Course: Computational Chemistry and Molecular Modelling of Biomolecules

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Course title Computational Chemistry and Molecular Modelling of Biomolecules
Course code UCH/060
Organizational form of instruction Lecture
Level of course Bachelor
Year of study not specified
Frequency of the course In each academic year, in the winter semester.
Semester Winter
Number of ECTS credits 4
Language of instruction English
Status of course Compulsory
Form of instruction Face-to-face
Work placements This is not an internship
Recommended optional programme components None
Course availability The course is available to visiting students
  • Řeha David, Mgr. Ph.D.
  • Kabeláč Martin, doc. Mgr. Ph.D.
  • Minofar Babak, Ing. Ph.D.
Course content
1.Introduction to quantum theory: Schrödinger equation and its approximations, valence bond theory, wave function. 2.Computational methods of quantum chemistry : ab initio approaches, semiempirical methodscommonly used programs in the computational chemistry. 3.Computational experiments and simulations: classical and ab initio molecular dynamics, Monte Carlo, calculations of statistical and thermodynamics values. 4.Intra- and intermolecular interactions in biomolecules. 5. Empirical force fields, molecular dynamics, homology modeling 6. Biopolymers -Nucleic acids and Proteins: structure and dynamics dominant effects during the process of protein folding, geometrical parameters of polypeptide chain, peptides, docking, combinatorial chemistry, QSAR methods. 7.Structural databases in chemistry and biology: Retrieving of structures, statistical methods, data sorting and handling.

Learning activities and teaching methods
Monologic (reading, lecture, briefing)
  • Preparation for classes - 30 hours per semester
  • Preparation for exam - 30 hours per semester
  • Class attendance - 50 hours per semester
Learning outcomes
To obtain a basic knowledge about methods used in theoretical chemistry, how to calculate the structures and properties of molecules with the stress on biopolymers.
basic orientation in quantum mechanics, theory of quantum chemical calcualtions and molecular modelling
no extra requirements

Assessment methods and criteria
Oral examination

basic knowledge of Integral and Differential calculus, General chemistry and Physics
Recommended literature
  • LEACH A., Molecular Modelling: Principles and Applications, Pearson Education EMA, January 2001.
  • YOUNG D., Computational Chemistry, A Practical Guide for Applying Techniques to Real World Problems , John Wiley and Sons Ltd., England 2001.

Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
Faculty: Faculty of Science Study plan (Version): Bioinformatics (1) Category: Informatics courses 3 Recommended year of study:3, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Biological chemistry (1) Category: Chemistry courses - Recommended year of study:-, Recommended semester: Winter