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Computations and Visualization of Molecules

Lecture Excercise/laboratory
2019, Winter Semester
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Credits 4
Hours per week 1 / 2 / 0
Examination C+Ex
Study Language Czech
Level []
Guarantor prof. Ing. Jaroslav Kvíčala, CSc.

Summary

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.

Syllabus

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.

Literature

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

VŠCHT Praha
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166 28 Praha 6 – Dejvice
IČO: 60461373
DIČ: CZ60461373

Datová schránka: sp4j9ch

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