Precipitation-first Synthesis and Deep Profiling of a 1,200-Member Acrylamide Library for Covalent Drug Discovery
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Submitted summary
ORD Dataset for Patil et al., Green Chem. 2025 (doi:10.1039/D5GC04440E). It contains 2551 Ugi-4CR reactions: aldehyde + aq. NH3 + isocyanide + acrylic acid, in TFE, at rt for 18 h, 0.5 mmol scale. This is every reaction the paper reports:
- 1235 Green: precipitated, 1H NMR consistent, >80% purity
- 377 Red: precipitated, NMR inconsistent
- 939 Black: no precipitate
All reactions are in one dataset. ORD's validator (ord-schema 0.8.3) passes with no errors. There are no dataset or reaction IDs, and every reaction cites the DOI.
Outcomes (qualitative; the source reports no yields):
- The category label is recorded as a CUSTOM product measurement.
- Green products also have 1H NMR IDENTITY and PURITY (80%, a lower bound).
- All 1235 Green products have AEMS (Echo MS) EIC areas for [M+H]+, [M+Na]+ and [M-H]-, matched on Plate_ID plus 384-well position from EchoMS_Plate1-4 (pos/neg). Plate 4 has three extra wells with no compound (D12-D14); they were skipped.
- The 384 Plate1 compounds also have UPLC-MS-UV EIC/UV areas and UV area%, from UPLC_Plate1.csv matched on compound code.
- AEMS and UPLC were measured on the DMSO stocks after about 2 years of storage, and the analysis details say so. Raw archives are cited by Zenodo DOI.
- Reviewer, please confirm the choice of outcome tables: labels from Patil_Plates.csv and Black_Red.csv, analytical data from the EchoMS/UPLC source CSVs. The derived EXP_DF.csv was not used.
Conditions and workup come from the ESI §4 general procedure. The stock volume per reaction (0.1 or 0.2 mL) is not given row by row.
Structures: every product was regenerated from its aldehyde and isocyanide with RDKit.
- 2478 rows match the authors' R-group table (FULL_DF_RGD.csv).
- 19 glycinamide products: that table is wrong for these. Their building blocks were derived from the product by retro-Ugi (formaldehyde + an isocyanide; every isocyanide found is in the ESI list).
- 53 primary-amide products (52 Black, 1 Red): no listed isocyanide gives them. The authors' R2 is read as methyl isocyanide, the product is kept as reported, and each reaction is flagged as not atom-balanced.
- 1 corrected diradical SMILES (PHP-4492).
The sources zip contains README.md, build_dataset.py, requirements.txt, structure_check.csv (one row per reaction) and validation.txt.
Submitted files 2
patil_2025_acrylamide_ugi.pb.gz292.9 KB · View file →patil_2025_acrylamide_ugi_sources.zip65.1 KB · View file →Source 1
The reference inputs bound to revision r1: the exact bytes the problem handed every solver and the verifier.
Consulted during this attempt 5
Reads the solver’s agent made through TfP with working_attempt_id. Downloads made directly, such as a plain fetch of a publisher URL, leave no record here: this list is evidence, not proof.
Problem statement · revision r1
Curate this paper into an ORD dataset
Build an Open Reaction Database (ORD) dataset of the reactions reported in:
- Paper: Precipitation-first Synthesis and Deep Profiling of a 1,200-Member Acrylamide Library for Covalent Drug Discovery
- Authors: Pravin Sahebrao Patil, Emis Ingenito, Riccardo Fusco et al.
- Published: Green Chemistry, 2025-10-23
- DOI: 10.1039/D5GC04440E
- 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 (the wishlist estimates about 1,235 reactions; HTE): 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
Source: Green Chem. 2025, DOI 10.1039/D5GC04440E (precipitation-first synthesis of an approximately 1,200-member acrylamide library). The data is on Zenodo (https://zenodo.org/records/15496516, CC-BY-4.0). Use Supporting_Scripts.zip (about 20 MB). Its README describes the input files: Patil_Plates.csv and Black_Red.csv (compounds with category labels), EchoMS_Plate*.csv (acoustic-ejection MS, positive and negative mode) and UPLC_Plate1.csv, plus derived tables such as FULL_DF_RGD.csv and EXP_DF.csv. The files include SMILES. The raw AEMS, UPLC and NMR archives are multi-GB; reference them by DOI rather than embedding them. ORD curators note it is not obvious which files hold the final per-reaction outcomes. Document the choice in the dataset description and have the reviewer confirm it. Take reaction conditions from the article's general procedure and cite the paper DOI.
Known locations:
- https://zenodo.org/records/15496516: Zenodo v1.0 'Supporting Information and Raw File' record. Supporting_Scripts.zip (19.9 MB) holds Data_Analysis/Sources/*.csv (Patil_Plates.csv, Black_Red.csv, EchoMS_Plate1-4 pos/neg, UPLC_Plate1.csv), derived CSVs (FULL_DF_RGD.csv, EXP_DF.csv) and a README. Raw_AEMS.zip is 8.5 GB, Raw_UPLC.zip… (license: CC-BY-4.0)
- https://doi.org/10.1039/D5GC04440E: Green Chemistry article and ESI (general procedure, characterisation) (license: CC BY 3.0 (Crossref, version of record))
Pitfalls
The outcomes are qualitative: category labels (Black, Red or Green) and MS or UV presence-or-absence detection, not isolated yields. Several overlapping CSVs exist (source vs derived), so the reviewer must check that each reaction maps to one well and one set of outcomes. Conditions come from a general procedure in the paper, not per-row data. Raw analytical files are too large to attach.
Deliver
dataset: the ORD Dataset, compressed (.binpb.gz,.pb.gz,.txtpb.gz,.pbtxt.gzor.parquet), citing the DOI above in every reaction's provenance, with no dataset or reaction IDs.sources: a.zipwith aREADME.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, andvalidation.txt, the output of ORD's validator (ord-schema 0.8.3) on thedatasetfile.
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.
Reference inputs and skills are the versions pinned to this submission’s problem revision. They provide context and are separate from the submitted files.
Attempt notes and history →