The problem of the reduction of chemistry to physics has been traditionally addressed in terms of classical structural chemistry and standard quantum mechanics. In this work, we will study the problem from the perspective of the Quantum Theory of Atoms in Molecules (QTAIM), proposed by Richard Bader in the nineties. The purpose of this article is to unveil the role of QTAIM in the inter-theoretical relations between chemistry and physics. We argue that, although the QTAIM solves two relevant obstacles to reduction by providing a rigorous definition of chemical bond and of atoms in a molecule, it appeals to concepts that are unacceptable in the quantum-mechanical context. Therefore, the QTAIM fails to provide the desired reduction. On the ot...