Course detail

Chemical Structure Modeling

FSI-TSMAcad. year: 2020/2021

The course is focused on acquiring basic knowledge in the field of computational chemistry in amount suitable for study of some engineering disciplines, e.g. nanotechnology. The course is oriented on obtaining practical skills in using chemical modelling software. Students will learn how a molecular geometry is represented in a computer and how the energy is calculated. At the end, students will learn how to use one of the commonly used modelling software packages.

Learning outcomes of the course unit

The course will help students to select their diploma project. Students will obtain basic knowledge in modelling of chemical structures, which help them in understanding of new technological processes applicable in development of advanced materials.


Chemistry (FSI-1CH), Organic and Macromolecular Chemistry (FSI-TOM).


Not applicable.

Recommended optional programme components

Not applicable.

Recommended or required reading

Leach, A. Molecular Modelling: Principles and Applications, 2nd ed.; Prentice Hall: Harlow England; New York, 2001.
Cramer, C. J. Essentials Of Computational Chemistry: Theories And Models; John Wiley & Sons, 2004.
Manuály programů Gaussian ( a AMBER (
Manuály počítačových programů SPARTAN a PEGAS

Planned learning activities and teaching methods

The course is taught through lectures explaining the basic principles and theory of the discipline. Exercises are focused on practical topics presented in lectures.

Assesment methods and criteria linked to learning outcomes

The student's assessment shall involve partly his performance in practice, partly results attained in a written test and a following discussion on topics selected at the examination.

Language of instruction


Work placements

Not applicable.


The aim of the course is to present theoretical background of methods that are commonly used in modelling of molecular structures. The main emphasis is placed on used approximations and their impact on the quality of obtained results. Students will obtain basic insight about computer representation of molecular systems and their characterization employing quantum chemical and molecular mechanics calculations. Students will exercise calculations of the interaction energy, find reaction pathway of simple reaction, and perform a short molecular dynamics simulation.

Specification of controlled education, way of implementation and compensation for absences

The presence of students at practice is obligatory and is monitored by a tutor. The way how to compensate missed practice lessons will be decided by a tutor depending on the range and content of missed lessons.

Classification of course in study plans

  • Programme B-FIN-P Bachelor's, 2. year of study, summer semester, 4 credits, compulsory-optional

Type of course unit



13 hours, optionally

Teacher / Lecturer


1. Experiment versus molecular modelling (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 modelling, periodic boundary conditions, and 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)

Computer-assisted exercise

26 hours, compulsory

Teacher / Lecturer


The calculation of selected theoretical examples and practical demonstrations are held throughout the semester (e.g. calculation of the interaction energy, the study of reaction mechanisms, molecular dynamic simulations).