Perhaps the hottest topic in the philosophy of chemistry is that of the relationship between chemistry and physics. The problem finds one of its main manifestations in the debate about the nature of molecular structure, given by the spatial arrangement of the nuclei in a molecule. The traditional strategy to address the problem is to consider chemical cases that challenge the definition of molecular structure in quantum–mechanical terms. Instead of taking that top-down strategy, in this paper we face the problem (...) of the reduction of molecular structure to quantum mechanics from a bottom-up perspective: our aim is to show how the theoretical peculiarities of quantum mechanics stand against the possibility of molecular structure, defined in terms of the spatial relations of the nuclei conceived as individual localized objects. We will argue that, according to the theory, quantum “particles” are not individuals that can be identified as different from others and that can be reidentified through time; therefore, they do not have the ontological stability necessary to maintain the relations that can lead to a spatially definite system with an identifiable shape. On the other hand, although quantum chemists use the resources supplied by quantum mechanics with successful results, this does no mean reduction: their “approximations” add certain assumptions that are not justified in the context of quantum mechanics or are even inconsistent with the very formal structure of the theory. (shrink)