Rather than manipulating the molecules into monomers so they can be assembled easily, we can use the Transformation language to express exactly how the reagents go together.
This shifts the burden of describing mixtures to writing comprehensive, accurate transformations.
Note:
One the surface, this doesn't seem to be a practical way to store mixtures in a database. Given the types of questions one wants to ask about mixtures (typically about the final molecules in the mixture), there would be a lot of computation required to answer them.