Course detail

Chemical Structure Modeling

FSI-TSMAcad. year: 2023/2024

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.

Language of instruction


Number of ECTS credits


Mode of study

Not applicable.

Entry knowledge

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

Rules for evaluation and completion of the course

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.
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.


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.
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.

Study aids

Not applicable.

Prerequisites and corequisites

Basic literature

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 (

Recommended reading

Manuály počítačových programů SPARTAN a PEGAS

Classification of course in study plans

  • Programme B-FIN-P Bachelor's, 2. year of study, summer semester, 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).