Generation of multimillion chemical space based on the parallel Groebke–Blackburn–Bienaymé reaction
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Submitted summary
ORD Dataset for Govor et al., BJOC 2024, 20, 1604 (doi:10.3762/bjoc.20.143): 2052 reactions, one for every entry of SI File 2, in a gzipped binary ord.Dataset with no dataset or reaction IDs. Every reaction's provenance cites the DOI.
- Coverage: preliminary TsOH screen (#1-580), preliminary Sc(OTf)3 screen (#581-1160), and the Sc(OTf)3 library run (#1161-2052, 892 entries). All three are in one dataset, and the dataset description and each reaction's notes say which section a reaction came from. There are 2028 unique products; the 24 made under both catalysts are the ones compared in the paper's Figure 2. The 547 zero-yield entries are kept as negative results.
- Each reaction: the amine, aldehyde and isonitrile are given as printed (salts kept) with their compound numbers, at 0.270 mmol each and all limiting. Catalyst is Sc(OTf)3 or TsOH at 0.027 mmol. iPr2NEt (0.270 mmol) is included when the amine is a salt. Solvent is MeOH 0.5 mL, rt, stirred, 16 h. Workup: concentration, then DMSO, filtration, LCMS and prep RP-HPLC (from SI File 3). Each product has its SMILES, the original CXSMILES, its number 4{a,b,c} and its Enamine ID, plus the isolated mass in mg and the yield in %.
- Checks: the table was parsed from the PDF's own cell rules. All SMILES parse in RDKit. A GBB reaction template reproduces the listed product for 2052/2052 rows; 8 of those match only when stereo is ignored, because the source's stereo labels are inconsistent. Yields recomputed from mg at the 0.270 mmol scale match the printed % (13 rows are off by 3-7 points and are kept as reported). Success rates per section are 61.6/66.9/85.2 %, matching the paper's 62/67/85 %.
- Validator: ord-schema 0.8.3
validate_datasetgives 0 errors and exit status 0. There are 74 warnings, all SMILES-vs-CXSMILES relative-stereo (&1) identifier mismatches. Details are invalidation.txtandREADME.mdin the sources zip. - Preflight: none was available. This Contract has only a review stage, with no sandbox stage to run locally.
Submitted files 2
govor2024_gbb_ord_dataset.pb.gz337.9 KB · View file →govor2024_gbb_ord_sources.zip260.6 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: Generation of multimillion chemical space based on the parallel Groebke–Blackburn–Bienaymé reaction
- Authors: E.V. Govor, Vasyl Naumchyk, Ihor Nestorak et al.
- Published: BJOC, 2024-07-16
- DOI: 10.3762/bjoc.20.143
- 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 2,000 reactions; Parallel synthesis): 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
Parallel Groebke-Blackburn-Bienaymé 3-component library synthesis (Enamine), about 700 unique products. The data is in SI File 2, a text-based PDF table (CC-BY 4.0). Each row gives the product SMILES (ChemAxon CXSMILES with |c:...,t:...| extensions), the amine, aldehyde and isonitrile IDs and SMILES, and the yield in mg and %. There are about 2052 rows, including zero-yield outcomes, which should be kept as negative results. General procedures and conditions are in SI File 3. Reactant structure drawings are in SI File 1 (ZIP of PDFs). Pitfalls: long SMILES wrap across several text lines inside table cells, so parse by column position (e.g. pdfplumber word coordinates) rather than by raw text order. Strip CXSMILES extensions before validation. Amines may appear as salts (e.g. 'Cl.' prefix). Rows are grouped under condition headings (preliminary experiments with TsOH vs Sc(OTf)3 catalyst, then the library runs), and those conditions must be carried into each reaction. An author-supplied spreadsheet version is reported to exist but is not public. Check with the ORD maintainers before starting to avoid duplicated effort. Cite DOI 10.3762/bjoc.20.143.
Known locations:
- https://www.beilstein-journals.org/bjoc/articles/20/143: Article landing page listing SI Files 1-4 (S1 ZIP 6.9 MB, S2 PDF 625 KB, S3 PDF 1.0 MB, S4 PDF 3.0 MB) (license: CC-BY 4.0 (Crossref VOR/AM/TDM; diamond OA))
- https://www.beilstein-journals.org/bjoc/content/supplementary/1860-5397-20-143-S2.pdf: SI File 2: 'Parallel synthesis of compound library 4'. 169-page text PDF table with columns #, ID, product structure as CXSMILES, internal ID, amine/aldehyde/isonitrile IDs and SMILES, yield (mg and %). About 2052 rows, grouped into condition sections (e.g. preliminary TsOH vs Sc(OTf)3 catalyst… (license: CC-BY 4.0 (stated in the SI file header))
- https://www.beilstein-journals.org/bjoc/content/supplementary/1860-5397-20-143-S1.zip: SI File 1: ZIP of 3 PDFs of drawn reactant structures (amines 1, aldehydes 2, isonitriles 3) (license: CC-BY 4.0)
- https://www.beilstein-journals.org/bjoc/content/supplementary/1860-5397-20-143-S3.pdf: SI File 3: experimental part (general procedures and conditions, characterization) (license: CC-BY 4.0)
Pitfalls
Rows run across many condition sections (catalyst and scale vary), so templating must track section headers. Wrapped SMILES make reconstruction errors likely, which can be checked with RDKit parse plus a GBB reaction template (amine + aldehyde + isonitrile -> product) against the listed product SMILES. Yields are isolated mg/%; confirm purification and analysis details in SI File 3. The 2052 rows exceed ORD's estimate of 2000; reconcile the count.
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 →