In molecules whose vibrational mode involves a rotational or pseudorotational mechanism (such as the Berry mechanism or the Bartell mechanism), Van der Waals strain can cause significant differences in potential energy, even between molecules with identical geometry. 
PF, for example, has significantly lower potential energy than PCl. 
Despite their identical trigonal bipyramidal molecular geometry, the higher electron count of chlorine as compared to fluorine causes a potential energy spike as the molecule enters its intermediate in the mechanism and the substituents draw nearer to each other.