Computer Science for Molecular Modeling 0600-S1-Spec-CI
Lecture 'Introduction to programming'
1. 1. Introduction to programming languages: Fortran, Pascal, C/C++ and others.
2. Program units and procedures.
3. Data types (integer, real, complex, logical, character).
4. Variables and constants.
5. Data structure (one- and multi-dimensional arrays).
6. Operators (scalar numeric, scalar relational, scalar logical).
7. Numeric expressions.
8. Array expressions.
9. Control statements (go to, if, case, do).
10. Internal subprograms, functions, procedures.
11. Specification statements (implicit, parameter, data).
12. Declaration statement.
13. Mathematical functions.
14. Numerical errors
15. Programming: numerical integration, systems of linear and nonlinear equations.
Lecture 'Molecular Modeling by Quantum Chemistry Methods'
1. Born-Oppeheimer approximation. Potential energy surface.
2. Molecular geometry optimization.
3. Stationary points, local minima and transition states. Reaction paths.
Kinetics of chemical reactions.
4. Variational methods.
5. One-electron approximation, Hartree-Fock methods: RHF, UHF and ROHF.
6. Basis sets in ab-initio calculations. Atomic orbitals and molecular orbitals. Contracted basis sets.
7. Effective core potentials (ECP) and Model core potentials (MCP).
8. Semi-Empirical Methods.
9. Density Functional Theory (DFT). History of DFT. Topology of the electron density distribution. Hohenberg-Kohn theorems. Kohn-Sham equations. Functional.
10. Elements of Statistical Thermodynamics.
11. Population analysis.
12. Methods for electron correlation. Configuration interaction. Moller-Plesset perturbation theory.
13. Intermolecular interactions.
Lecture 'Molecular Symmetry and Group Theory'
1. Symmetry operations and elements.
2. Combining Symmetry Operations. Symmetry Point Groups.
3. Point Groups of Molecules. Systematic Point Group Classification.
4. Optical Activity and Symmetry.
5. Irreducible and reducible representations. Character Tables.
6. Techniques and Relationships for chemical applications.
7. Symmetry and chemical bonding.
8. Vibrational Spectroscopy. Vibrational modes and their symmetries.
Symmetry-Based selection rules and their general consequences. Spectroscopic activities.
2. Laboratory: 'Introduction to programming' – practical implementation of the program of the lecture in the computer lab.
1. Introducion to GAMESS and MOLDEN – input files
2. Hartree-Fock method for closed- and open-shell sysstems. RHF, ROHF UHF, and ROHF. Energy, geometry optimization, Koopmans theorem, core and valence ionization potentials.
2. The importance of choosing a base in quantum chemical calculations.
3. Molecular orbitals: occupied and virtual in different basis sets.
4. Pseudopotentials and semiempirical methods.
5. Geometry optimization and analysis of normal modes.
6. Thermochemistry.
7. Studies of reaction mechanism.
Total student workload
Learning outcomes - knowledge
Learning outcomes - skills
Learning outcomes - social competencies
Teaching methods
Prerequisites
Assessment criteria
Assessment methods: Written examination (65%), laboratory (40%).
Assessment criteria:
fail - 0-49%
satisfactory - 50-60%
satisfactory plus - 61-65%
good - 66-75%
good plus - 76-80%
very good - 81-100%
Practical placement
not applicable
Bibliography
1. Christopher Negus, Christine Bresnahan, Linux Bible, 8th Edition, Wiley, 2012
2. Christoper Negus, Red Hat Fedora Linux 3 Bible, Wiley, 2005
3. Justin Davies, Roger Whittaker, William von Hagen, SUSE Linux 9 Bible, Wiley, 2005
4. Arnold Robbins, Unix in a Nutshell, 4th Edition, O'Reilly, 2005
5. Bill Ball, David Pitts, Red Hat Linux 7 Unleashed, Sams, 2000
1. A. Hinchlife, Computational Quantum Chemistry, John Wiley & Sons, New York 1995.
2. F. Jensen, Introduction to Computational Chemistry, Wiley 2008
Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: