Course detail

Chemical Structure Modeling

FSI-TSMAcad. year: 2015/2016

Introduction in modelling of chemical structures. Students familiarize with basic methods of the energy of molecules or molecular systems by using the quantum chemistry. Basic types of interaction and their function expressions are discussed. The SPARTAN software package is used for determination of the energy minimum of a quantum system. Calculations of structures and energies. Computer design of a chemical synthesis by using the PEGAS software package.

Language of instruction

Czech

Number of ECTS credits

2

Mode of study

Not applicable.

Guarantor

prof. RNDr. Jaroslav Koča, DrSc.

Department

Institute of Physical Engineering (ÚFI)

Learning outcomes of the course unit

The course makes easy orientation of students at a choice of diploma project. Getting basic knowledge in the field of modelling of chemical structures will enable them to improve their understanding new technological processes applicable in development of modern materials.

Prerequisites

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

Co-requisites

Not applicable.

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 (lecture notes allowed at preparation).

Course curriculum

Not applicable.

Work placements

Not applicable.

Aims

In the course students familiarize with introduction in modelling of chemical structures in the range suitable for studies of engineering branches, e. g. nanotechnology. Students get acquainted with basic methods of calculations of molecule/molecular system energy by using the quantum chemistry. The aim of the course is to elucidate the basic interactions and carrying out the minimisation of quantum system energy by using the SPARTAN and PEGAS software packages.

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.

Recommended optional programme components

Not applicable.

Prerequisites and corequisites

Basic literature

Cramer, C. J. Essentials Of Computational Chemistry: Theories And Models; John Wiley & Sons, 2004.
Leach, A. Molecular Modelling: Principles and Applications, 2nd ed.; Prentice Hall: Harlow England; New York, 2001.
Manuály programů Gaussian (http://www.gaussian.com/) a AMBER (http://ambermd.org/)

Recommended reading

Manuály počítačových programů SPARTAN a PEGAS

Classification of course in study plans

  • Programme B3901-3 Bachelor's

    branch B-FIN , 2 year of study, summer semester, compulsory-optional

Type of course unit

 

Lecture

13 hod., optionally

Teacher / Lecturer

RNDr. Petr Kulhánek, Ph.D.

Syllabus

Introduction. Basic methods of calculations of the molecule/molecular system energy. Description of the geometry by using the Cartesian and internal co-ordinates.

The molecular mechanics. Basic types of interactions and their function expressions.

Summary of quantum chemistry methods.

Energy minimisation, relaxation, fixation, driving. Basic categories of minimisation techniques, their advantages and difficulties. The concept of potential energy surface (PES). Stationary points on the PES.

The SPARTAN software package. Basic functions. The methodology of conformational behaviour study.

The computer design of a chemical synthesis. The PEGAS software package.

Computer-assisted exercise

26 hod., compulsory

Teacher / Lecturer

RNDr. Petr Kulhánek, Ph.D.

Syllabus

The calculation of supportive theoretical examples and practical demonstrations and testing take place during the whole semester.