Calculation of Molecular Structures and Properties

1. 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

2. 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

3. 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

4. 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. 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, McGraw-Hill 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

6. 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

7. 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