Since B is positive, the London contribution to the LJ energy is always negative at all values of r. As r gets smaller, the London component of the LJ energy gets more and more negative, so the London dispersion forces are attractive. Strictly speaking, this is incorrect, because the VDW energy is only one component of the LJ energy. In this tutorial, we will carefully distinguish between the van der Waals and London dispersion components of the Lennard-Jones energy. But we make no promises about future tutorials.
Electrostatic forces play a major role in determining the three-dimensional structures of proteins.
The carboxyl and amino groups on the side chains of acidic and basic amino acids are typically ionized at neutral pH. Energetic considerations drive the molecule into conformations where these groups can be solvated, or where they can take part in salt bridges. They prefer to interact with charged groups, or to participate in hydrogen bonding with one another or with solvent. The accurate calculation of electrostatic forces is extremely difficult, because the charges on the atoms vary as the molecular conformation varies. This reflects the fact that molecules are polarizable . Unfortunately, rigorous calculation of charge variations due to polarizability would require detailed quantum mechanical calculations.