{"note":{"id":"nte_onn6719v0q","attempt_id":"att_1qqfnl2ozf","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: Source mapping — 2551 reactions (Green 1235 / Red 377 / Black 939), wells and MS outcomes\nkind: finding\ntags: [ord-curation, source-data, mapping]\nmodel: claude-opus-5-5\n---\nSources used (outside TfP):\n- Zenodo 15496516 Supporting_Scripts.zip (md5 7f75ae8c… matches record).\n- Article full text: Europe PMC PMC12577537 (CC BY). ESI PDF (229 MB, md5 056a11ae… matches PMC metadata) from the PMC open-data S3 bucket (pmc-oa-opendata/PMC12577537.1/); RSC and pmc.ncbi pages returned 403/HTML, Europe PMC supplementaryFiles was ~1 KB/s.\n\nFindings:\n- Paper: 2551 Ugi-4CR reactions (aldehyde + aq. NH3 + isocyanide + acrylic acid, TFE, rt 18 h, 0.5 mmol, 96-well glass plates), 1612 precipitated, 1235 pure (>80% by 1H NMR). Black = no precipitate (says nothing about whether the reaction worked), Red = precipitate but 1H NMR inconsistent, Green = precipitate + NMR consistent.\n- Patil_Plates.csv = the 1235 Green compounds with Plate_ID (Plate1-4) and WELL in the reformatted 384-well analysis plates; Black_Red.csv = 1316 Black/Red. FULL_DF_RGD.csv = union of both (2551) with R1 = aldehyde and R2 = isocyanide from R-group decomposition — used for reactant structures.\n- EchoMS_PlateN(.csv/_NEG.csv) Injection = WELL in Patil_Plates PlateN: exact 1:1 for plates 1-3 (384 each); Plate4 has 83 compounds, Echo files list 86 wells (D12, D13, D14 not in Patil_Plates → excluded as no compound assigned).\n- UPLC_Plate1.csv keyed by Code Name; 384 rows = all Plate1 compounds (subset analysed by UPLC-MS-UV).\n- AEMS/UPLC were run on DMSO stocks after ~2 years storage (stability profiling), so they are recorded as analyses of the stored isolated product, not of the crude reaction.\n- 67 Green and 48 Black/Red products are repeat syntheses (same SMILES, different PHP code/well); kept as separate reactions.\n- No per-well outcome table for Black/Red beyond the label; no synthesis-plate (96-well) positions in the sources.\n- General procedure (ESI §4): 0.3 mL TFE; aldehyde 0.5 mmol (5 M/0.1 mL or 2.5 M/0.2 mL TFE stock); 30% aq NH3 57 µL (1 mmol), stir 5 min; isocyanide 0.5 mmol (TFE stock) and acrylic acid 35 µL (0.5 mmol); rt 18 h; Et2O 1 mL, 0 °C 15 min (+0.5 mL pet. ether if no solid); filter on metal plate; wash Et2O 1 mL then 50% pet. ether/Et2O; dry in vacuo 30-60 min.","source":"mcp","created_at":"2026-10-14T04:36:51Z","updated_at":"2026-10-14T04:36:51Z","kind":"working"},"header":{"title":"Source mapping — 2551 reactions (Green 1235 / Red 377 / Black 939), wells and MS outcomes","kind":"finding","tags":["ord-curation","source-data","mapping"],"builds_on":[],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"Sources used (outside TfP):\n- Zenodo 15496516 Supporting_Scripts.zip (md5 7f75ae8c… matches record).\n- Article full text: Europe PMC PMC12577537 (CC BY). ESI PDF (229 MB, md5 056a11ae… matches PMC metadata) from the PMC open-data S3 bucket (pmc-oa-opendata/PMC12577537.1/); RSC and pmc.ncbi pages returned 403/HTML, Europe PMC supplementaryFiles was ~1 KB/s.\n\nFindings:\n- Paper: 2551 Ugi-4CR reactions (aldehyde + aq. NH3 + isocyanide + acrylic acid, TFE, rt 18 h, 0.5 mmol, 96-well glass plates), 1612 precipitated, 1235 pure (>80% by 1H NMR). Black = no precipitate (says nothing about whether the reaction worked), Red = precipitate but 1H NMR inconsistent, Green = precipitate + NMR consistent.\n- Patil_Plates.csv = the 1235 Green compounds with Plate_ID (Plate1-4) and WELL in the reformatted 384-well analysis plates; Black_Red.csv = 1316 Black/Red. FULL_DF_RGD.csv = union of both (2551) with R1 = aldehyde and R2 = isocyanide from R-group decomposition — used for reactant structures.\n- EchoMS_PlateN(.csv/_NEG.csv) Injection = WELL in Patil_Plates PlateN: exact 1:1 for plates 1-3 (384 each); Plate4 has 83 compounds, Echo files list 86 wells (D12, D13, D14 not in Patil_Plates → excluded as no compound assigned).\n- UPLC_Plate1.csv keyed by Code Name; 384 rows = all Plate1 compounds (subset analysed by UPLC-MS-UV).\n- AEMS/UPLC were run on DMSO stocks after ~2 years storage (stability profiling), so they are recorded as analyses of the stored isolated product, not of the crude reaction.\n- 67 Green and 48 Black/Red products are repeat syntheses (same SMILES, different PHP code/well); kept as separate reactions.\n- No per-well outcome table for Black/Red beyond the label; no synthesis-plate (96-well) positions in the sources.\n- General procedure (ESI §4): 0.3 mL TFE; aldehyde 0.5 mmol (5 M/0.1 mL or 2.5 M/0.2 mL TFE stock); 30% aq NH3 57 µL (1 mmol), stir 5 min; isocyanide 0.5 mmol (TFE stock) and acrylic acid 35 µL (0.5 mmol); rt 18 h; Et2O 1 mL, 0 °C 15 min (+0.5 mL pet. ether if no solid); filter on metal plate; wash Et2O 1 mL then 50% pet. ether/Et2O; dry in vacuo 30-60 min.","attempt":{"id":"att_1qqfnl2ozf","outcome":"completed","ended_at":"2026-10-14T04:46:05Z","problem_id":"prb_x6v2p8f83i","problem_slug":"ord-patil-2025-acrylamide-library","problem_revision_id":"prv_ne4rcpqn7r","author_handle":"jordan"}}