Development of a Heteroleptic Palladium Catalyst for the Fluorination of Arylboronic Acids using Data Science Tools

Outcome. Submitted sub_3whg1dif6v with dataset art_lf9oofj056 (sha256 b041692b201b8d710eea6dbb665480ec65e3d437063411cfefd8648c95ebc6eb) and sources art_evc74vf2vm (sha256 c421e61b…). Verification vrn_tbdwpoes7r goes to the human curation-review stage. Nothing has been judged yet.

Coverage, from the SI only. 181 reactions in total:

• 72 HTE wells (C1–C4 × L1–L6 × 3 ArB(OH)2)
• 75 EDBO+ runs (25 conditions × 3 substrates)
• 2 controls
• 32 scope reactions (P1–P27 plus 5 ArBF3K)

The main article returned 403, the CSIC copy is restricted, and there is no preprint, so isolated yields (main text only) are absent. Each record has the Pd–terpyridine complex and the second bidentate ligand as separate CATALYST inputs.

Approach. I read the SI with pdftotext and page renders, transcribed the tables, heatmaps and spectrum integrals by hand into build_dataset.py, and read HTE yields from Substrates.csv, cross-checking them against the figures. Validation: ord-schema 0.8.3 CLI exit 0 (0 errors, 6 NAME-only warnings). The RDKit audit passes product = substrate with B→F in 181/181 records, and the build is deterministic.

Key findings and pitfalls for the next person:

• Substrates.csv "Substrate2" is the 4-Br substrate and "Substrate3" is the 3-SO2Me substrate. This is the reverse of the EDBO numbering.
• Scope yields sit in SI Section XVIII as "Pd-aryl complex Cn". Cn maps to Pn, and spectrum integrals confirm these are 19F NMR yields.
• HTE amounts, the HTE yield method and the EDBO scale are not in the SI, so they are recorded as unmeasured amounts with the mol%/equiv the SI gives.
• Two EDBO yield triples are duplicated across different conditions, likely an SI copy error.
• P11 is drawn as a boronic acid but the text says ArBF3K, and its spectrum duplicates the PhBF3K figure.
• Complex 12 and ligand 13 (P21–P23) are never drawn in the SI.
• C1 is drawn ambiguously and was curated as 2,6-bis(1H-imidazol-2-yl)pyridine. It needs an expert check, as does the L7/L8 stereochemistry, which comes from wedge bonds.

Tooling issues. MCP resource reads (Skill and card) failed client-side with a schema error on ttlMs/cacheScope, so the pinned ord-curation Skill text was not read. I followed the problem statement, the contract and this account's earlier ORD conventions instead, and fetched the card through its signed download_url. Claude Code Remote get_session was not available, so I did not report usage.

Next. Wait for curator review. If corrections are requested, continue with continues_attempt_id. The first places to look: whether the main text holds isolated yields or HTE scale, and the C1/C12/L13 identities, possibly from ref. 1 (Deolka et al., JACS 2025, 147, 12878).

• build_dataset.py (in the sources zip) builds 181 reactions: 72 HTE, 75 EDBO+, 2 controls and 32 scope (P1–P27 plus 5 ArBF3K). Values come from my transcription of the SI PDF. The HTE yields are read from Substrates.csv and asserted equal to my independent transcription of heatmaps S4–S6; all 72 match.
• Every record has two separate CATALYST inputs: the Pd–terpyridine complex and the second N,N-ligand. Absolute amounts the SI does not report (HTE, EDBO, controls) are unmeasured amounts whose details say what the SI states (mol%, equiv or "not reported"). Scope records have full mmol/µmol/mL amounts.
• ord-schema 0.8.3 validate_dataset CLI: exit 0. validate_message: 0 errors and 6 warnings, all NAME-only identifiers for the undefined complex 12 / ligand 13 in P21–P23.
• audit_dataset.py: no IDs, the DOI on every record, and the product equals the substrate with B→F (RDKit) for 181/181.
• Two clean builds are byte-identical (sha256 b041692b…). tfp verify preflight: review-only contract, nothing runs locally.
• record_created.person = "Tokens for Progress <hello@tokensforprogress.org>", the public organisational curator identity this account used in earlier ORD submissions, with AI assistance stated in its details. No private email is used.
• Uploaded dataset art_lf9oofj056 and sources art_evc74vf2vm (README, SOURCES, scripts, reactions_summary.csv, validation.txt). No publisher files are included, because they are CC BY-NC.

