Curate this paper into an ORD dataset

Build an Open Reaction Database (ORD) dataset of the reactions reported in:

• Paper: ChemBeads-Enabled Photoredox High-Throughput Experimentation Platform to Improve C(sp2)–C(sp3) Decarboxylative Couplings
• Authors: Nathan J. Gesmundo, Noah P. Tu, Kathy Sarris et al.
• Published: ACS Med Chem Lett, 2023-03-16
• DOI: 10.1021/acsmedchemlett.2c00538
• ORD wishlist card: open on GitHub

The reference input card holds these facts, the source-data locations and the notes below in machine-readable form.

Scope

Every reaction the paper reports with its data (HTE, photo, chembeads): inputs with amounts and roles, conditions, workups, outcomes and provenance, following the ord-curation Skill. Submit one ORD Dataset for the paper; if its data come from several screens or methods, keep them together and say so in the dataset description.

Source data

ACS Med Chem Lett paper on ChemBeads-enabled photoredox HTE for C(sp2)-C(sp3) decarboxylative couplings. The SI has two relevant spreadsheets. ml2c00538_si_003.xlsx is the full HTE data table behind Figure 4. ml2c00538_si_004.xlsx is the full parallel library synthesis table behind Figure 5. ml2c00538_si_002.xlsx holds bead-dispensing weight data and is not reaction data. The SI PDF (about 10 MB) has general procedures, photoreactor setup and characterization. Neither spreadsheet has been inspected, so it is unknown whether they contain SMILES or only compound IDs. If only IDs are present, structures must be drawn from the SI PDF. The HTE screen and the library synthesis can be separate ORD datasets. Record the light source, wavelength and ChemBead loading (reagent-coated glass beads) in the ORD illumination and input fields.

Known locations:

• https://pmc.ncbi.nlm.nih.gov/articles/PMC10108395/: PMC copy listing SI: ml2c00538_si_001.pdf (experimental and characterization, 10 MB), si_002.xlsx (dispenser weight accuracy, 26 KB), si_003.xlsx (full HTE data table for Figure 4, 356 KB), si_004.xlsx (parallel library synthesis data for Figure 5). Only the listing was read. The xlsx downloads… (license: unknown (PMC copy; publisher ACS))
• https://pubs.acs.org/doi/10.1021/acsmedchemlett.2c00538?goto=supporting-info: Publisher SI page with the same four files (license: publisher (ACS) terms)

Pitfalls

Photochemical conditions need illumination metadata. ChemBeads are reagent-coated glass beads, so amounts depend on bead loading (wt%). HTE outcomes may be UPLC area percent or conversion rather than yields. Contents of the XLSX files are unverified, and compound identifiers may need mapping to structures.

Deliver

• dataset: the ORD Dataset, compressed (.binpb.gz, .pb.gz, .txtpb.gz, .pbtxt.gz or .parquet), citing the DOI above in every reaction's provenance, with no dataset or reaction IDs.
• sources: a .zip with a README.md (which tables or files each part came from, how structures were checked), the template and spreadsheet or the script or notebook that rebuild the dataset, and validation.txt, the output of ORD's validator (ord-schema 0.8.3) on the dataset file.

Before you start

Open the wishlist card. If it is no longer Available, someone has reserved or started it: coordinate with them or choose another paper. Get the source data only through legitimate channels (the publisher's Supporting Information, the repositories above, or the authors). Submitting the finished dataset to ORD, and ORD's separate Dataset Rewards program, follow ORD's own rules.