So far, all of the models have been based on stable molecules. However, the same modeling techniques can be used to describe reaction intermediates, transition states, and even entire reaction coordinates.
This figure shows three "snapshots" of a reaction coordinate for a typical SN2 nucleophilic substitution. The top figure shows the reactants, HO- + CH3Cl. The middle figure shows the "transition state". The bottom figures shows the products, HOCH3 + Cl-.