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Research Center for Complex Molecular Systems and Biomolecules
Center for Biomolecules and Complex Molecular Systems   
Supported by the Ministry of Education, Czech Republic      
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Details of Program of 3rd Summer School of Theoretical and Computational Chemistry
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Word of Introduction

Quantum Chemistry (Petr Nachtigall)   Introduction to Quantum Chemistry and Correlation Energy
  1. Basic approximations used for solving more-electrons stationary Schrodinger equation
    • approximations concerning Hamiltonian, approximations concerning wavefunction
    • Born-Oppenheimer approximation, perturbation theory, variational principle, MO LCAO approximation, independent electrons model
  2. Hierarchy of quantum chemistry methods
    • ab initio methods, semi-empirical methods, empirical methods

Correlation Energy (Petr Nachtigall)
  1. Hartree-Fock method
    • HF equations for two--electron system, coulombic and exchange integral, SCF equations
    • Closed- and open-shell systems, Hartree-Fock-Roothan equation
    • Basis for MO-LCAO expansion
    • Hartree-Fock limit, correlation energy definition, Koopman's and Brillouin theorem
  2. Post Hartree-Fock methods
    • Configuration interaction method, Moller-Plesset perturbation theory method, coupled-cluster method

Unix for beginners (Daniel Svozil)   Linux for Beginners   Basic Linux Commands
  1. Introduction to the system
  2. Filesystem and basic commands (tree hierarchy, file and directory related commands), Midnight Commander
  3. Text files commands (more, grep, tail, cat)
  4. Text editing with mcedit

Vibrational Dynamics (Ota Bludsky)   Molecular Symmetry   Rotational and vibrational Molecular Spectra
  1. Molecular symmetry and spectroscopy
    • Introduction to group theory, molecular Hamiltonian and its symmetry
  2. Rovibronic states calculations
    • Harmonic approximation and rigid rotor model, normal coordinates
    • Anharmonicity and rovibronic interaction, perturbation theory, effective Hamiltonians, spctroscopy constants, variational calculations of rovibronic states, spectra calculations of large molecules and clusters
    • Nonrigid molecules, failure of the harmonic approximation
  3. Current trends in theoretical molecular spectroscopy

Molecular Dynamics (Pavel Jungwirth, Jiri Kolafa)   Quantum Molecular Dynamics
  1. Classical molecular dynamics
  2. Quantum molecular dynamics
Resonances (Petra Zdanska)
  1. Resonance phenomenon: open and closed resonator
  2. Resonances due to wave character of particles (electrons or atoms)
    • in spectroscopy
    • in collision processes
  3. Fingerprints of resonance phenomenon in measurables
  4. Interactions which lead to resonance phenomenon
    • Feshbach type of resonance
    • Shape type of resonance
  5. Methods to calculate resonance positions and widths

Proteins (Jiri Vondrasek)   Proteins and Life

Statistical Thermodynamics (Anatol Malijevsky)
  1. What is statistical thermodynamics?
    • Axioms, statistical ensembles, partition function and thermodynamic quantities
  2. Simple models
    • Ideal gas, ideal crystal
  3. Intermolecular interactions
    • Pair-additive potentials: models and quantum chemistry results, three-particle potentials
  4. Real gas
    • Virial expansion, pros and cons
  5. Dense liquid and gas
    • Inner structure of liquid - pair distribution function, computer pseudo-experiments, theory of integral equations, perturbation theory, pair-distribution function and thermodynamic quantities
  6. Some philosophical aspects of statistical thermodynamics
    • Probability and entropy, third law of thermodynamics: axiom or proof?, negative absolute temperatures, arrow of time

Visualization (Martin Kabelac)   Empirical Potentials and Their Use for The Study of Biomolecules
  • How to create (build) a molecule in computer?, structure visualization, 3D visualization (3D glases, virtual reality), rendering and raytracing, computer animations

Quantum Chemistry Codes (Zdenek Havlas)   Quantum Chemistry Programs
  1. General aspcts of programming languages for scientific applications
  2. Hardware for computational chemistry
  3. The most often used quantum chemistry codes
  4. Gaussian program, its computational capabilities, comparison to other codes

DFT (Petr Nachtigall, Vladimir Sychrovsky)   Introduction to DFT
  1. Theorems leading to the formulation of DFT methods
  2. Exchange and correlation density functionals
    • LDA (LSD) approximation
    • GGA and hybrid functionals
  3. Pros and cons of DFT

Energy Hypersurface (Zdenek Havlas)   Potential Energy Surface
  1. Theoretical foundations: Born-Oppenheimer approximation
  2. Critical points on the energy hypersurface, optimization methods, coordinate systems
  3. Energy derivatives
  4. Equilibrium and rate processes
  5. Critical points on the energy hypersurface occuring during the electronic state change
  6. Photophysical and photochemistry processes
  7. Problem of multiple local minima
  8. Superposition error
  9. Molecular dynamics and energy hypersurface
NMR, EPR (Vladimir Sychrovsky)   Calculations of the NMR Spectra Parameters

Molecular Interactions (Pavel Hobza)
  1. Covalent and non-covalent interactions
  2. Non-covalent interactions in natural sciences
  3. Origin of non-covalent interactions
  4. Perturbation and variational calculations of non-covalent interactions, their advantages and disadvantages
  5. Energy, entropy and free (Gibbs) energy and molecular complexes, energy surfaces
  6. Experimental detection of molecular clusters
Structural Databases (Bohdan Schneider)   Structural Database in Chemistry and Biology

RNA (Bohdan Schneider)   RNA Functional Diversity
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