Mereology is the logic of part—whole concepts as they are used in many different contexts. The old chemical metaphysics of atoms and molecules seems to fit classical mereology very well. However, when functional attributes are added to part specifications and quantum mechanical considerations are also added, the rules of classical mereology are breached in chemical discourses. A set theoretical alternative mereology is also found wanting. Molecular orbital theory requires a metaphysics of affordances that also stands outside classical mereology.