Non-bonded Interactions

As the name implies non-bonded interactions act between atoms which are not linked by covalent bonds. Like most things this is simple to state but can be confusing to apply in practice! In most approaches then atoms which are involved in a bond angle are also not regarded as having a non-bonded interaction. 1-4 interactions (those between the end atoms involved in a dihedral angle) are sometimes given an additional scaled down nonbonded interaction. Similarly the interaction between a metal ion and its liganding atoms is usually regarded as non-bonded and treated by the kind of approach set out here but are sometimes represented by the bond and bond angle terms of the potential energy function (e.g., in representing the iron atom in the haem group found in globins).

Electrostatic interactions

As mentioned in the introduction to this section electromagnetic interactions dominate on the molecular scale and provide the fundamental basis for all the different bonded and non-bonded interactions discussed here. This is clearest in the case of electrostatic interactions where charges on nuclei and electrons interact according to Coulomb's law:

where and are the magnitude of the charges, is their separation, the permittivity of free space and the relative dielectric constant of the medium in which the charges are placed (if you do not remember this consult your high school Physics textbook!). The strictly correct way to use the law would be to consider every nucleus and electron seperately, plug it into the Schrödinger equation and apply quantum chemical methods to solve the equation for the spatial configuration of nuclei we are interested. As already mentioned this is completely impractical for biomolecular systems. So instead we wish to develope a useful model for the interactions between nuclear centres (commonly called "atoms") without having to explicitly deal with the electrons in a system.

The simplest approach is just to place formal charges on each atom which is chemically regarded as charged e.g., a lysine residue would have a charge on +1 electons on its terminal nitrogen atom. Because it is The most common approach is to place a partial charge at each atomic centre. This is a charge which can take a fraction of an electron

Click here if you would like to see an example of a salt bridge.

Non-bonded Interactions

Electrostatic interactions

Induction and Dispersion

Repulsion terms

Hydrogen bonding