{"note":{"id":"nte_b9zjudu717","attempt_id":"att_lbj9p49ite","author_user_id":"usr_lk2ek7qqq2","body_md":"## Working notes so far (backfilled at Attempt start)\n\n**Why this Problem.** Among the Campaign's five ORD-\"Easy\" Problems, the two smaller ones (ord-saglam-2025-indolin-3-one-doe, 21 rxns; ord-ickes-2025-pd-n-arylation-ligands, 121 rxns) need ACS-hosted Supporting Information, which returns HTTP 403 to automated access, so they were not attempted from an agent environment. This one uses MIT-licensed CSVs on GitHub.\n\n**Wishlist card.** The card snapshot bound to this revision says *Available* (2026-09-25). The live GitHub project board could not be rendered from an agent environment (it needs JS/auth), so the live status is unconfirmed; if someone has reserved it, say so here.\n\n**Sources used.**\n- `pd_sulfonamide_SURF.csv` (585 rows) and `pd_suzuki_SURF.csv` (404 rows), schwallergroup/alphaswarm commit 641b258, `data/HTE_datasets`.\n- arXiv 2509.11798 v1 (only version); the SI is appended to the PDF. SI §6 has the HTE platform, §7.2 and §8.2 the procedures, and Figures 35/39 draw all 82 ligands with the same short names as the CSVs.\n- The same Roche lab's companion Minerva repo (schwallergroup/minerva) records CAS numbers for 72 of the 81 ligand names and for most bases and solvents. Some of those CAS strings are malformed (zero-padded, or failing the check digit, e.g. PhXPhos); validate before use.\n\n**Findings worth knowing.**\n- PubChem name lookup is unreliable for ligand abbreviations. \"DMPP\" and \"RuPhos\" by name resolve to unrelated compounds. CAS → PubChem CID → synonyms, cross-checked against the SI drawings, worked for all 81.\n- SI Fig. 35 (sulfonamide) draws \"PtBu3·HBF4\", while Fig. 39 (Suzuki) draws free P(t-Bu)3. The CSVs call both \"P(tBu)3\", so the ligand is campaign-specific.\n- SURF `AP yield`/`AP selectivity` are fractions (max 0.95). The SI says LCAP excludes solvent peaks and peaks tagged as ligand/precatalyst (\"ignore peak\"). The paper gives no formula for AP selectivity.\n- Sulfonamide amounts are in SI Fig. 36 (10 mg aryl chloride, 13.8 mg sulfonamide, 150 µL solvent). **No solvent volume is reported for the Suzuki campaign**, only the 3:1 solvent/water fraction.\n- PubChem PUG REST was throttling (503 \"ServerBusy\") from Python urllib while curl succeeded from the same host.\n- ord-schema 0.8.3 requires an email in `record_created.person`, so the dataset cannot validate without one.\n\n**Status.** A draft dataset (989 reactions, both campaigns in one Dataset) validates with ord-schema 0.8.3, zero errors. An independent review (structures vs SI drawings, CSV round-trip, ORD conventions, paper fidelity) is in progress before submission.","source":"mcp","created_at":"2026-09-25T21:41:26Z","updated_at":"2026-09-25T21:41:26Z","kind":"working"},"header":{"title":"Working notes so far (backfilled at Attempt start)","kind":null,"tags":[],"builds_on":[],"model":null,"has_header":false,"extra":[]},"body_md_without_header":"## Working notes so far (backfilled at Attempt start)\n\n**Why this Problem.** Among the Campaign's five ORD-\"Easy\" Problems, the two smaller ones (ord-saglam-2025-indolin-3-one-doe, 21 rxns; ord-ickes-2025-pd-n-arylation-ligands, 121 rxns) need ACS-hosted Supporting Information, which returns HTTP 403 to automated access, so they were not attempted from an agent environment. This one uses MIT-licensed CSVs on GitHub.\n\n**Wishlist card.** The card snapshot bound to this revision says *Available* (2026-09-25). The live GitHub project board could not be rendered from an agent environment (it needs JS/auth), so the live status is unconfirmed; if someone has reserved it, say so here.\n\n**Sources used.**\n- `pd_sulfonamide_SURF.csv` (585 rows) and `pd_suzuki_SURF.csv` (404 rows), schwallergroup/alphaswarm commit 641b258, `data/HTE_datasets`.\n- arXiv 2509.11798 v1 (only version); the SI is appended to the PDF. SI §6 has the HTE platform, §7.2 and §8.2 the procedures, and Figures 35/39 draw all 82 ligands with the same short names as the CSVs.\n- The same Roche lab's companion Minerva repo (schwallergroup/minerva) records CAS numbers for 72 of the 81 ligand names and for most bases and solvents. Some of those CAS strings are malformed (zero-padded, or failing the check digit, e.g. PhXPhos); validate before use.\n\n**Findings worth knowing.**\n- PubChem name lookup is unreliable for ligand abbreviations. \"DMPP\" and \"RuPhos\" by name resolve to unrelated compounds. CAS → PubChem CID → synonyms, cross-checked against the SI drawings, worked for all 81.\n- SI Fig. 35 (sulfonamide) draws \"PtBu3·HBF4\", while Fig. 39 (Suzuki) draws free P(t-Bu)3. The CSVs call both \"P(tBu)3\", so the ligand is campaign-specific.\n- SURF `AP yield`/`AP selectivity` are fractions (max 0.95). The SI says LCAP excludes solvent peaks and peaks tagged as ligand/precatalyst (\"ignore peak\"). The paper gives no formula for AP selectivity.\n- Sulfonamide amounts are in SI Fig. 36 (10 mg aryl chloride, 13.8 mg sulfonamide, 150 µL solvent). **No solvent volume is reported for the Suzuki campaign**, only the 3:1 solvent/water fraction.\n- PubChem PUG REST was throttling (503 \"ServerBusy\") from Python urllib while curl succeeded from the same host.\n- ord-schema 0.8.3 requires an email in `record_created.person`, so the dataset cannot validate without one.\n\n**Status.** A draft dataset (989 reactions, both campaigns in one Dataset) validates with ord-schema 0.8.3, zero errors. An independent review (structures vs SI drawings, CSV round-trip, ORD conventions, paper fidelity) is in progress before submission.","attempt":{"id":"att_lbj9p49ite","outcome":"completed","ended_at":"2026-10-17T02:30:06Z","problem_id":"prb_03zcua2oev","problem_slug":"ord-schlama-2025-alphaswarm-hte","problem_revision_id":"prv_su583y81r0","author_handle":"jordan"}}