Course: Molecular Structure Modelling in Biosciences

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Course title Molecular Structure Modelling in Biosciences
Course code UCH/617
Organizational form of instruction Lecture + Lesson
Level of course Doctoral
Year of study not specified
Frequency of the course In each academic year, in the winter semester.
Semester Winter
Number of ECTS credits 5
Language of instruction Czech
Status of course Compulsory-optional
Form of instruction unspecified
Work placements unspecified
Recommended optional programme components None
Lecturer(s)
  • Kutý Michal, Mgr. Ph.D.
  • Kabeláč Martin, doc. Mgr. Ph.D.
  • Řeha David, Mgr. Ph.D.
Course content
Content of lectures: 1. Introduction to quantum theory: Schrödinger equation and its approximations, operators, wave function. 2. Computational methods of quantum and theoretical chemistry: ab initio approaches, semiempirical methods, 3. empirical force fields, molecular mechanics; commonly used programs in the computational chemistry. 4. Potential energy surface, methods of localization of minima and transition states 5. Computational experiments and simulations: classical molecular dynamics, Monte Carlo, calculations of statistical and thermodynamics values, simulations of spectra 6. Intra- and intermolecular interactions in biomolecules. Content of practices: 1. Introduction to UNIX operating system, basic commands, work with text editors. 2. Applications of the quantum chemical programs (GAUSSIAN) , programs for empirical calculations (molecular mechanics and dynamic -AMBER). 3. Computer graphics: building of the molecule, vizualization of the results obtained by computational experiments (MOLDEN, VMD).

Learning activities and teaching methods
Monologic (reading, lecture, briefing), Laboratory
  • Preparation for classes - 50 hours per semester
  • Preparation for exam - 50 hours per semester
  • Class attendance - 50 hours per semester
Learning outcomes
Theoretical prediction and interpretation of experimental results became necessary in modern chemistry. Due to rapid development of computer hardware the very exact theoretical data became available. This set of lectures gives an introduction to the theoretical study of small molecules as well as large biomolecules (mainly proteins and nucleic acids). After a brief explanation of basic principles of quantum chemistry, the lectures are going to be focused on the intermolecular interactions, structure and dynamics of the biomolecules. The exercises will give the insight how to obtain the structure and properties of relative small molecules (tens of atoms) using ab initio methods as well as how to provide the computer experiments of larger systems (hundreds or thousands atoms) of the biological interest. Students will become familiar with UNIX operating system, molecular modeling and computer graphics.
The knowledge abou common computational methods and their theoretical principles will be obtained. Practical part covers work with programs Gaussian and Hyperchem.
Prerequisites
The course of General and Physical Chemistry was succesfully finished - obligatorily Graduation Chemical Structure and Spectroscopy course is recommended.

Assessment methods and criteria
Oral examination, Development of laboratory protocols

Passing the oral exam and protocols from the project tasks.
Recommended literature
  • Leach, A.. Molecular Modelling: Principles and Applications, Pearson Education EMA, 2001..
  • Nebeda, I., Kolafa , J. Kotrla , M. Úvod do počítačových simulací , Karolinum 1998.
  • P. Atkins, J. de Paula. Fyzikální chemie, ČVUT Praha 2013..
  • Slavíček, P. Ončák M., Šištík, P. Stručný úvod do teoretické a počítačové chemie, dostupné volně na old.vscht.cz/fch/cz/pomucky/Prirucka_TeorChem.pdf.
  • 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): Biophysics (1) Category: Physics courses - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Secondary Schools Teacher Training in Chemistry (1) Category: Pedagogy, teacher training and social care - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Secondary Schools Teacher Training in Chemistry (1) Category: Pedagogy, teacher training and social care - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Biophysics (1) Category: Physics courses - Recommended year of study:-, Recommended semester: Winter