1. - 2014/2015 - 3D Structures of Biological Macromolecules Part 6: Atomic and Molecular Orbitals Jürgen Sühnel jsuehnel@fli-leibniz.de Supplementary Material: www.fli-leibniz.de/www_bioc/3D/ Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena / Germany

2. Rutherford Model (Planetary Model) Atoms are not single particles but consist of subparticles (electrons, neutrons, protons). Most of the atomic mass is concentrated in the (small) nucleus. However: The laws of classical mechanics, predict that the electron will release electromagnetic radiation while orbiting a nucleus. Because the electron would lose energy, it would collaps into the nucleus. Hence, atoms should be unstable.

3. The electrons can only travel in certain orbits at a certain discrete set of distances from the nucleus with specific energies. These orbits are associated with definite energies and are also called energy shells or energy levels. Thus, the electrons do not continuously lose energy as they travel in a particular orbit. They can only gain and lose energy by jumping from one allowed orbit to another, absorbing or emitting electromagnetic radiation with a frequency ν determined by the energy difference of the levels according to the Planck relation: where h is Planck‘s constant. Bohr Model - 1913

4. Hydrogen Atom: Schrödinger Equation H  = E 

5. Hydrogen Atom: Schrödinger Equation

6. Hydrogen Atom Wave Functions – Generalized Form

7. Hydrogen Atom Wave Functions

8. Hydrogen Atom Wave Functions – Radial Distribution Function

9. Hydrogen Atom: Schrödinger Equation  Wave function is like a vibrating string or membrane, but the vibration is in three dimensions  Labelled by three quantum numbers: n = 1, 2, 3, … ℓ = 0, 1, …, n-1 m = -ℓ, -ℓ+1, …, ℓ-1, ℓ  For historical reasons, ℓ = 0, 1, 2, 3 is also known as s, p, d, f

10. Hydrogen Atom

15. Electron Configuration

17. Hybrid Orbitals - sp

18. Hybrid Orbitals – sp 2

19. Hybrid Orbitals – sp 3

20. Molecular Orbitals: Valence Electrons of Methane

21. Molecular Orbitals: Oxygen Molecule

22. Molecular Orbitals: Benzene (  orbitals only)

23. Valence Shell Electron Pair Repulsion (VSEPR) A – central atom X –  bonds (double and triple bonds count as one X) E – lone pairs

24. Valence Shell Electron Pair Repulsion (VSEPR)

25. Electron Structure of Water

26. Lone electron pairs in the  - or  -system, aromaticity Aniline:  lone pairaromatic ring system

27. Lone electron pairs in the  - or  -system, aromaticity Pyridine:  lone pairaromatic ring system

28. Quinone:  lone pairsnon-aromatic ring system Lone electron pairs in the  - or  -system, aromaticity