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.
Detailed plan
| Learning activities | Content | Preparations |
|---|---|---|
| Lecture 1 (1 Nov) | Introduction | |
| Lecture 2 (2 Nov) | Potential energy surfaces | |
| Lecture 3 (3 Nov) | Molecular Mechanics | |
| Lecture 4 (8 Nov) | Molecular dynamics | |
| Lecture 5 (9 Nov) | Introduction to QM | |
| Lecture 6 (15 Nov) | Hartree-Fock, Basis sets | |
| Lecture 7 (16 Nov) | Correlated Methods | |
| Lecture 8 (17 Nov) | Density Functional Theory | |
| Lecture 9 (22 Nov) | Qualitative Structure Activity Relation (QSAR) in Drug Discovery | |
| Lecture 10 (23 Nov) | Molecular Docking in Drug Discovery | |
| Lecture 11 (24 Nov) | Applications of Molecular Modeling | |
| Lecture 12 (29 Nov) | Research paper presentation | Mandatory to present one paper |
|
Lecture 13 (30 Nov) |
Research paper presentation | |
|
Lecture 14 (1 Dec) |
Research paper presentation | |
| Lecture 15 (7 DEC) | Invited lecture | |
| Lecture 16 (TBA) | Summary and repetion |
Preparations before course start
Recommended prerequisites
Basic classes in chemistry and mathematics för K och BIO.
Literature
No information insertedSupport for students with disabilities
Students at KTH with a permanent disability can get support during studies from Funka:
Examination and completion
Grading scale
A, B, C, D, E, FX, F
Examination
- 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.
The section below is not retrieved from the course syllabus:
Laboratory Work ( LAB1 )
Written exam ( TEN1 )
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).
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
No information inserted
Contacts
Round Facts
Start date
1 Nov 2021
Course offering
- Autumn 2021-50532
- Autumn 2021-50598
Language Of Instruction
English