1.  Introduction. (allowance 2/0) 
 a.  Theoretical, Computational and Quantum Chemistry.What can be modeled and to which accuracy?  b.  History, present and future of molecular modelling and simulations.  c.  Molecular Mechanics vs Wave Function methods. Literature sources. 

2.  Force fields and molecular representations of matter. (allowance 8/0) 
 a.  Intramolecular (bonding) interactions, Nonbonded interactions. Electrostatic (Coulomb, Dipolar) interactions. London (van der Waals) interactions. Hydrogen bonds. Constraints and Restraints. United atom and other coarsegrained approaches. Nonpairwise interactions. The chemical accuracy of the force fields.Molecular mechanics MM3, AMBER, OPLS, BIO+.  b.  Methods for Simulating Large systems. Nonbonded Cutoffs. Shifted potential and shifted force. Switching functions. Neighbor lists.  c.  Boundaries. Periodic Boundary conditions. Stochastic forces at spherical boundary.  d.  Longrange interactions. The Ewald Sum. The Reaction field method. 

3.  Energy Minimization and related analysis techniques. (allowance 5/0) 
 a.  Comparison of methods. Advanced techniques: Simulated Annealing, Branchandbound, simplex. What's the big deal about the minimum anyway?  b.  Introduction to Equilibrium Statistical Mechanics. Phase space, ergodicity, and Liouville's theorem.  c.  Ensemble theory, thermodynamic averages. Microcanonical Ensemble. Canonical Ensemble. Other ensembles. Statistical mechanics of fluids. 

4.  Monte Carlo. (allowance 2/0) 
 a.  MC integration and Markov chains. The Metropolis method. Biased Monte Carlo (MC). 

5.  Molecular Dynamics. (allowance 8/0) 
 a.  Classical mechanics: equations of motion. Finite Difference methods. Verlet algorithm. Velocity verlet. The Time step: practical issues. Multiple timestep algorithms.  b.  Constraint Dynamics. Fundamental concepts. SHAKE and RATTLE. Temperature: MaxwellBoltzmann distribution of velocities.  c.  Temperature control. Velocity scaling. Andersen's method. NoseHoover dynamics. Calculating properties from MD trajectories. Hybrid MC.  d.  Free Energy. Perturbation methods. Thermodynamic integration. Brownian dynamics and the Langevin Equation. 

6.  Elementary Quantum Chemistry. (allowance 5/0) 
 a.  The molecular Hamiltonian and the BornOppenheimer approximation. Electronic and Nuclear Schrödinger equations.  b.  Variational Principle and Perturbation Theory.  c.  Hydrogen atom. The shape of atomic orbitals. Helium atom.  d.  Molecular Orbital Theory. The LCAOMO approximation and the Secular equation. Electron Spin and Antisymmetry Principle. Manyelectron Wave Functions: Hartreeproduct and Slater Determinant. The HartreeFock Selfconsistent Field method. 

7.  Basis sets of atomic orbitals. (allowance 5/0) 
 a.  STO vs GTO functions. Diffuse and polarization functions. Correlationconsistent basis sets. Extrapolation to the complete basis limit.  b.  Effective core potentials.  c.  Alternative approaches: Planewaves. 

8.  Introduction to the ab initio theories. (allowance 2/0) 
 a.  The HartreeFock approximation. Restricted and unrestricted WF.  b.  Electron Correlation: dynamical and static correlation. Configuration Interaction: Brillouin Principle. Truncated CI. FullCI. Size consistency. MollerPlesset Perturbation Theory.CoupledCluster theory.  c.  Multiconfigurational SCF and multireference methods. 

9.  Introduction to the Density functional theory. (allowance 3/0) 
 a.  HohenbergKohn principles. KohnSham DFT. "Classical" exchangecorrelation functionals: The Jacob's Ladder. Hybrid functionals and the adiabatic connection. Timedependent DFT. Semiempirical version of DFT.  b.  Longrange corrected functionals and dispersion corrections.  c.  General performance overview of ab initio and DFT methods. 

10.  Molecular modelling. (allowance 5/0) 
 a.  Computers in Chemistry. Basics of Linux / Unix. Software for electronic structure calculations. Visualization software and other applications. Molecular graphics. Practical aspects of electronic structure calculations.  b.  Molecule specifications. Coordinate systems and Zmatrix. Singlepoint energy calculations. Gradient optimization calculations.  c.  Optimal geometries and conformations. Vibrational frequency analysis. Zero point energy. Calculations of vibrational spectra, IR / Raman active modes.  d.  Thermochemistry.  e.  Calculations in solvents. Solvent models: COSMO, IEFPCM. 

11.  Energy calculations. (allowance 10/0) 
 a.  Reaction Free Energies in GasPhase and Solution: The Menshutkin Reaction.  b.  Bond Enthalpies of the Hydrides.  c.  Vertical and adiabatic ionization potentials and electron affinities.  d.  Bond dissociation enthalpies. Model phenol and aniline derivatives.  e.  Examples of calculations of electron transitions, selected model systems. Comparison with experiment.přesun řádku tabulky ve směru šipky Visualisation of electron transitions.  f.  Fluorescence spectra. Singlettriplet tranistions.Simulations of optical bands. 

12.  Energy calculations (continued). (allowance 5/0) 
 a.  Interaction energy calculation. Supermolecular approach. Basis set superposition error. Counterpoisse corrections.  b.  Intermolecular perturbation theories. SAPT.  c.  Quantum chemical calculations of the interaction energies: noble gases, two atomic moleculeatom, two atomic moleculetwo atomic molecule, aromaticaromatic molecules, hydrogen and halogen bonds. 

13.  Electric and magnetic property calculations. (allowance 5/0) 
 a.  Partial charges. Population analysis. Spin distribution. Electrostatic potentials. Dipole moment. First and secondorder polarizabilities and hyperpolarizabilities.  b.  Spin atomic nucleus. The principle of NMR. Spin of the electron. GIAO method. Chemical shift. Tensor for magnetic shielding. Simulating C13 and H1 NMR Chemical Shifts.  c.  EPR principle. Calculations of Fermi coupling constants.  d.  Examples of calculations of the magnetic properties of molecules. 
