Nanoscale synthesis and affinity ranking
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Submitted summary
ORD Dataset for Gesmundo et al., Nature 2018 (doi:10.1038/s41586-018-0056-8): 5,532 reactions
dataset: gesmundo_2018_nanoscale.pb.gz, one ORD Dataset with no dataset or reaction IDs. Every reaction cites the DOI in provenance.doi. ord-schema 0.8.3 validate_dataset: 0 errors. 205 warnings, all real data values: LC-UV yields >100%, yields/conversions <1%, and one −1.3% yield reported by the authors.
Contents (one Dataset; the parts are listed in Dataset.description):
| Part | n | Outcome |
|---|---|---|
| SI §3.2–3.6 optimisation screens (ED Fig. 6): Suzuki ×2, C–N ×2, diverse nucleophiles | 672+162+384+360+1,536 | LC-UV yield (PhPh internal standard / standard curves), conversion, UV area |
| SI §5.2/6.2/7.2 nano-libraries (Fig. 2a/b/c) | 38+144+200 | LC-UV yield (standard curves), conversion |
| SI §8.2/8.3 384-member CHK1 library (Fig. 3), variable + single condition | 1,536+384 | relative conversion, UV area |
| SI §5.1/6.1/7.1/8.6 bench-scale syntheses | 19+18+20+59 | isolated yield and mass |
Key curation choices
- Built from the per-screen sheets only.
Compiled Yield Data,prelim-screening-csv,big-library-csvand the MOESM4–9 copies are excluded to avoid double counting. - Diverse screen yield column:
Calc'd % Yield Updated(the older column's 171 negative values are set to 0). - C–N Screen 2 has duplicate injections of wells L11–L14; each well is one reaction with two measurements.
- MFCD-only building blocks are resolved from an MFCD→SMILES map built across 8 sheets (396 IDs, 0 conflicts).
- Precatalysts are given full structures (ligand + 2-aminobiphenyl Pd palladacycle, G2 Cl / G3 OMs) plus their trade names. Bases have full structures.
- Amounts, concentrations, times and atmosphere come from the SI.
- Every reaction passes a formula-balance check (5,532/5,532).
- SI errors found and resolved: the compound 36 MFCD, and the "MEBD" typo (= MTBD).
- ASMS/affinity data are out of scope.
record_createduses the RFC 2606 placeholder e-mailcurator@example.org, which ord-schema requires. Replace it with the submitter's address at ORD submission.
sources: gesmundo_2018_sources.zip contains README.md (sheet → reaction mapping, decisions, how structures were checked), the Python scripts that rebuild the dataset from the publisher files, validation.txt, structure_checks.txt and reactions_summary.csv (one row per reaction, for spot checks).
Submitted files 2
gesmundo_2018_nanoscale.pb.gz331.8 KB · View file →gesmundo_2018_sources.zip145.2 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 4
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: Nanoscale synthesis and affinity ranking
- Authors: Nathan J. Gesmundo, Bérengère Sauvagnat, Patrick J. Curran et al.
- Published: Nature, 2018-04-19
- DOI: 10.1038/s41586-018-0056-8
- 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: 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
Nanomole-scale (1536-well) Pd-catalysed coupling screens (Suzuki, C-N amination, amide/diverse nucleophile couplings) and library syntheses from Gesmundo et al., Nature 2018 (doi:10.1038/s41586-018-0056-8). Reaction data is in the article's Source Data Excel files (Fig. 2-4 and Extended Data Figs. 2-6, 8-10) on nature.com. Rows give reactant and product SMILES, plate position, catalyst (trade names such as XPhos Pd G3), base (e.g. P2-Et, BTMG, BTTP), solvent, LC-UV areas and a calculated percent yield from a product-to-internal-standard ratio. Reagent volumes are in the plate-map sheets. Concentrations, stoichiometry, temperature and time must be taken from the Supplementary Information PDF. Pitfalls: (1) some sheets identify building blocks only by MFCD number, so resolve SMILES from other sheets; (2) the 'Compiled Yield Data' sheet repeats rows from the individual screen sheets, so do not double-count; (3) some sheets have two yield columns (e.g. 'Calc. Percent Yield' and 'Calc'd % Yield Updated'), so state which one is used; (4) affinity-selection mass spectrometry (ASMS) binding data is not reaction data and is out of scope; (5) catalyst and base names need structures. The ORD Dataset must cite the paper DOI.
Known locations:
- https://www.nature.com/articles/s41586-018-0056-8: Article landing page; lists the Supplementary Information PDF (MOESM1) and 11 Source Data files (Fig. 2, 3, 4; ED Fig. 2-6, 8-10) as XLS/XLSX (license: Springer Nature, closed-access article (Crossref: springer.com/tdm only))
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-018-0056-8/MediaObjects/41586_2018_56_MOESM9_ESM.xlsx: Source Data for ED Fig. 6 (catalyst/base survey, 0.78 MB). Sheets: Suzuki Coupling Screen 1 (687 rows), Suzuki 2 Optimization (162), C-N Coupling Screen 1 (384), C-N Coupling Screen 2 (364), Diverse Coupling Screen (1,536), Compiled Yield Data (2,110), plus plate maps. Columns include Core SMILES… (license: Springer Nature source data; no CC license stated)
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-018-0056-8/MediaObjects/41586_2018_56_MOESM2_ESM.xls: Source Data for Fig. 2 (library synthesis; 1.3 MB per HEAD); MOESM3-8 and MOESM10-12 are the other figure source data files (HEAD checked only on MOESM2/3/9/12) (license: Springer Nature source data; no CC license stated)
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-018-0056-8/MediaObjects/41586_2018_56_MOESM1_ESM.pdf: Supplementary Information PDF (procedures, concentrations and amounts, compound data) (license: Springer Nature; closed)
Pitfalls
Yields are LC-UV estimates against an internal standard, not isolated yields; conversion and yield columns coexist. Screens are spread across many sheets and files with overlap (compiled vs per-screen), so reviewers must check for deduplication. Many reactions give 0% yield (valid negative data). Precatalysts are named by trade name. Reaction conditions such as temperature, time and concentrations live in the SI PDF, not in the spreadsheets. It may need 2 datasets if library synthesis and condition screens are kept separate.
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 →