Předmět Seminář chemického modelování (N342026)

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Materiál	Typ	Datum	Počet stažení

Sylabus

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 Internet3. 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 representation6. 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 demonstration8. 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/Chem3D9. 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 chart11. Comparison of strength and conformational rigidity of ester and amide (peptide bond) bonds12. Seminar, individual work with CS/ChemDraw-CS/Chem3D programs13. Assignments of individual projects14. Individual project

Literatura

D: Caffery ML Dobosh PA, Richardson DM, Laboratory Excercises using Hyperchem, Hypercube 1998.D: Spartan 04 Windows, Tutorial and User Guide, Wavefunction 2001.

Garant

Drašar Pavel prof. RNDr. DSc.