Headings denoted with an asterisk ( * ) is retrieved from the course syllabus version Autumn 2021
Content and learning outcomes
Course contents
The course's theoretical content includes:
Introduction to 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
Modeling of enzymatic catalysis
Intended learning outcomes
After completion of the course the student shall be able to
demonstrate in-depth knowledge and analytical ability in molecular modeling adequate for the level of educational level of the course, and critically review others' work in the field [LAB1, PRO1]
demonstrate good ability to explain and analyze complex concepts in molecular modeling based on relevant research literature, and in a pedagogical way communicate the knowledge in writing and orally [PRO1]
be able to reflect on and describe how scientific issues in the field's research can contribute to sustainable societal development [PRO1]
Detailed plan
Lecture 1 (31 Oct)
Introduction + Potential energy surfaces
Lecture 2 (1 Nov)
Molecular Mechanics
Lecture 3 (2 Nov)
Molecular dynamics
Lecture 4 (7 Nov)
Solvation models
Lecture 5 (8 Nov)
Introduction to QM
Lecture 6 (9 Nov)
Hartree-Fock, Basis sets
Lecture 7 (14 Nov)
Correlated Methods
Lecture 8 (15 Nov)
Density Functional Theory
Lecture 9 (16 Nov)
No lecture
Lecture 10 (21 Nov)
Qualitative Structure Activity Relation (QSAR) in Drug Discovery
Lecture 11 (22 Nov)
Molecular Docking in Drug Discovery
Lecture 12 (23 Nov)
Applications of Molecular Modeling
Lecture 13 (28 Nov)
Research paper presentation
Mandatory to present one paper
Lecture 14 (29 Nov)
Research paper presentation
Lecture 15 (30 Nov)
Research paper presentation
Lecture 16 (TBA)
Invited lecture
Lecture 17 (After X-Mas)
Summary and repetion
Preparations before course start
Literature
Announced at course start.
Support for students with disabilities
Students at KTH with a permanent disability can get support during studies from Funka:
LAB1 - Laboratory work, 1.5 credits, Grading scale: P, F
PRO1 - Project, 6.0 credits, Grading scale: P, 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.
Grading criteria are specified in the course PM.
Other requirements for final grade
Required for final grade: 90% attendance at lectures, written critical reflection for selected scientific articles, approved written project report and completed oral project presentation (PRO1); and attendance on computer exercises and completed exercise reports (LAB1).
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.
