6. Solvatation, QM/MM calculations and molecular dynamics

6.1 Solvatation

In most cases, the molecules studied are not in the vapor phase, and so cannot be treated as isolated molecules. They are usually solvated. There are several ways of treating a solute in a solvent. When there are specific interactions between solute and solvent, such as hydrogen bonds, the solute-solvent molecule pair must be treated explicitly, as a "supermolecule". Otherwise, to describe the effect of the solvent on the solute's properties, it is generally sufficient to consider the solute inside a cavity immersed in a continuum with a dielectric constant equal to that of the solvent. The origin of such a methodology, known as the polarizable continuum, is the Born-Kirkwood-Onsager model