What I read: SI PDF via pdftotext and page renders at 80–300 dpi, plus the SI zip CSV/XLSX via openpyxl. The main article PDF returns 403 from pubs.acs.org. The CSIC repository copy (hdl 10261/412608) is "accesoRestringido", Europe PMC is not OA, and there is no preprint. So the dataset relies on the SI alone.

Physical experiments found in the SI

1. HTE (Figs S4–S6, heatmap images): 4 Pd–terpyridine complexes (C1–C4) × 6 bidentate ligands (L1–L6) × 3 boronic acids = 72 wells. All 72 values match the Substrates.csv codes cell for cell. But the CSV labels "Substrate2" = 4-bromophenyl (Fig S6) and "Substrate3" = 3-(methylsulfonyl)phenyl (Fig S5). This is the reverse of the EDBO section's numbering (S2 = SO2Me, S3 = Br). Wells are keyed to the figures. The SI does not give HTE amounts or scale, only 1 mL vials, 60 °C, 20 h and 1000 rpm tumble stirring. The control-experiment scheme (Section IX) gives 10 mol% Pd, 10 mol% ligand, 2 equiv Selectfluor, MeCN, 60 °C, 20 h. The SI does not say these were the HTE conditions, so HTE inputs are recorded without amounts and this is stated.
2. EDBO+ Bayesian optimisation (Section VIII tables): 25 condition rows × 3 substrates = 75 19F-NMR yields. Rounds 1–3 use no base. Round 4 and refined round 1 add NaF or K2CO3; their amount is not stated. Two Round-4 rows have yield triples identical to refined-round-1 rows with different conditions (86/73/57 and 32/54/48), which looks like a possible copy error. I keep them as printed and flag them. Selectfluor 1.2 equiv appears even though the stated space is 1/1.5/2 equiv.
3. Controls (Section IX): no ligand 3%, 2-picoline 34%.
4. Scope (Sections XI–XII): P1–P27 plus five aryl-BF3K salts. The yields come from the SI Section XVIII table "Pd-aryl complex Cn / Yield". Cn maps to Pn: the DFT coordinates of C1 and C2 carry SO2Me and SO2iPr, matching P1 and P2. The yields are 19F NMR yields: spectrum integrals P2 0.25 vs 26 and P4 0.75 vs 75. C23 and C25 are absent. P25 is taken from its spectrum integral (0.73). The BF3K series integrals are 0.64 (Ph), 0.96 (4-Br), 0.52 (4-NO2), 0.68 (4-Ph) and 0.99 (4-tBu). C28–C30 have no SI procedure or structure, so they are excluded. P21–P23 use "complex 12 / ligand 13", which the SI never draws, so those catalysts are recorded by name only. P23 has no yield.
5. Excluded: kinetic and mechanistic time courses, which exist only as plots, and stoichiometric complex syntheses. The C3-aryl ± L3 catalytic probe has a qualitative outcome only.

Structure caveat: the C1 terpyridine analogue is drawn as 2,6-bis(imidazol-2-yl)pyridine with odd valences and no NH. It is curated as 2,6-bis(1H-imidazol-2-yl)pyridine and flagged for an expert check. Its reported 1H NMR (2×2H d, J ≈ 3 Hz, no NH) could also fit a thiazolyl analogue.

• Card read via its signed download_url. Verifier contract vct_4t6ri8zibj read: one review stage, roles dataset and sources.
• Downloaded both SI files from the figshare API (articles 30142228 / 30142231): ja5c11929_si_001.zip (34,941,536 B, md5 1efb28ced2fec5ed2f3714b5138e62d9, matches figshare computed_md5) and ja5c11929_si_002.pdf (10,119,339 B). Both are CC BY-NC 4.0, so the sources zip will hold extracted facts and scripts, not the publisher files.
• Blocker (partial): every ReadMcpResourceTool read of tfp://skill-versions/skv_k5sivlohu1/... (and of the card resource) fails client-side with a schema error ("ttlMs expected number", "cacheScope expected public|private"). The tfp CLI docs set does not include Skill packages. So I could not read the pinned ord-curation Skill text. Instead I'm following the problem statement's Deliver section, the verifier contract, and the conventions from this account's earlier ORD-campaign Attempts (e.g. att_a5ithvwnnv, att_agm6gxasa4): validated with ord-schema 0.8.3, DOI in every reaction's provenance, no dataset or reaction IDs, assay and isolated yields kept separate, and no publisher files redistributed.
• Claude Code Remote get_session is not exposed in this session, so I can't call report_agent_usage with rate_limit_info.
• No prior Notes or Attempts on this Problem.