This work is part of series of other posts avaialble here:
I post this in case anyone is interested in experimenting further along these lines, or in collaborating with me on an organic synthesis related project. This notebook shows my representation of various organic chemical reactions in Wolfram Language.
Hi Leonardo, interesting work! ..do you have SOCIAL (ex: like LinkedIn), so we can connect?
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"}]
Hi Claudio
I just created a LinkedIn page for myself: linkedin.com/in/leonardo-cabana-5463451b6
Feel free to connect with me there. I’m new at social media, so please excuse my rudimentary LinkedIn profile. Thank you for your interest in the chemistry code that I published. I look forward to hearing from you.
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.
Here is the link to my first notebook:
https://community.wolfram.com/groups/-/m/t/2073460
In the 1st notebook I practice the basic graph- and molecule-related functions, gradually learning increasingly better ways to represent and make changes to molecules.
In the 2nd notebook, I summarize the final products of the research form the 1st notebook.
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!
Nice and interesting! Looks like this notebook was published as private. Can you republish it with public permissions so we an take a look? Thank you.
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.
Please see my new post about Organic Synthesis in WL:
– you have earned Featured Contributor Badge 
Your exceptional post has been selected for our editorial column Staff Picks http://wolfr.am/StaffPicks and Your Profile is now distinguished by a Featured Contributor Badge and is displayed on the Featured Contributor Board. Thank you!
Thank you for posting! I was honored to receive the Featured Contributor Badge, but I also feel encouraged when I get some comments :-). Please let me know if you have any questions or opinions about this project. And please see my more recent posts here that take my organic synthesis model even further.
Here is the link to my most recent article:
Organic Chemistry 4: Experimental Functions for Chemical Synthesis in WL
