Course memo Autumn 2023
Course presentation
Headings denoted with an asterisk ( * ) is retrieved from the course syllabus version Autumn 2023
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 (30 Oct) | Introduction + Potential energy surfaces | |
Lecture 2 (31 Oct) | No lecture | |
Lecture 3 (1 Nov) | Molecular Mechanics | |
Lecture 4 (6 Nov) | Molecular dynamics | |
Lecture 5 (7 Nov) | Applications of Molecular Dynamics | |
Lecture 6 (8 Nov) | Introduction to QM | |
Lecture 7 (13 Nov) | Hartree-Fock, Basis sets | |
Lecture 8 (14 Nov) | Correlated Methods | |
Lecture 9 (15 Nov) | Density Functional Theory | |
Lecture 10 (20 Nov) | Applications of Quantum Chemistry | |
Lecture 11 (21 Nov) | Solvation models | |
Lecture 12 (22 Nov) | Qualitative Structure Activity Relation (QSAR) in Drug Discovery | |
Lecture 13 (27 Nov) | Molecular Docking in Drug Discovery | |
Lecture 14 (28 Nov) |
Research paper presentation | Mandatory to present one paper |
Lecture 15 (29 Nov) |
Research paper presentation | |
Lecture 16 (TBA) | Invited lecture | |
Lecture 17 (After X-Mas) | Summary and repetion |
Preparations before course start
Recommended prerequisites
Basic classes in chemistry and mathematics för K och BIO.
Literature
No information insertedEquipment
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.
Software
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.
More information will be given at the first lectures.
Support 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
Course Coordinator
Teachers
Examiner
Round Facts
Start date
30 Oct 2023
Course offering
- Autumn 2023-10010
- Autumn 2023-50782
Language Of Instruction
English