C8855 Advanced Molecular Modelling Methods

Faculty of Science
Spring 2023
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Ivo Durník (seminar tutor)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research - Faculty of Science
Contact Person: RNDr. Petr Kulhánek, Ph.D.
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. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Learning outcomes
Student will have basic knowledge in the field of computational chemistry including knowledge about methods to analyze complicated energy functions and knowledge about molecular dynamics simulations, molecular complexes and chemical reactions. Student will be able to include solvent in the calculations. Students will be able to work with a selected program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996. xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022.
  • Enrolment Statistics (recent)
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