PřF:C7790 Intro. to Mol. Mod. - Course Information
C7790 Introduction to Molecular Modelling
Faculty of ScienceAutumn 2024
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Július Zemaník (lecturer) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is offered to students of any study field.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 3/30, only registered with preference (fields directly associated with the programme): 0/30 - Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Learning outcomes
- Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system; - Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week. - Listed among pre-requisites of other courses
- Enrolment Statistics (recent)
- Permalink: https://is.muni.cz/course/sci/autumn2024/C7790