We study isomerizations in quantum mechanics. We consider a neutral molecule composed of N quantum electrons and M classical nuclei and assume that the first eigenvalue of the corresponding N-particle Schr¨odinger operator possesses two local minima with respect to the locations of the nuclei. An isomerization is a mountain pass problem between these two local configurations, where one minimizes over all possible paths the highest value of the energy along the paths. Here we state a conjecture about the compactness of min-maxing sequences of such paths, which we then partly solve in the particular case of a molecule composed of two rigid sub-molecules that can move freely in space. More precisely, under appropriate assumptions on the multipoles of the two molecules, we are able to prove that the distance between them stays bounded during the whole chemical reaction. We obtain a critical point at the mountain pass level, which is called a transition state in chemistry. Our method requires to study the critical points and the Morse indices of the classical multipole interactions, as well as to improve existing results about the van de ... mehrr Waals force. This paper generalizes previous works by the second author in several directions.