Molecular Modeling using Qunatum Chemical Methods 0600-S2-O-MMCK
Lectures:
1. 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.
2. Basis sets. Minimal STO-nG basis sets. Gaussian basis sets for molecular calculations. Primitive and contracted basis sets. Auxiliary functions.
3. The closed-shell restricted Hartree-Fock method. The open-shell Hartree-Fock methods. SCF procedure. Direct SCF calculations.
4. 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.
5. Methods for large systems. Effective core potentials, ECP. Model core potentials, MCP. Semiempirical methods. Zero-differential overlap. The MNDO, AM1, PM3, ZINDO, CNDO methods.
6. 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-reference methods. Size consistency and size extensivity.
7. 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.
8. General introduction to the perturbation theory. Møller-Plesset perturbation theory MP2. Properties of MPn approximations. Quality of MPn calculations.
9. 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.
Computer Laboratory:
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.
Total student workload
Learning outcomes - knowledge
Learning outcomes - skills
Learning outcomes - social competencies
Teaching methods
Type of course
Course coordinators
Learning outcomes
Student knows the theoretical basis of the computational methods of quantum chemistry; knows at least one software package well
used to calculate the electronic structure, properties and reactivity of atoms and molecules; knows the relationship between the results of theoretical calculations and various experimental techniques.
K_W08
Student is familiar with the Gamess USA computer program and is able to use it to solve selected chemical problems.
The student is able, using theoretical methods, to determine the properties of molecules, including spectroscopic ones, and to study the pathways of chemical reactions, consciously choose the optimal method; is able to independently carry out calculations, use them to analyze experimental data and critically evaluate the results.
K_U10
The student independently and effectively works with a large amount of information, perceives the relationships between phenomena and correctly draws conclusions using the principles of logic. He thinks creatively in order to improve existing or create new solutions. It is focused on the continuous acquisition of knowledge, skills and experience; sees the need for continuous improvement and improvement of professional competences; knows the limitations of their own knowledge and understands the need for further education. Works systematically and has a positive attitude to the difficulties standing in the way of achieving the assumed goal; meet deadlines; understands the need to work systematically on any projects. Understands the importance of computer science and computational quantum chemistry in chemical sciences and practice. Fully independently implements the agreed goals, making independent and sometimes difficult decisions; can independently search for information in the professional literature.
K_K01, K_K02, K_K03, K_K05, K_K06, K_K07
Assessment criteria
Assessment methods:
lecture - written examination
computer laboratory – self-computational projects
Assessment criteria:
lecture:
fail- less than 50pts (less than 50 %)
satisfactory- 50-60pts (50-60%)
satisfactory plus- 61-65pts (61-65%)
good – 66-75pts (66-75%)
good plus- 76-80pts (76-80%)
very good- 81-100pts (81-100%)
computational laboratory:
fail- less than 50pts (less than 50 %)
satisfactory- 50-60pts (50-60%)
satisfactory plus- 61-65pts (61-65%)
good – 66-75pts (66-75%)
good plus- 76-80pts (76-80%)
very good- 81-100pts (81-100%)
Bibliography
1. Frank Jensen, 'Introduction to Computational Chemistry' , Wiley, Germany, 2008.
2. A. Szabo and N. S. Ostlund, Modern Quantum Chemistry, Dover, 1996.
3. A. Hinchlife, Modelling molecular structures, Wiley, 2000.
4. A. Hinchliffe, Computational quantum chemistry, Wiley, 1988.
5. C. J. Cramer, Essentials of computational chemistry: theories and models, Wiley, 2002.
Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: