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- 2014/2015 -
3D Structures of Biological Macromolecules3D Structures of Biological Macromolecules
Part 6: Atomic and Molecular OrbitalsPart 6: Atomic and Molecular Orbitals
Jürgen SühnelJürgen Sü[email protected]@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