{"note":{"id":"nte_rr9ikvlkp3","attempt_id":"att_m1oaktrtok","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: Scope, code→structure map and column semantics (from SI + repo processing scripts)\nkind: approach\ntags: [ord-curation, robowski, structures, scope]\nbuilds_on: [nte_0rjbsdszw9]\nmodel: claude-opus-5-5\n---\n**Scope.** One Dataset built from the six raw tables in `summary_of_reaction_yield_data`: E1 774 + SN1_simple 832 + SN1 (Fig. 3) 864 + Ugi 3234 + Hantzsch HPLC 31+31 + PBA 756 = **6,522 reactions**.\n- No row has `is_outlier`=1. The paper's counts (775/930/1085) are larger than what the repo deposits.\n- The Hantzsch UV-Vis cube (~2,440–2,582 spectra) is published only as resampled/viewer data, so it is out of scope.\n- The 9,362 wishlist estimate is not reached for that reason.\n\n**Codes → structures** (SI §4.1–4.2, Tables S5–S7; checked with RDKit formula vs HRMS):\n- **E1:** 13a/E1OH02 9-butyl-9H-fluoren-9-ol → 13b/E1DB02 9-butylidene-9H-fluorene.\n- **Simple SN1:** 14a/SN1OH03 9-phenylfluoren-9-ol → 14b/SN1Br03 9-bromo-9-phenylfluorene.\n- **SN1 (Fig. 3):**\n  - 15a/SN1OH01 anthracen-9-yldiphenylmethanol → 15b/\"SN1Br01\" 10-(diphenylmethylene)-9,10-dihydroanthracen-9-ol, plus 15d/SN1Br01s1 anthraquinone.\n  - The CCDC code for 15b is SN1Br01.\n  - The SI name says \"4a,9,9a,10-tetrahydro\", but HRMS C27H20O fits the 9,10-dihydro structure, so I use that.\n- **Ugi-type:** 16a/ald001 4-nitrobenzaldehyde, am001 n-butylamine, ic001 TosMIC, pTSA·H2O; product 16e/IIO029A, the imidazolium-olate.\n- **Hantzsch:** 19c p-anisaldehyde, 19a ethyl acetoacetate, NH4OAc; products 19d, 19e, 19j, 19k (Table S7 names).\n- **PBA:** K3[Fe(CN)6]/K3[Co(CN)6] (A site), Mn(NO3)2/FeCl2/Co/Ni/Cu nitrates (B site), Na3-citrate. Reaction: styrene + TBHP, CTAB, MeCN/H2O → styrene oxide + benzaldehyde (Methods).\n\n**Column semantics** (read from the repo's processing scripts):\n- E1 and simple SN1: `yield` = product/(product + remaining substrate).\n- SN1 Fig. 3:\n  - `yield` = conversion of 15a.\n  - `yield#SN1Br01` = 15b by mass balance; it goes negative when unmixing over-fits 15d.\n  - `pc#carbocat` is an absorbance metric, not a concentration, so it is not curated.\n- Ugi `IIO029A` = [16e].\n- Hantzsch `_y_` are replicate-averaged HPLC yields that already include the product stoichiometry.\n\n**Conflict noted:** for the Fig. 3 SN1, SI §4.2.3 gives 4 h but the Fig. 3 caption says 24 h. I use 4 h from the experimental procedure and flag it in the reaction notes.\n","source":"mcp","created_at":"2026-10-14T04:37:31Z","updated_at":"2026-10-14T04:37:31Z","kind":"working"},"header":{"title":"Scope, code→structure map and column semantics (from SI + repo processing scripts)","kind":"approach","tags":["ord-curation","robowski","structures","scope"],"builds_on":["nte_0rjbsdszw9"],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"**Scope.** One Dataset built from the six raw tables in `summary_of_reaction_yield_data`: E1 774 + SN1_simple 832 + SN1 (Fig. 3) 864 + Ugi 3234 + Hantzsch HPLC 31+31 + PBA 756 = **6,522 reactions**.\n- No row has `is_outlier`=1. The paper's counts (775/930/1085) are larger than what the repo deposits.\n- The Hantzsch UV-Vis cube (~2,440–2,582 spectra) is published only as resampled/viewer data, so it is out of scope.\n- The 9,362 wishlist estimate is not reached for that reason.\n\n**Codes → structures** (SI §4.1–4.2, Tables S5–S7; checked with RDKit formula vs HRMS):\n- **E1:** 13a/E1OH02 9-butyl-9H-fluoren-9-ol → 13b/E1DB02 9-butylidene-9H-fluorene.\n- **Simple SN1:** 14a/SN1OH03 9-phenylfluoren-9-ol → 14b/SN1Br03 9-bromo-9-phenylfluorene.\n- **SN1 (Fig. 3):**\n  - 15a/SN1OH01 anthracen-9-yldiphenylmethanol → 15b/\"SN1Br01\" 10-(diphenylmethylene)-9,10-dihydroanthracen-9-ol, plus 15d/SN1Br01s1 anthraquinone.\n  - The CCDC code for 15b is SN1Br01.\n  - The SI name says \"4a,9,9a,10-tetrahydro\", but HRMS C27H20O fits the 9,10-dihydro structure, so I use that.\n- **Ugi-type:** 16a/ald001 4-nitrobenzaldehyde, am001 n-butylamine, ic001 TosMIC, pTSA·H2O; product 16e/IIO029A, the imidazolium-olate.\n- **Hantzsch:** 19c p-anisaldehyde, 19a ethyl acetoacetate, NH4OAc; products 19d, 19e, 19j, 19k (Table S7 names).\n- **PBA:** K3[Fe(CN)6]/K3[Co(CN)6] (A site), Mn(NO3)2/FeCl2/Co/Ni/Cu nitrates (B site), Na3-citrate. Reaction: styrene + TBHP, CTAB, MeCN/H2O → styrene oxide + benzaldehyde (Methods).\n\n**Column semantics** (read from the repo's processing scripts):\n- E1 and simple SN1: `yield` = product/(product + remaining substrate).\n- SN1 Fig. 3:\n  - `yield` = conversion of 15a.\n  - `yield#SN1Br01` = 15b by mass balance; it goes negative when unmixing over-fits 15d.\n  - `pc#carbocat` is an absorbance metric, not a concentration, so it is not curated.\n- Ugi `IIO029A` = [16e].\n- Hantzsch `_y_` are replicate-averaged HPLC yields that already include the product stoichiometry.\n\n**Conflict noted:** for the Fig. 3 SN1, SI §4.2.3 gives 4 h but the Fig. 3 caption says 24 h. I use 4 h from the experimental procedure and flag it in the reaction notes.\n","attempt":{"id":"att_m1oaktrtok","outcome":"completed","ended_at":"2026-10-14T04:44:15Z","problem_id":"prb_ipe3ti07ku","problem_slug":"ord-jia-2025-robotic-reaction-hyperspaces","problem_revision_id":"prv_dfo7y0cf2w","author_handle":"jordan"}}