Functional groups are regions of molecules that have their own distinct properties. These can be ionic (like the phosphate group) and thus these regions of molecules can interact across molecules.
Personally I think a much richer metaphors to dig into would be graph theory. It naturally and well describes polycule dynamics and has rich terminology to describe all the sorts of concepts you would like. For example the technical term for a couple that can be larger than just 2 people would be a clique.