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open-reaction-database / ord-data

Official data repository for the Open Reaction Database
https://open-reaction-database.org
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Huffman islatravir biocatalytic cascade dataset submission #91

Closed michaelmaser closed 3 years ago

michaelmaser commented 3 years ago

Details the synthesis of islatravir by enzymatic catalysis.

Notebook used for generation is attached, which includes links to the paper and images of each reaction scheme from the SI for visualization.

Huffman_islatravir_dataset.ipynb.zip

brilee commented 3 years ago

I notice there's a lot of solutions in this one. Do you want to review and give the macros in https://github.com/open-reaction-database/ord-schema/pull/599 a whirl?

The 1H NMR, 13C NMR, 31P NMR, HRMS data is nice.

michaelmaser commented 3 years ago

Thanks for the feedback, Brian!

  • in rxn1 sulfur pentahydrate is drawn as the hexahydrate

Are you sure? Just loaded the SMILES from the pbtxt into RDKit and see the pentahydrate below: cuso4_5h2o

  • in rxn2, water solvent is doubly specified?

Yes, the substrate is a solution in water, but the crude_component can't be specified as a solution if you want to include the mass of the compound (since they know the exact amount of the substrate, I wanted to use it). So, I added the crude substrate as it's mass, with an input of the proper volume of water at the same addition order. Then, one of the reagents is also added as an aqueous solution, which was treated normally as a single input.

I notice there's a lot of solutions in this one. Do you want to review and give the macros in open-reaction-database/ord-schema#599 a whirl?

Cool, thanks! For the sake of time, I'm hoping to submit ASAP since this dataset will be referenced in the manuscript. Would be happy to try it out after/with the next dataset!

The 1H NMR, 13C NMR, 31P NMR, HRMS data is nice.

Thanks!

brilee commented 3 years ago

Ah, double-checked the pentahydrate and it's correct - my bad. Everything else seems good to me

michaelmaser commented 3 years ago

No worries, thanks again! @skearnes @connorcoley any concerns before I submit?

connorcoley commented 3 years ago

Just changing the PR so you're merging into a branch and not main, but I'll trust Brian's review and the process!

skearnes commented 3 years ago

Thanks @michaelmaser --- can you please create the second PR to merge that branch into main now?