  In this paper, a topological classification of molecules and their chemical
reactions is proposed on a single particle level . We consider zero-dimensional
electronic Hamiltonians in a real-space tight-binding basis with spinless
time-reversal symmetry and an additional spatial reflection symmetry. The
symmetry gives rise to a perplectic structure and suggests a $\mathbb{Z}_2$
invariant in form of a pfaffian, which can be captured by an entanglement cut.
We apply our findings to a class of chemical reactions studied by Woodward and
Hoffmann, where a reflection symmetry is preserved along a one-dimensional
reaction path and argue that the topological classification should contribute
to the rate constants of these reactions. More concretely, we find that a
reaction takes place experimentally whenever the reactants and products can be
adiabatically deformed into each other, while reactions that require a change
of topological invariants have not been observed experimentally.
