Leveraging Data Science to Elucidate Ligand Features for Pd-Catalyzed Enantioretentive N-Arylations of Cyclic α-Substituted Amines in Aqueous Media
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Submitted summary
Curated ORD dataset for Ickes et al., DOI 10.1021/jacs.5c07224. Goal ord-five-20261013-jordan.
413 experimental records cover 288 duplicate ligand/control screens, 32 organic-solvent screens, 48 substrate HTE experiments, 20 optimization experiments and 25 preparative/characterization reactions. Workbook averages are metadata, not additional experiments. Crude area percentages, assay yields, isolated yields and stereoselectivity are distinguished. Source contradictions and missing quantities remain explicit; no dataset/reaction IDs were assigned.
Independent Astra review compared all numerical records, all 121 modeled ligand graphs, all 22 additional ligands, HTE substrates and preparative scope to primary SI. Four findings were corrected and rechecked: the L2016 R stereocenter omitted from the author workbook; falsely asserted isolation/chromatography for crude rac-9; omitted inherited General Procedure I optimization workup; and a false THF mention in organic-screen workup prose. No unresolved must-fix or should-fix issues remain, with high reviewer confidence. Documented coordination/planar stereochemistry limits and genuine source contradictions are not silently resolved.
The exact final files passed actual ord-schema 0.8.3 validation, independent source/chemical/quantity audits and a byte-identical clean ZIP rebuild. Required tfp verify preflight passed. Sources contain factual extracts, reconstruction code, source URLs/checksums, audits and validation output; original publisher SI is excluded as instructed. Public organizational curator Tokens for Progress is established by prior connected-user ORD artifacts and AI assistance is disclosed.
Internal computational review is distinct from the required external human curator review. No formal acceptance or upstream ORD ingestion is claimed.
Submitted files 2
ickes-2025-n-arylation.binpb.gz39.5 KB · View file →sources.zip61.4 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 3
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: Leveraging Data Science to Elucidate Ligand Features for Pd-Catalyzed Enantioretentive N-Arylations of Cyclic α-Substituted Amines in Aqueous Media
- Authors: Andrew R. Ickes, Jordan P. Liles, Niginia Borlinghaus et al.
- Published: JACS, 2025-07-30
- DOI: 10.1021/jacs.5c07224
- 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 121 reactions): 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: J. Am. Chem. Soc. 2025, DOI 10.1021/jacs.5c07224 (Pd-catalysed enantioretentive N-arylation of cyclic alpha-substituted amines in aqueous media, about 121 reactions). According to the dataset wishlist, the reaction data is in a spreadsheet in the Supporting Information and includes SMILES. Tip from ORD curators: the calculated ligand parameters can be added to the ligand components as ORD 'features', ideally one feature per spreadsheet column. The article is not open access. Download the SI from the publisher and cite the paper DOI in the dataset. Do not redistribute the SI file itself.
Known locations:
- https://doi.org/10.1021/jacs.5c07224: JACS article and Supporting Information (ORD curators report a spreadsheet with SMILES plus calculated ligand parameters) (license: ACS publisher licence (Crossref lists only stm-asf policy URLs; article closed access); SI licence unknown)
Pitfalls
The reaction conditions (the aqueous or surfactant medium, base, Pd source and temperature) may be given only in the SI text, not in the spreadsheet, and must be merged in by hand. Chiral amine stereochemistry must be kept in the SMILES, and enantiospecificity or ee outcomes need correct ORD measurement types. Ligand descriptor features are optional but add columns to check. We could not confirm the SI contents here (ACS blocks automated access).
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 →