According to classical molecular chemistry, molecules have a structure, that is, they are sets of atoms with a definite arrangements in space and held together by chemical bonds. The concept of molecular structure is central to modern chemical thought given its impressive predictive power. It is also a very useful concept in chemistry education, due to its role in the rationalization and visualization of microscopic phenomena. However, such a concept seems to find no place in the ontology described by quantum mechanics, since it appeals to classical notions such as the position of the atomic nuclei or the individuality of electrons. Although this problem has attracted the attention of several authors, the discussion is far from settled. Some authors adopt an explicitly reductionist position and advocate to reconstruct the concept of molecular structure within the framework of the quantum theory. Others, although acknowledging the conceptual discontinuity between quantum mechanics and molecular chemistry, keep the hope of future reduction alive. From an explicitly non-reductionist position, on the contrary, others authors conceive molecular structure as an emergent phenomenon. The purpose of this article is to propose a different line of argumentation to address this problem. By contrast to reduction and emergence, the admission of a multiplicity of ontologies, not necessarily linked by hierarchical connections, cancels the need of finding a relation of dependence between the molecular level and the quantum level. This ontologically pluralist position can be applied to the issue of molecular structure, in order to argue that it is possible to admit the existence of structure in the ontology of molecular chemistry, in spite of the fact that it does not exist in the quantum world.
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