HELM has a limited approach to bond formation; essentially single bonds are created between monomers connecting numbered R groups.
It is theoretically possible to create a monomers which has an R group connected via a double bond. However, what happens when you connect it? If you connect to another monomer with a double-bond, you have no way of knowing what the final bond order should be.
Bond order choice is not the only problem. Real-life examples can include other changes to the molecule. For example:
This non-ribosomal peptide synthesis step not only requires the user to choose the bond order of the R3 to R1 connection, but the cyclisation forms a double bond where there are no R groups.
Furthermore, the final product is not easily recognised as a combination of two amino acids you started with.
Click chemistry poses similar problems. In this example: if you add two R groups to the alkyne you would end up with a pentavalent carbon or would have to reduce the bond order. The azide poses similar problems.
HELM is a product notation. It does not encode reactions and monomers are based on the final structure and not starting materials. The wide variety of synthetic pathways cannot be encoded in a notation like HELM and we will not attempt to do so.
Since this is the case, the user should look for common monomers first and then add other fragments as needed. In the click chemistry case, you could represent it like this:
The structure in black would be defined as a CHEM monomer, but the others as peptide monomers. This way we have recognisable amino acids.
It would also be possible to define the final structure as a single monomer, but in this case the final product would be unwieldy and contain multiple functional groups that could be attached to further a peptide chain, so the approach shown would be preferred.
The HELM notation allows R groups to be anything, so they can be defined as azide and alkyne, however the web-editor doesn’t support this yet. (It is on our list of things to do.)
For the case combining two amino acids, we recommend that the end product is used as a monomer.