SubjectsSubjects(version: 953)
Course, academic year 2023/2024
Chemical Modelling: Seminar - B342007
Title: Seminář chemického modelování
Guaranteed by: Department of Chemistry of Natural Compounds (342)
Faculty: Faculty of Food and Biochemical Technology
Actual: from 2019
Semester: winter
Points: winter s.:3
E-Credits: winter s.:3
Examination process: winter s.:
Hours per week, examination: winter s.:0/3, MC [HT]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
State of the course: taught
Language: Czech
Teaching methods: full-time
Teaching methods: full-time
Note: course can be enrolled in outside the study plan
enabled for web enrollment
Guarantor: Drašar Pavel prof. RNDr. DSc.
Interchangeability : N342026
Annotation -
The seminar is aimed to provide students with basics of molecular modelling, and prediction of basic observables that are dependent on the structure of molecule.
Last update: Fialová Jana (18.12.2017)
Aim of the course -

Students will be able to:

Use chemical software for representation of molecules in 2D and 3D

Predict basic observable quantities on the basis of correctly drawn structure

Last update: Fialová Jana (18.12.2017)
Literature -

A: Caffery ML Dobosh PA, Richardson DM, Laboratory Excercises using Hyperchem, Hypercube 1998.

A: Spartan 04 Windows, Tutorial and User Guide, Wavefunction 2001.

Last update: Fialová Jana (18.12.2017)
Learning resources -

Last update: Fialová Jana (18.12.2017)
Syllabus -

1. Chemical structure editors (CS/ChemDraw, ACD/ChemSketch, MDL/IsisDraw, BioRad/DrawItAll). Transfer of 2D representation of a molecule into a text editor (MS Word) or into a graphical editor (Corel Draw, Adobe Illustrator)

2. Application of chemical structure editor for the calculation of SMILES and INCHI identificators and for data retrieval for a given structure on the Internet

3. Application of chemical structure editors (CS/ChemDraw, ACD/ChemSketch) for the prediction (calculation) of a compound name and composition and observable (physico-chemical) properties (solubility, refraction index, dielectric constant, boiling and melting point, tautomeric forms, log P)

4. Prediction of spectral data using chemical structure editors CS/ChemDraw, ACD/ChemSketch (MS spectra and NMR spectra)

5. 3D Representation of compounds using ACD/ChemSketch and conversion of structural formulae from CS/ChemDraw into CS/Chem3D, correct expression of chirality in 2D notation as well as in 3D representation

6. Optimization of 3D structures using CHARMM in ACD/ChemSketch and using MM2, extraction of intermolecule distances and torsion angles, XYZ coordinates and 3D notation of a structure in MDL/MOL file and Z-matrix. Transfer of 3D representation of a molecule into a text editor (MS Word) or into a graphical editor (Corel Draw, Adobe Illustrator)

7. Optimization of 3D structures using Gaussian 09W program from CS/Chem3D environment, comparison with MM results. Parameter selection (methods, basis sets, etc.), local minima explanation and its demonstration

8. Calculation of charge/electron distribution in a compound and its rendering by differently colored molecular surfaces. Calculation of van der Waals radii and its rendering in CS/Chem3D

9. Calculation of IR spectra using Gaussian 09W program from CS/Chem3D environment. Parameter selection (methods, basis sets, etc.)

10. Calculation of heat of formation and heat of combustion (energy) and construction of conformational analysis chart

11. Comparison of strength and conformational rigidity of ester and amide (peptide bond) bonds

12. Seminar, individual work with CS/ChemDraw-CS/Chem3D programs

13. Assignments of individual projects

14. Individual project

Last update: Fialová Jana (18.12.2017)
Registration requirements -


Last update: Fialová Jana (18.12.2017)