OrgSyn example from ord_schema

Mostly minor comments, besides workup for reaction 2 & 3.

Reaction 1:

[X] DMAP has reaction_role = REACTANT - Think I would consider it a REAGENT since it's not contributing atoms to the product.

[ ] You have 3 ADDITIONs of 50 mL DCM in the workup, then an EXTRACTION with details of "3 x 50 mL". It seems like the procedure has 1 addition (to wash the reaction flask on transferring to the sep funnel) then 2 extractions. Is this how we handle extractions (ADDITION, then EXTRACTION)? Or, should they just be EXTRACTIONs?

I think this has always been vague. To me, doing 3 additions then an extraction makes the most sense because otherwise the process isn't linear. When I think about the linear workup steps, keep_phase means that material becomes what we're tracking throughout the rest of the workup. This is tricky since our workups are linear sequences but this is not a sequential operation.

[X] Could the ADDITION step between the concentration and chromatography be considered a DISSOLUTION?

[X] I think I would consider the purification FLASH_CHROMATOGRAPHY. They load onto a column and collect fractions as usual, just that the stationary phase is alumina (our note in the proto says to specify this). Seems like we added OTHER_CHROMATOGRAPHY for things like prep TLC, prep HPLC and things.

[X] The analytical data is great

[X] Want to add experimenter name to provenance?

How do we know if Richard or Steve ran the reactions? Just kidding, I'll add Richard as the experimenter for all three

Reaction 2:

[X] Thinking reaction_role for Cu(OAc)2, DTBM-SEGPHOS, and PPh3 could probably be CATALYST

That's fair. Changed

[X] N,N-dibenzyl-O-pivaloylhydroxylamine has preparation SYNTHESIZED, but doesn't reference reaction 1, want to add this?

[X] Want to specify this reactant is_limiting=False? Have it noted for the styrene and could be derived from amounts, just noting.

[X] dimethoxy(methyl)silane has addition order 5, but was added after THF (addition order 6)

Thanks, not sure why I flipped those originally

[X] setup and observation details are nice

[X] The workup seems to be missing?

I swear I had added those to the Jupyter notebook months ago, but it doesn't look like it. The new version should have it.

[X] Funny consequence of using Python floats for HRMS data, making note here to remind myself to create issue later. Precision/number of sig figs is way beyond instrument precision, and could change the resulting delta between expected and measured. In the worst case scenario, this change would bring a measurement outside the acceptable range for publication. Not crucial right now, but worth noting for auto SI generation down the line. Possible solutions are to handle as strings or round to 4 decimals. Found same thing for isolated_weight in analysis.

[X] Analytical data is really nice

Reaction 3:

[X] Basically all the same comments from step 2

[X] Yield in the paper is 87%, vs 86% in the dataset, perhaps copied from reaction 2

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open-reaction-database / ord-data

OrgSyn example from ord_schema #95