Quantum-Chemical Molecular Modelling
Unit Code	ASC 11
Credits	5
Prerequisites	ASC 1 to 5 (semester I), basic course of quantum chemistry
TEACHING STAFF	Prof. Artur Michalak, Dr. Mariusz Mitoraj, Monika Srebro

COURSE DESCRIPTION: The course covers practical aspects of molecular modelling with quantum-chemical methods. The lectures and practical exercises (computer lab) cover the following topics: using quantum chemical software - general rules; input data for quantum chemical calculations; available software; Born-Oppenheimer approximation; potential energy surface (PES), stationary points on PES; Practical aspects of geometry optimization of molecular systems; optimization of minima (reactants, products) and saddle points (transition states); reaction paths on PES; Commonly used computational methods; variational and perturbational methods; Hartree-Fock method (HF); restricted and unrestricted HF (RHF and UHF); ab initio and semiempirical methods; basis sets in ab initio calculations; molecular orbitals, electron density, population and bond-order analysis; visualisation methods; chemical bond; differential density (deformation density); delocalized and localized orbitals; localization methods; vibrational analysis; normal modes; electron correlation; configuration interaction methos (CI), Moller-Plesset perturbational method (MP); Density functional theory (DFT) and Kohn-Sham (KS) method; practical aspects of DFT calculations; exchange-correlation functional choice; modeling of large systems; hybrid methods (QMMM); solvent effects; continuum models; chemical reactivity; single- and two reactant reactivity indices; interaction energy partitioning methods; modelling the elementary reactions of complex processes; thermodynamic properties; free-energy of chemical reactions; ab initio molecular dynamics approaches.

OBJECTIVE OF THE COURSE:

To build upon and extend the theoretical concepts introduced during the bachelor degree programme
To develop the competence and confidence of the students in performing quantum-chemical calculations and interpreting their results
To highlight modern methods of computational chemistry
To identify appropriate method for particular applications

INTENDED LEARNING OUTCOMES:
After completing this unit the student should be able to:

Choose and apply the appropriate computational method to a given problem
Discuss in a comprehensive way the basic theoretical background of various computational methods and their applicability to various problems
Estimate the degree of reliability of the results
Explain to a non-specialists how computational quantum chemistry can be expected to provide valuable information in different areas of chemistry and related disciplines

TEACHING AND LEARNING ACTIVITIES:

TERM	NAME	L	S/E	P
1	Quantum-Chemical Molecular Modelling	30	0	60

Student centered learning: 45 hours; Total student effort: 135 hours

LANGUAGE OF INSTRUCTION: English

RECOMMENDED READING:

(i) web page of the course;
(ii) selected articles from scientific journals;
(iii) F. Jensen, Introduction to Computational Chemistry, Wiley, 1999;
(iv) W. Koch, M.C. Holthausen, A Chemist's Guide to Density Functional Theory, Wiley, 2001;
(v) A.R. Leach, Molecular Modeling. Principles and Applications. Pearson Education 2001;
(vi) Encyclopedia of Computational Chemistry. Wiley, 1998. (selected articles)
RECOMMENDED WEBSITES: http://www.chemia.uj.edu.pl/~michalak/mmod

SCHEDULE AND LEARNING METHOD:

Weeks	Type	Duration	Course description
1	L	6	Basics ideas of quantum chemistry; review of the methods, input/output for/from quantum chemical calculatains; basis sets in ab initio calculations
2	L	4	Geometry optimization
2	P	2	Running simple ab initio calculations
3	L	2	Conformational analysis, the global minimum problem
3	P	4	Geometry optimization and interpretation of results of ab initio calculations
4	L	2	Electronic structure description; population analysis and bond-orders
4	P	4	Complex geometry optimizations and conformational analysis
5	P	4	The global minimum problem
6	L	2	Vibrational analysis, determination thermodynamical properties
6	P	4	Molecular orbitals - interpretation and visualization
7	L	2	Modeling chemical reactions, transition state optimization, reactivity indices
7	P	4	Electron density, deformation density and localized orbitals
8	L	2	Modeling of complex chemical processes - examples from catalysis
8	P	4	Structure and bonding - complex examples
9	L	2	Molecular spectroscopy from ab initio calculations
9	P	4	Vibrational analysis and thermochemistry
10	L	2	Advanced methods for electron correlation
10	P	4	Molecular spectroscopy from ab initio calculations
11	L	2	Molecular dynamics
11	P	4	Reactivity indices
12	L	2	Modeling large systems; hybrid (QM/MM)methods; solvation models
12	P	4	TS optimization
13	P	6	Structure, bonding, and reactivity complex examples
14	P	6	MP2 and CI, ionization potential and electron affinity
15	P	6	Solvent effects, hybrid methods

ASSESSMENT:

Test (50%), and practicals evaluation (50%)

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