Computational Chemistry - Molecule Visualization - AM110007
Title: Computations and Visualization of Molecules
Guaranteed by: Department of Organic Chemistry (110)
Faculty: Faculty of Chemical Technology
Actual: from 2020
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 [HT]
Capacity: unlimited / unlimited (unknown)
Min. number of students: unlimited
State of the course: taught
Language: English
Teaching methods: full-time
Teaching methods: full-time
Note: course can be enrolled in outside the study plan
enabled for web enrollment
Guarantor: Kvíčala Jaroslav prof. Ing. CSc.
Rybáčková Markéta Ing. Ph.D.
Interchangeability : N110024
Examination dates   
Annotation -
The course is targeted mainly on the student with zero knowledge of computational chemistry, oriented on inorganic, organic and macromolecular chemisty. Students will learn how to use Gaussian, Firefly and Orca computational programs. Special attention is devoted to visualization of the computational results, namely optimized geometries, infrared and NMR spectra, canonical and localized molecular orbitals, electrostatic potential and reaction mechanisms. For this, both commercial (GaussView) and free of charge (WxMacMolPlt, Avogadro, AscalaphDesigner) visualization programs will be used.
Last update: Kvíčala Jaroslav (22.10.2019)
Aim of the course -

Students will be able to:

work with Gaussian16 program, perform ab initio and DFT computations

work with GaussView6 program and its use for visualization of the results of Gaussian16 computations

work with Firefly program and its use for ab initio and DFT computations

work with WxMacMolPlt and AscalaphDesigner programs and their use for visualization of the results of Firefly computations

work with Orca program and its use for ab initio and DFT computations

work with Avogadro program and its use for visualization of the results of Orca computations

Last update: Kvíčala Jaroslav (21.10.2019)
Literature -

A: J. B. Foresman and A. Frisch, Exploring Chemistry with Electronic Structure Methods, 3rd ed., Gaussian, Inc.: Wallingford, CT, 2015. ISBN: 978-1-935522-03-4

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

Last update: Kvíčala Jaroslav (21.10.2019)
Learning resources -

Electronic version of lectures

Last update: Kubová Petra (14.10.2019)
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.

Last update: Kvíčala Jaroslav (22.10.2019)
Registration requirements -


Last update: Kubová Petra (14.10.2019)
Course completion requirements -

The subject is finished by examination consisting of theoretical and experimental part. Student can approach the examination after obtaining assessment based on three finished computational projects.

Last update: Kvíčala Jaroslav (21.10.2019)