Shields_Arylation

[Jesus00-1]

Shields Arylation S42 and S45. Paper: https://doi.org/10.1038/s41586-021-03213-y

Best,
Jesus

[Jesus00-1]

I merged into the main branch, but the check is failing. Which branch in the repo should I merge to?

Best,
Jesus

[Jesus00-1]

uploading the zip files.

experiment_index_extended.zip
experiment_index_S42.zip

[skearnes]

I merged into the main branch, but the check is failing. Which branch in the repo should I merge to?

Best,
Jesus

That check is ok to fail; I'll change the target branch when we're ready to merge. The Submission/process_submission check is the important one.

A couple things:

• It looks like you committed the template reaction pbtxt; please remove that.
• The second pbtxt file is much smaller than the one from Uploading dataset pbtxt for Shields Doyle Paper #51; just checking that you're only intending to submit the 60k-line file?

[michaelmaser]

Looks good for the most part. Couple things:

1. The vessel type given is WELL_PLATE, which is true, though the reactions are actually set up in VIALs of material GLASS in a well plate, not in the plate wells directly. @skearnes @connorcoley, don't know that we've discussed this yet. How should this be captured? Also, the pressure control is listed as SEALED, but no VesselAttachment is listed. I assume the vials are capped, which can be captured by adding a CAP VesselAttachment; please add this.
2. There is only one workup step (ALIQUOT) included, which contains string details describing several more steps. The full workup is described as:

The plate was removed from the glovebox, opened, and diluted to a 900 uL total volume with N,N-dimethylacetamide. The plate was stirred for 5 min and a 75 uL sample was taken and filtered into an HPLC analysis plate. The filter was rinsed with 400 uL acetonitrile/water (4:1) solution and analyzed by UHPLCMS.

This should be captured by the full workup step sequence: ADDITION -> STIRRING -> ALIQUOT -> FILTRATION -> ADDITION.

3. The INTERNAL_STANDARD is listed in a separate reaction.outcome, though it is analyzed in the same analyses key as the desired product. This can be captured by adding the internal standard to the set of products in the first (and only) outcome. Its peak area measurement can also be added and linked to the same UHPLCMS analysis that the product is measured with. These values are not included in the dataset, only the ultimate processed reaction yields. I don't know that this is necessarily a problem (@skearnes @connorcoley?), but do you have the raw peak areas for the internal standard?

[michaelmaser]

Looks great. Thanks for working through this, Jesus!