- 2014/2015 -

3D Structures of Biological Macromolecules3D Structures of Biological Macromolecules

Part 6: Atomic and Molecular OrbitalsPart 6: Atomic and Molecular Orbitals

Jürgen SühnelJürgen Sühneljsuehnel@fli-leibniz.dejsuehnel@fli-leibniz.de

Supplementary Material: www.fli-leibniz.de/www_bioc/3D/

Leibniz Institute for Age Research, Fritz Lipmann Institute,Leibniz Institute for Age Research, Fritz Lipmann Institute,Jena Centre for BioinformaticsJena Centre for Bioinformatics

Jena / GermanyJena / Germany

Rutherford Model (Planetary Model) 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.

•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 Bohr Model - 1913

Hydrogen Atom: Schrödinger EquationHydrogen Atom: Schrödinger Equation

H = E

Hydrogen Atom: Schrödinger EquationHydrogen Atom: Schrödinger Equation

Hydrogen Atom Wave Functions – Generalized FormHydrogen Atom Wave Functions – Generalized Form

Hydrogen Atom Wave FunctionsHydrogen Atom Wave Functions

Hydrogen Atom Wave Functions – Radial Distribution FunctionHydrogen Atom Wave Functions – Radial Distribution Function

Hydrogen Atom: Schrödinger EquationHydrogen 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 knownas s, p, d, f

Hydrogen AtomHydrogen Atom

Hydrogen AtomHydrogen Atom

Hydrogen AtomHydrogen Atom

Hydrogen AtomHydrogen Atom

Hydrogen AtomHydrogen Atom

Electron ConfigurationElectron Configuration

Electron ConfigurationElectron Configuration

Hybrid Orbitals - spHybrid Orbitals - sp

Hybrid Orbitals – spHybrid Orbitals – sp2 2

Hybrid Orbitals – spHybrid Orbitals – sp3 3

Molecular Orbitals: Valence Electrons of Methane Molecular Orbitals: Valence Electrons of Methane

Molecular Orbitals: Oxygen Molecule Molecular Orbitals: Oxygen Molecule

Molecular Orbitals: Benzene (Molecular Orbitals: Benzene ( orbitals only) orbitals only)

Valence Shell Electron Pair Repulsion (VSEPR)Valence Shell Electron Pair Repulsion (VSEPR)

A – central atomX – bonds (double and triple bonds count as one X)E – lone pairs

Valence Shell Electron Pair Repulsion (VSEPR)Valence Shell Electron Pair Repulsion (VSEPR)

Electron Structure of WaterElectron Structure of Water

Lone electron pairs in the Lone electron pairs in the - or - or -system, aromaticity-system, aromaticity

Aniline: lone pair aromatic ring system

Lone electron pairs in the Lone electron pairs in the - or - or -system, aromaticity-system, aromaticity

Pyridine: lone pair aromatic ring system

Quinone: lone pairs non-aromatic ring system

Lone electron pairs in the Lone electron pairs in the - or - or -system, aromaticity-system, aromaticity