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Here is the url for my first notebook:

https://community.wolfram.com/groups/-/m/t/2073460

Sorry for the delays. I am cleaning up the code from my 2nd notebook, fixing bugs, and then I will post it again in a 3rd notebook with examples of multi-step synthesis.

Regarding my mention of "Wolfram Summer School 2020" in the original version of my notebook, I was not a student of this year's session, but I did apply for admission. I began working on my 1st notebook while I was (optimistically) waiting to hear if I would be accepted into WSS 2020. I wanted to get a head start, just in case. But there were so many great applicants, and not everyone could be squeezed in, and I didn't make the cut. But I totally understand. I've enjoyed watching the WSS 2020 student project presentations. Very exciting minds working at the cutting edge!

Hi Jason,

Thank you for your encouragement and the very useful info about the "ReplaceStructure" method. I only recently started learning WL, so I know that there are other chemistry-related functions I need to explore. I will definitely look into your specific suggestion for joining molecules.

This is great work! I look forward to reading through the code more thoroughly.

In the long run we definitely need a chemical reaction data structure that can operate on a list of molecules to make this easier on you. Until we get that, another approach you could take for chemical reactions is using the "ReplaceSubstructure" method:

alkyne = Molecule["1-octyne"]
primaryalkylhalide = Molecule["benzyl bromide"]

The trick here is to join the two molecules into one disconnected structure, then search for a single substructure matching the bromly group and terminal alkyne, and replace it with the joined version:

joinMolecules[list : {__Molecule}] := 
 Molecule@StringRiffle[MoleculeValue[list, "SMILES"], "."]

MoleculeModify[
 joinMolecules[{alkyne, primaryalkylhalide}], {"ReplaceSubstructure", 
  MoleculePattern["[CH2][Br].[CH1]#[C]"] -> "CC#C"}]