Chemical Structure Modeling (FSI-TSM)

Academic year 2020/2021
Supervisor: prof. RNDr. Jaroslav Koča, DrSc.  
Supervising institute: ÚFI all courses guaranted by this institute
Teaching language: Czech
Aims of the course unit:
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.
Learning outcomes and competences:
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.
Prerequisites:
Chemistry (FSI-1CH), Organic and Macromolecular Chemistry (FSI-TOM).

Links to other subjects:
compulsory co-requisite: CAD [3CD]
compulsory co-requisite: Organic and Macromolecular Chemistry [TOM]
Course contents:
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.
Teaching methods and criteria:
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.
Controlled participation in lessons:
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.
Type of course unit:
    Lecture  13 × 1 hrs. optionally                  
    Computer-assisted exercise  13 × 2 hrs. compulsory                  
Course curriculum:
    Lecture 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 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).
Literature - fundamental:
1. Leach, A. Molecular Modelling: Principles and Applications, 2nd ed.; Prentice Hall: Harlow England; New York, 2001.
2. Cramer, C. J. Essentials Of Computational Chemistry: Theories And Models; John Wiley & Sons, 2004.
3. Manuály programů Gaussian (http://www.gaussian.com/) a AMBER (http://ambermd.org/)
Literature - recommended:
4. Manuály počítačových programů SPARTAN a PEGAS
The study programmes with the given course:
Programme Study form Branch Spec. Final classification   Course-unit credits     Obligation     Level     Year     Semester  
B-FIN-P full-time study --- no specialisation -- Cr,Ex 4 Compulsory-optional 1 2 S