Biginelli dataset

[connorcoley]

Paper: https://pubs.acs.org/doi/full/10.1021/cc010044j
SI: https://pubs.acs.org/doi/suppl/10.1021/cc010044j/suppl_file/cc010044j_s.pdf

Files used for the enumeration attached. It ended up being a little more custom than desired.

Currently, this ignores one small detail in procedure, so let me know if I should revise the submission to include it: "If solutions could not be prepared because of insufficient solubility (2h, 2r), the particular building block was added manually to the urea/thiourea and catalyst components were added directly into the vial."

biginelli.zip

[connorcoley]

Current validation errors are the following:

dataset: Reaction.workups[2].input: Reaction input components require an amount
dataset: Reaction.outcomes[0].products[0].measurements[1]: Purity measurements should be defined as percentage values
dataset: Reaction.workups[4].input: Reaction input components require an amount

In the paper, "washed with cold (4 °C) EtOH" does not specify an amount (which isn't unusual for washing steps). And purity is reported as ">90%" across all compounds, without a reaction-specific value, which I feel is best reflected by the string_value instead of a percentage.

Thoughts re: relaxing these validations (@michaelmaser @skearnes )?

[skearnes]

Thoughts re: relaxing these validations (@michaelmaser @skearnes )?

Agreed that both could be downgraded to warnings.

[brilee]

On naming: suggestion to sub /Biginelli Condensation Dataset/ with /Microwave-assisted Biginelli Condensation Dataset/

Stirring - I see no stirring was specified, but I think we should assume stirring unless otherwise specified because it would be an odd thing to drop.

Everything else LGTM

[connorcoley]

I've updated the name, but haven't added stirring. I think assuming stirring might actually be incorrect, since these are microwave reactions

[michaelmaser]

Currently, this ignores one small detail in procedure, so let me know if I should revise the submission to include it: "If solutions could not be prepared because of insufficient solubility (2h, 2r), the particular building block was added manually to the urea/thiourea and catalyst components were added directly into the vial."

Thinking this should probably be included, would it be possible to add to the loop? Looking at the notebook now

I've updated the name, but haven't added stirring. I think assuming stirring might actually be incorrect, since these are microwave reactions

Think I agree here, microwave reactions often go unstirred

[brilee]

SGTM for leaving the description unstirred

[brilee]

When spotchecking products, I noticed that in reaction 3, the urea has a phenylthiourea as a reagent, but there's no phenyl group on the product. I think this was caused by the paper's misleading use of φ (lowercase phi, the phenylthiourea) vs Φ (uppercase phi, the plain thiourea). This switchup appears wherever Φ is the urea specified, so it's probably a mistake in the urea input structure enumeration.

[connorcoley]

When spotchecking products, I noticed that in reaction 3, the urea has a phenylthiourea as a reagent, but there's no phenyl group on the product. I think this was caused by the paper's misleading use of φ (lowercase phi, the phenylthiourea) vs Φ (uppercase phi, the plain thiourea). This switchup appears wherever Φ is the urea specified, so it's probably a mistake in the urea input structure enumeration.

Good catch. I've made the phenylthiourea (NC(NC1=CC=CC=C1)=S) $\Omega$ now. It seems like only one product actually uses the phenylthiourea, and most use NC(N)=S

Thinking this should probably be included, would it be possible to add to the loop? Looking at the notebook now

I've added this as a condition detail, but have left the procedure as reflected by the inputs as-is. The statement in the methods section is a little unclear (to me) so I've copied it verbatim.

Archive.zip

[brilee]

structures LGTM