Although the MPculeID format meets the basic requirements for a database ID format and overcomes certain key limitations of previous chemical identifiers, MPculeIDs have limitations of their own. For example, similar graphs do not in general produce similar Weisfeiler-Lehman hashes; these hashes therefore cannot be used to search for similar molecules, including molecules containing a particular substructure or functional group. There are also limits to the current implementation of MPculeIDs in the MPcules database that are not limitations of the basic format. As we have explained, when generating graph hashes for use in MPculeIDs, the graphs can be augmented with atom or bond features. Depending on how the graphs are augmented, different hashes will be produced, which can change if and how species are distinguished. As an example, consider chiral molecules. Different enantiomers have the same connectivity but are thought of as distinct because of their optical, structural, and (in some cases) reactive properties. Because they are by definition non-superimposable, enantiomers can be distinguished by their MPculeIDs in the association stage (where the graphs are augmented with Cartesian coordinates). However, MPculeIDs in the collection stage cannot distinguish between enantiomers because we do not augment the graphs with any information about chirality.