C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 2007 - for the purpose of the accreditation
Extent and Intensity
1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
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 also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10
fields of study / plans the course is directly associated with
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.
Syllabus
  • 1. Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. 2. Molecular mechanics. Basic interactions and their expression. 3. Quantum chemistry methods. 4. Molecular dynamics, basic equations. 5. Potential energy hypersurfaces (PES). Stationary points on PES. 6. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. 7. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy.
Literature
  • REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. 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
Assessment methods (in Czech)
Kurs sestává ze sedmi dvouhodinových přednášek. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt.
Language of instruction
Czech
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
Teacher's information
http://www.chemi.muni.cz/~jkoca/#TEACHING MATERIAL
The course is also listed under the following terms Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.