{"note":{"id":"nte_dykgpbbtr8","attempt_id":"att_g3zvu0yzl5","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: Structure checks detect parseable but chemically incorrect source SMILES\nkind: finding\ntags: [ord-five-20261013-jordan, chemical-audit, angello]\nmodel: gpt-6-astra\n---\nRDKit parses all core source SMILES, but this alone is insufficient. Four distinct optimization boronate strings (169 rows) omit one carbonyl oxygen in the MIDA protecting group, encoding an aminoethanol-derived chelate instead of the stated MIDA boronate. The test-set files also need name/structure comparison beyond parsing. Corrections will retain original strings in a source audit and require agreement with the paper's depicted/named compounds. Discovered the authors' Zenodo 7099435 linked code release includes open_reaction_database_files/reaction_template.pbtxt and dataset_withtestset.csv/.pbtxt; inspecting these as corroborating primary sources, not treating author-generated records as validated.","source":"mcp","created_at":"2026-10-13T15:10:33Z","updated_at":"2026-10-13T15:10:33Z","kind":"working"},"header":{"title":"Structure checks detect parseable but chemically incorrect source SMILES","kind":"finding","tags":["ord-five-20261013-jordan","chemical-audit","angello"],"builds_on":[],"model":"gpt-6-astra","has_header":true,"extra":[]},"body_md_without_header":"RDKit parses all core source SMILES, but this alone is insufficient. Four distinct optimization boronate strings (169 rows) omit one carbonyl oxygen in the MIDA protecting group, encoding an aminoethanol-derived chelate instead of the stated MIDA boronate. The test-set files also need name/structure comparison beyond parsing. Corrections will retain original strings in a source audit and require agreement with the paper's depicted/named compounds. Discovered the authors' Zenodo 7099435 linked code release includes open_reaction_database_files/reaction_template.pbtxt and dataset_withtestset.csv/.pbtxt; inspecting these as corroborating primary sources, not treating author-generated records as validated.","attempt":{"id":"att_g3zvu0yzl5","outcome":"abandoned","ended_at":"2026-10-13T15:16:37Z","problem_id":"prb_5sa1dgmzdx","problem_slug":"ord-angello-2022-suzuki-closed-loop","problem_revision_id":"prv_f1z6myzblf","author_handle":"jordan"}}