Adds Nielsen deoxyfluorination dataset

open-reaction-database / ord-data

Official data repository for the Open Reaction Database

https://open-reaction-database.org

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Adds Nielsen deoxyfluorination dataset #110

Closed michaelmaser closed 3 years ago

michaelmaser commented 3 years ago

Dataset created from notebook in ord-schema by @connorcoley.

skearnes commented 3 years ago

Thanks @michaelmaser! A few comments:

[x] The SI says "8 x 40 mm" glass vial; should this be included somewhere? I assume the 1 mL annotation is inferred from that size?
[x] Add volume_includes_solutes = False to the solvents (including in the workup)?
[x] The chloroform added in the workup should be deuterated (also update the corresponding description).
[x] The non-synthesized SFs (PyFluor and PBSF) should be indicated in build_compound.
[x] The vendor for PyFluor should be specified.
[x] Please add the names of the SFs so the records are easier to read.
[x] The logic to build out the table doesn't seem to correctly copy preparations (I expected to see SYNTHESIZED for the randomly chosen reaction shown in the notebook).

michaelmaser commented 3 years ago

Thanks, @skearnes! Think I got everything. Added a record_modified for posterity.

skearnes commented 3 years ago

Thanks, @skearnes! Think I got everything. Added a record_modified for posterity.

Thanks! Would you mind attaching the updated notebook---or linking to a PR on ord-schema with the changes?

michaelmaser commented 3 years ago

Thanks! Would you mind attaching the updated notebook---or linking to a PR on ord-schema with the changes?

Sure thing, attached here. Happy to create a PR, maybe next office hours. example_nielsen.ipynb.zip

skearnes commented 3 years ago

Thanks! One more question: where is the stereochemistry information coming from for e.g. 1a in the example reaction? I don't see that in the SI or paper anywhere?

skearnes commented 3 years ago

Thanks! One more question: where is the stereochemistry information coming from for e.g. 1a in the example reaction? I don't see that in the SI or paper anywhere?

Nevermind; was looking at the wrong structure.

michaelmaser commented 3 years ago

Thanks! Any idea why the check_file_types is failing?

skearnes commented 3 years ago

I think it's because the target branch is out of date, and the job does a comparison vs. main. If you update nielsen it should work, but I wouldn't worry about it.

michaelmaser commented 3 years ago

Worked, thanks!