Molecular Modeling

To learn to model the most probable conformations of molecules, the geometry of molecular aggregates in the basic and excited electronic states by the methods of quantum molecular theory (quantum chemistry).

Students will learn how to use quantum chemical simulations for solving of different tasks including environmental effects in solvatation shells.

General Physics, Biophysics

1. Molecular modeling. Close. Visualization techniques. Software packages. 2. Electric charges. The law of the pendant. Point loads, dipoles, multipoles. Polarization. 3. Intermolecular forces. Interaction of charge with dipole. Interdipolar interaction. Inductive and dispersive energy. Morse potential. 4. Molecular mechanics. 5. The potential energy surface of a molecule. Geometry optimization. Search for conformations. 6. Introduction to quantum molecular theory. Schrödinger's equation. 1D and 2D potential pit. Hydrogen atom H, molecule H2 and ion H2 +. Bases and methods. 7. Half-length models. Hiukeli's theory. ZINDO, PM3, AM1. Density functional methods. 8. Ab-initio models. Hartry and Fock method. 9. Applications. Simulation of electronic and vibrational absorption spectra by quantum molecular theory methods.

Be able to evaluate the experimental molecular optical absorption spectrum by simulated semi-semipiral methods. Calculate the oscillation spectrum by density functional methods. To evaluate the intermolecular electron transfer process by quantum chemical methods.