Theoretical Chemistry 0600-SP/W-EN-TCh

Lectures:
1. A general introduction to the vi editor and to the Linux (Unix) system.
2. A general introduction to the Gamess packet of programs. Preparation of input files for Gamess. Definition of a molecular structure using Z-Matrix. Molden – a molecular visualization program. Running Gamess.
3. Molecular symmetry and Group Theory. Symmetry operations and Elements. Symmetry point groups. Systematic point group classification. Representations of groups. Irreducible and reducible representations. Molecular orbital symmetries.
4. Basis sets. Minimal STO-nG basis sets. Gaussian basis sets for molecular calculations. Primitive and contracted basis sets. Auxiliary functions.
5. The closed-shell restricted Hartree-Fock method. The open-shell Hartree-Fock methods. SCF procedure. Direct SCF calculations.
6. Locating minima and Saddle points on a potential energy surface. Calculations of gradients and Hessians. Optimization methods. Numerical and analytical gradients. Hessian matrix, force constants. Frequencies of vibrations along normal modes of atomic displacement. Stationary points and saddle points. Vibrational frequency analysis. Zero-point energy correction.
7. Methods for large systems. Effective core potentials, ECP. Model core potentials, MCP. Semiempirical methods. Zero-differential overlap. The MNDO, AM1, PM3, ZINDO, CNDO methods.
8. Methods for electron correlation. Configuration interaction method with single, double and triple excitations.(CIS, CISD, CISDT). Full CI method. Multi-configurational SCF (MC SCF) method. Multi-refernce CI. Size consistency and size extensivity.
9. Introduction to the Density Functional Theory. The Hohenberg-Kohn Theorems. The Kohn-Sham equations. Local (LDA) and non-local density approximations (NLDA). Quality of DFT results.
10. General introduction to the perturbation theory. Møller-Plesset perturbation theory MP2. Properties of MPn approximations. Quality of MPn calculations.
11. Studies of reaction mechanisms. Thermodynamic functions. Transition state theory. Locating transition states and following reaction pathways. Intrinsic reaction coordinate (IRC). Rates of reaction. Computational thermochemistry from Gamess. Computation of heat of reactions at different temperatures and pressures.
12. Calculation of electric properties. Multipole moments. Multipole expansion. First- and second-order properties. Calculation of Nuclear Quadrupole Coupling Constant. Population analysis.
13. Intermolecular interactions. The supermolecular approach. The symmetry-adapted perturbation theory. The physical interpretation of the electrostatic, induction and dispersion components of interaction energy. Two- and three-body interactions. The hydrogen bond.
14. Molecular mechanics and molecular dynamics. Protein Data Bank. The force field (CHARMM). Simulations with the VMD and NAMD programs and protein structure analysis.

Computer Labs:
Most of problems discussed during the lectures will be illustrated in numerous practical exercises in the computer laboratory. Each meeting will be divided into two parts. One of them will be devoted to show how to use a computer program, usually Gamess, to solve a particular problem in computational chemistry. Exemplary problems will be presented as well as many practical advices how to use the computer codes efficiently. During the second part of the meeting students will get a small project to work on it. The individual work of students should give them initial skills to apply computational methods of the theoretical chemistry in their further academic and professional careers.