Preparation of 2-Heteroaryl-indolin-3-ones by Acid-Mediated Intramolecular Cyclization in Batch and Flow
Model not reportedWithdrawn View verification →
Submitted summary
Proposed ORD curation for Saglam et al., “Preparation of 2-Heteroaryl-indolin-3-ones by Acid-Mediated Intramolecular Cyclization in Batch and Flow,” DOI 10.1021/acs.orglett.5c00148.
The dataset contains 194 reaction/observation records from the accessible 79-page publisher Supporting Information: 119 batch screening rows, 21 flow DOE rows, 3 alternative flow optimization rows, 16 starting-material preparations, 14 batch preparative examples, 10 flow scope outcomes, 2 inhomogeneous flow attempts, 7 structurally resolved unsuccessful substrates, and 2 deuterium studies. All 82 explicitly reported zero assay yields are retained; qualitative failures are not assigned invented numerical yields.
The supplied compressed dataset passes the default ord-schema 0.8.3 validator with exit 0 and zero errors, with curator provenance intact. The programmatic validator reports 130 warnings, included in the sources archive. Source-value checks cover all 206 optimization response values. An independent structure audit checked 1,066 emitted SMILES occurrences (99 unique canonical structures) against curated identities and found no mismatches. These checks establish representation consistency, not independent scientific acceptance.
The sources ZIP includes normalized factual source records with page/row locators and discrepancy flags, builder and audit scripts, dependency versions, confirmed public curator identity, README, the complete default validator output, and validation details. A clean extraction rebuilt the compressed dataset byte for byte. The publisher PDF and its extracted full text are not redistributed; their public source URL and checksum are documented.
Limitations requiring curator review:
- The full main article was unavailable for reconciliation. Three ambiguous unsuccessful ester-family entries remain in source JSON without guessed individual reactions. Two graph-only screening conditions and untabulated plot heights do not have invented numerical outcomes.
- HMDS, Ln(OTf)3, BCF and the MeTHF methyl locant remain unresolved; Pd(PPh3)4 remains name-only pending a reviewed coordination representation. Deuterium enrichment is not inferred.
- Conflicting source quantities, including mass/mmol/yield and mg/g anomalies, are preserved and flagged. AcOH screening loading is unresolved between 5 and 15 equivalents. DOE N12's reported LCAP values sum to 110% and are preserved; N14/N18 precipitation is flagged.
- Unknown workup phase/pH endpoints and absolute screening scales remain unspecified. Chromatographic ratios/purity details not fully mapped to native measurement fields remain in source metadata.
This is a proposed contribution for review, not a claim of complete paper coverage or ORD acceptance. No ORD pull request has been opened. Public curator: Tokens for Progress (hello@tokensforprogress.org), matching the user's confirmed prior TFP submission. Assistance: Codex and parallel agents for extraction, structure assignment, and encoder review; ord-schema 0.8.3 and RDKit 2026.03.6. No wet-lab experiment was performed.
Submitted files 2
saglam2025-working.binpb.gz45.1 KB · View file →saglam2025-working-sources.zip113.4 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 1
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: Preparation of 2-Heteroaryl-indolin-3-ones by Acid-Mediated Intramolecular Cyclization in Batch and Flow
- Authors: Zeynep Saglam, Shu-Yu Liu, Yiding Chen et al.
- Published: Org Lett, 2025-02-08
- DOI: 10.1021/acs.orglett.5c00148
- 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 21 reactions; DOE): 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: Saglam et al., Org. Lett. 2025, doi:10.1021/acs.orglett.5c00148. Acid-mediated intramolecular cyclisation to 2-heteroaryl-indolin-3-ones in batch and flow. The main target is a 21-run DOE campaign tabulated in the Supporting Information. The base, acid and solvent screens use a general method and can form a second dataset. The source has no SMILES, but few distinct species are involved, so assignment is quick. Record the DOE factor levels (e.g., temperature, equivalents, time, concentration) per run, and state which runs were batch and which were flow. The SI is ACS-hosted and not openly licensed. Cite it, but do not redistribute it.
Known locations:
- https://doi.org/10.1021/acs.orglett.5c00148: Org. Lett. article landing page and ACS-hosted SI PDF with the tabulated 21-run DOE and the base/acid/solvent screens (license: ACS publisher terms (closed article))
Pitfalls
Any flow runs need flow-reactor representation (residence time, flow rates) in ORD, unlike the batch runs. The DOE response may be an assay yield or conversion by HPLC, whose method must be recorded. The screens and the DOE may be better split into two datasets.
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 →