This is extensively discussed in Parts XVe and XVf. It boils down to the following : If it is found out or conceded that a molecule (any molecule) is a true Substance in the metaphysical sense, a molecule must then be one single being, one single ens. And this means that the constituent atoms in the molecule, as particles, cannot exist actually in it, because then the molecule would be an aggregate of more than one Substances, and thus not one single being anymore. So these atoms must exist in the molecule only virtually. And their properties, in so far as they are conserved in the molecule, are not properties of these atoms anymore but of the molecule.
If the constituent atoms are considered apart (from each other and from the molecule), then they become, in such consideration, actual. And if the molecule is chemically disintegrated, then also the constituent atoms change, now not only in consideration, from virtual to actual. Indeed, in the molecule the conserved qualitative contents of the constituent atoms have been integrated into the molecule's whole, i.e. integrated into the molecule's substantial Form. And only when considered apart, these qualitative contents may, as terms, be predicated of (the term representing) the molecule.