SubjectsSubjects(version: 878)
Course, academic year 2020/2021
Computations and Visualization of Molecules - N110024
Title: Výpočty a vizualizace molekul
Guaranteed by: Department of Organic Chemistry (110)
Actual: from 2019
Semester: winter
Points: winter s.:4
E-Credits: winter s.:4
Examination process: winter s.:
Hours per week, examination: winter s.:1/2 C+Ex [hours/week]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Is provided by: M110007
For type:  
Note: course can be enrolled in outside the study plan
enabled for web enrollment
Guarantor: Kvíčala Jaroslav prof. Ing. CSc.
Z//Is interchangeable with: M110007, AM110007
Annotation -
Last update: Kvíčala Jaroslav prof. Ing. CSc. (04.09.2012)
The course is targeted mainly on the student with zero knowledge of computational chemistry, oriented on inorganic, organic and macromolecular chemisty. It concentrates on practical use of Gaussian and PCGamess computational programs. Special attention is devoted to vizualization of the computational results, as optimized geometries, infrared and NMR spectra, electrostatic potential and reaction mechanisms, using both commercial (GaussView) and free of charge available (Molekel, WxMacMolPlt, ArgusLab etc.) programs.
Aim of the course -
Last update: Cibulka Radek prof. Ing. Ph.D. (20.08.2013)

Students will be able to:

work with Gaussian 03 program, perform ab initio and DFT computations

work with GaussView program and employ it for the visualisation of the results of Gaussian 03 computations

work with Firefly program and employ it for ab initio and DFT computations

work with Molekel and WxMacMolPlt programs and employ it for the visualisation of the results of Firefly computations

Literature -
Last update: Kvíčala Jaroslav prof. Ing. CSc. (14.08.2013)

A: J. B. Foresman, A. Frisch, Exploring Chemistry with Electronic Structure Methods, 2nd ed. Gaussian, Inc., Pittsburgh, USA, 1996. ISBN 0-9636769-3-8.

Learning resources -
Last update: Kvíčala Jaroslav prof. Ing. CSc. (14.08.2013)

Electronic version of lectures

Syllabus -
Last update: Kvíčala Jaroslav prof. Ing. CSc. (20.08.2013)

1. Overview of commercial and free of charge available computational and vizualization programs. Computational methods (molecular mechanics, semiempirical, SCF ab initio, post-SCF, DFT).

2. Short overview of theoretical principles of computational methods, summary of approaches and approximations in the MO-LCAO method. Basic principles of DFT methods.

3. Gaussian03W program, basic keywords. GaussView program as the interface for Gaussian03W, building the molecule, input deck for Gaussian03W.

4. Computation of the molecule energy, geometry optimalization. Computations of vibration frequencies, vizualization of infrared spectra.

5. Vizualization of calculation results, canonical and localized orbitals using GaussView program. Natural bond orbital method, calculation of charges.

6. Calculations using post-SCF methods. The use of DFT method for the calculations of NMR shielding and coupling constants, vizualization of the NMR spectra. Simulation of reaction mechanisms.

7. Calculation of reaction path (IRC), vizualization of reaction mechanisms using GaussView. Freezing the bond lengths, bond angles and torsion angles.

8. Calculations of the molecules in simulated solvents, SCRF methods (Onsager, PCM and SCF-PCM).

9. Multilayer methods (ONIOM) as the approach for obtaining acceptable results for large systems.

10. Import of the data from Cambridge Crystallographic Data Centre or from the results of crystallographic experiments into GaussView program.

11. Free of charge available computational programs, Gamess, Orca and PCGamess. Free of charge available programs for building the molecule, WxMacMolPlt, ChemSketch and ArgusLab.

12. The use of Firefly program for the calculation of localized molecular orbitals and reaction mechanisms (IRC).

13. Free of charge available vizualization programs Molekel, Avogadro and WxMacMolPlt. Vizualization of the results of the computations of localized molecular orbitals.

14. The use of ArgusLab program for the calculations of docking substrate in the enzyme molecule. Import of data from Cambridge Crystallographic Data Centre or crystallographic experiments using the OpenBabel and ArgusLab programs.

Registration requirements -
Last update: Kvíčala Jaroslav prof. Ing. CSc. (14.08.2013)

General and Inorganic Chemistry I, Organic Chemistry I

Teaching methods
Activity Credits Hours
Účast na přednáškách 1,5 42
Práce na individuálním projektu 1,5 42
Příprava na zkoušku a její absolvování 1 28
4 / 4 112 / 112
Coursework assessment
Form Significance
Report from individual projects 50
Oral examination 50