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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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submission 47465522 #192

Open qai222 opened 2 months ago

qai222 commented 2 months ago

reaction optimization plate from 10.1039/d3dd00167a

processing script: https://github.com/qai222/ord_submission/blob/master/dataset_47465522/process.py

comments:

skearnes commented 1 month ago

reaction optimization plate from 10.1039/d3dd00167a

processing script: https://github.com/qai222/ord_submission/blob/master/dataset_47465522/process.py

comments:

  • pd catalysts were added as solutions and then the solvents were removed to leave solid solutes before adding other reactants/reagents.
  • stirrers were added between reaction inputs
  • ambiguous reaction role for copper cocatalyst
  • some of the preparation were done in glove box, not sure where to put this info

Maybe here? https://github.com/open-reaction-database/ord-schema/blob/main/proto/reaction.proto#L44

  • the vial was sealed during some of the processes, not sure where to put this info

Maybe here? https://github.com/open-reaction-database/ord-schema/blob/main/proto/reaction.proto#L778

  • one option is VesselType.PRESSURE_FLASK but this seems odd when vials are actually used
    • no place to specify heater type (heated tumble stirrer)

Maybe here? https://github.com/open-reaction-database/ord-schema/blob/main/proto/reaction.proto#L574

  • measurements are relative peak area against internal standard, normalized to 100%. I used type=ProductMeasurement.ProductMeasurementType.AREA to record them
skearnes commented 1 month ago

Other details that don't have an obvious home can go here: https://github.com/open-reaction-database/ord-schema/blob/main/proto/reaction.proto#L778

skearnes commented 1 month ago

Might also consider this for the vessel sealing: https://github.com/open-reaction-database/ord-schema/blob/main/proto/reaction.proto#L601

skearnes commented 1 month ago

Might also consider this for the vessel sealing: https://github.com/open-reaction-database/ord-schema/blob/main/proto/reaction.proto#L601

And here: https://github.com/open-reaction-database/ord-schema/blob/main/proto/reaction.proto#L495

qai222 commented 1 month ago

The previous comments were solved by using fields of ReactionNotes and ReactionConditions.

One thing about the addition of pd catalyst. This ReactionInput was added as a solution and its solvent was removed using an evaporator before adding other ReactionInput:

  1. what should be the Texture of this ReactionInput? I'm using SOLID as this is the form in which this ReactionInput was immediately before mixing with other ReactionInput.
    • in this dataset the author did not describe the addition device so I left it unspecified. There could be a situation where a liquid handler is described for a ReactionInput whose texture is SOLID, which could be confusing.
  2. the removed solvent (and the concentration of the solution) could be useful but it's only included in an unstructured way, especially when this removed solvent is different from the solvent used in the actual reaction

FWIW Here is the related text from the paper

Inside a glovebox, a solution of each palladium precatalyst was prepared by dissolving 20 μmol of each
in a sufficient quantity of 2-methyltetrahydrofuran to give 2000 μL of solution. 100 μL of each solution
was then dosed to 8 x 24 well plates, and the solvent was removed in vacuo using the Genevac for 1 h.
The plates were stored in the glovebox and used within 1 year of creation.