Download Computational chemistry (Quantum chemical calculations)

Dr. Vasile Chiş
Biomedical Physics Department, Faculty of Physics
Babeş-Bolyai University, Cluj-Napoca
Calculation of Molecular Structures and Properties
Molecular structures and molecular properties by quantum chemical methods
Bio
Nanotechnology
Computational chemistry (Quantum chemical calculations)
- a branch of theoretical chemistry (molecular physics)
- the overlap area between computer science and chemical-physics
major goals
- to create efficient mathematical approximations and
computer programs
to calculate the properties of molecules (such as total
energy, dipole and quadrupole moment, vibrational frequencies,
reactivity, different spectroscopic quantitities and cross sections for
collision of molecules with different atomic or subatomic
projectiles)
- to apply these programs to concrete physico-chemical systems
Calculation of Molecular Structures and Properties
Molecular structures and molecular properties by quantum chemical methods
Computational chemistry

Molecular modelling
1. Why computing molecules?
electronic structure calculations
• electronic structure theory can be used as a very useful tool, providing new insights
into physico-chemical problems.
• provide useful results for those involved in experimental research.
• interpret the properties of the novel developed materials
• modelling the biochemical compounds
• modelling the intermolecular interactions
•…
Computational chemistry is one of the most rapidly advancing and exciting fields in the natural sciences today
"Many experimental chemists use various kinds of spectroscopy in their research even though they are not
spectroscopists. In a similar manner, more and more scientists are applying computational techniques as another
weapon in their arsenal"
Delano P. Chong in Recent Advances in Density Functional Methods, Part I, World Scientific, 1995
2. What should we learn?
-
the theory behind "molecular modeling"
to use program packages designed for molecular electronic structure theory
to use some molecular visualization packages
to do calculations at different levels of theory and to interpret the results
to make correlations between the experimental and theoretical data
3. Contents of this course
Hartree-Fock Theory
Basis sets
Electron Correlation Methods
Basis set superposition error
Density Functional Theory
Geometry optimizations
Calculation of vibrational spectra
Calculation of NMR and ESR spectra
Calculation of UV-VIS spectra
Visualisation of molecular orbitals, molecular electrostatic
properties, etc.
4. Can we do research?
pure theoretical studies
coupled experimental and theoretical investigation on the structure and
properties of molecular systems
improving codes for specific physico-chemical problems
5. Where can we publish the results?
Journal of Molecular Structure
Journal of Molecular Structure (Theochem)
Journal of Molecular Spectroscopy
Chemical Physics
Chemical Physics Letters
Journal of Molecular Modelling
International Journal of Quantum Chemistry
Journal of Computational Chemistry
Journal of Chemical Physics A
The Journal of Chemical Physics
Molecular Physics
Chemical Reviews
Theoretical Chemistry Accounts
… and many others
6. References
1. P.W. Atkins, Molecular Quantum Mechanics, Oxford University Press, 1983
2. R.G. Parr, W. Yang, Density Functional Theory of Atoms and Molecules, Oxford University Press, New York, 1989
3. W.J. Hehre, L. Radom, P.v.R. Schleyer, J.A. Pople, Ab Initio Molecular Orbital Theory, John Willey & Sons, New York,
1986
4. F.J ensen, Introduction to Computational Chemistry, John Wiley and Sons, New York, 2001
5. A. Szabo, N.S. Ostlund, Modern Quantum Chemistry; Introduction to Advanced Electronic Structure Theory, McGrawHill Publishing Company, New York, 1989
6. W. Koch M.C. Holthausen, A chemist's guide to DFT, Wiley-VCH, 2001
7. D.C. Young Computational chemistry, Wiley, 2001
8. A. Leach, Molecular Modelling - principles and applications, Prentice Hall, 2001
9. V. Barone, P. Cimino, O. Crescenzi, M. Pavone, Ab Initio computation of spectroscopic parameters as a tool for the
structural elucidation of organic systems, J. Mol. Struct., (Theochem), 811, 323-335 (2007)
10. C. J. Cramer, Essentials of Computational Chemistry, John Wiley & Sons (2002)
11. P.M.W. Gill, DFT, HF and the SCF
12. D. Rohr, Electronic Structure Methods, Vrije Universiteit Amsterdam
7. Research reports
1. Scaling the calculated vibrational frequencies
2. Calculation of NMR spectra: the influence of the method and basis set
3. Calculation of ESR spectra for paramagnetic compounds
4. Computational studies in molecular electronics
5. Modelling the intra and inter-molecular hydrogen bonds
6. Computational recipes for large molecules: the ONIOM method
7. Modelling the hydrogen bond interactions
8. Basis set superposition error – is it important?
9. Adsorbed molecules on metallic surfaces
10. Semiempirical methods: are they reliable?
…
depending on your interest!
8. Examples
Ab Initio methods


Used to solve the molecular Schrödinger equation associated with
the molecular Hamiltonian
Methods that do not include empirical or semi-empirical parameters
in their equations


derived directly from theoretical principles, with no inclusion of experimental
data
the only approximations made are usually mathematical in nature (e.g. using a
simpler functional form or getting an approximate solution for a complicated
differential equation).

Able to provide accurate and reliable theoretical results

Computationally expensive