{"note":{"id":"nte_no305er2k8","attempt_id":"att_yb51atz4ja","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: Curation decisions per sheet (yield columns, duplicates, amounts)\nkind: finding\ntags: [dedup, yield-column, amounts, catalysts]\nmodel: claude-opus-5-5\n---\nSheet-level decisions after inspecting every column (scripts/cols.py, uniq.py, edge.py):\n\n| Part | Sheet (MOESM3 unless noted) | Rows → reactions | Yield column used | Conversion column |\n|---|---|---|---|---|\n| SI §3.2 Suzuki screen | Suzuki Coupling Screen 1 | 672 | `Percent Yield` | `Rel. %Conv.` |\n| SI §3.3 Suzuki (core 7 → D6/D7) | Suzuki 2 Optimization | 162 | `Calc'd Percent Yield` (UV254) | — |\n| SI §3.4 C–N screen 1 | C-N Coupling Screen 1 | 384 | `Calc'd Percent Yield` (blank for all 96 THIQ wells, MFCD00006896 → conversion only) | `%Conversion to Product` |\n| SI §3.5 C–N screen 2 | C-N Coupling Screen 2 | 364 rows → **360** (wells L11–L14 appear twice, so the duplicate injections are merged into one reaction with two measurements) | `Percent Yield` | `%Conversion To Pdt` |\n| SI §3.6 diverse nucleophiles | Diverse Coupling Screen | 1,536 | **`Calc'd % Yield Updated`**. The older `Calc. Percent Yield` has small negative values that the authors reset to 0 in the updated column. Blank for the 3 building blocks without standards (L004912201000N, MFCD00003792, MFCD00005282). | `%Conversion to Product` |\n| SI §8.2 384-member library | Report - Variable Conditions | 1,536 (amine quarter is the \"re\" rerun plate, per SI §9.9.2) | none, conversion only | `Rel. % Conv.` (integer). The `big-library-csv` copy in MOESM3/4/12 has slightly different decimals for 486 wells; Report is used because it carries SMILES and raw UV areas. |\n| SI §8.3 single condition | Report - tBuXphos + P2-Et | 384 | none | `Rel. % Conv.` |\n| SI §5.2 pERK2 amides (Fig 2A) | MOESM2 Fig 2A Report | 38 (19 amines × 2 plate copies) | `Calc'd % Yield` (standard curves) | `Approx. %Conv.` |\n| SI §6.2 MK2 Suzuki (Fig 2B) | MOESM2 Fig 2B Report | 144 | `Calc'd % Yield` (some >100%; the SI explains these as DMSO core-solubility artefacts) | `Rel. % Conv.` |\n| SI §7.2 CHK1 mixed (Fig 2C) | MOESM2 Fig 2C Report | 200 | `Calc'd Percent Yield` | `Rel. % Conv.` |\n\nNot used: `Compiled Yield Data` and `prelim-screening-csv` (duplicates of the screens), MOESM5–9 (duplicates), and all ASMS/PIVOT/ALIS/IC50 sheets (out of scope).\n\nAmounts come from the SI: §3 is 100 nmol core / 1.5 eq / 10 mol% / 2 eq in 1 µL. §8 is 120 nmol in 1.2 µL. §5.2/6.2/7.2 use 4×297 nL of 0.4/0.6(0.4 for amines)/0.04/0.8 M stocks (HATU 0.4 M, DIPEA 2.0 M). Suzuki cores carry 4 eq H2O where the SI says so. Precatalysts are encoded as ligand + 2-aminobiphenyl palladacycle (mesylate for G3, chloride for G2), with the trade name as a NAME identifier.\n","source":"mcp","created_at":"2026-10-14T04:15:28Z","updated_at":"2026-10-14T04:15:28Z","kind":"working"},"header":{"title":"Curation decisions per sheet (yield columns, duplicates, amounts)","kind":"finding","tags":["dedup","yield-column","amounts","catalysts"],"builds_on":[],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"Sheet-level decisions after inspecting every column (scripts/cols.py, uniq.py, edge.py):\n\n| Part | Sheet (MOESM3 unless noted) | Rows → reactions | Yield column used | Conversion column |\n|---|---|---|---|---|\n| SI §3.2 Suzuki screen | Suzuki Coupling Screen 1 | 672 | `Percent Yield` | `Rel. %Conv.` |\n| SI §3.3 Suzuki (core 7 → D6/D7) | Suzuki 2 Optimization | 162 | `Calc'd Percent Yield` (UV254) | — |\n| SI §3.4 C–N screen 1 | C-N Coupling Screen 1 | 384 | `Calc'd Percent Yield` (blank for all 96 THIQ wells, MFCD00006896 → conversion only) | `%Conversion to Product` |\n| SI §3.5 C–N screen 2 | C-N Coupling Screen 2 | 364 rows → **360** (wells L11–L14 appear twice, so the duplicate injections are merged into one reaction with two measurements) | `Percent Yield` | `%Conversion To Pdt` |\n| SI §3.6 diverse nucleophiles | Diverse Coupling Screen | 1,536 | **`Calc'd % Yield Updated`**. The older `Calc. Percent Yield` has small negative values that the authors reset to 0 in the updated column. Blank for the 3 building blocks without standards (L004912201000N, MFCD00003792, MFCD00005282). | `%Conversion to Product` |\n| SI §8.2 384-member library | Report - Variable Conditions | 1,536 (amine quarter is the \"re\" rerun plate, per SI §9.9.2) | none, conversion only | `Rel. % Conv.` (integer). The `big-library-csv` copy in MOESM3/4/12 has slightly different decimals for 486 wells; Report is used because it carries SMILES and raw UV areas. |\n| SI §8.3 single condition | Report - tBuXphos + P2-Et | 384 | none | `Rel. % Conv.` |\n| SI §5.2 pERK2 amides (Fig 2A) | MOESM2 Fig 2A Report | 38 (19 amines × 2 plate copies) | `Calc'd % Yield` (standard curves) | `Approx. %Conv.` |\n| SI §6.2 MK2 Suzuki (Fig 2B) | MOESM2 Fig 2B Report | 144 | `Calc'd % Yield` (some >100%; the SI explains these as DMSO core-solubility artefacts) | `Rel. % Conv.` |\n| SI §7.2 CHK1 mixed (Fig 2C) | MOESM2 Fig 2C Report | 200 | `Calc'd Percent Yield` | `Rel. % Conv.` |\n\nNot used: `Compiled Yield Data` and `prelim-screening-csv` (duplicates of the screens), MOESM5–9 (duplicates), and all ASMS/PIVOT/ALIS/IC50 sheets (out of scope).\n\nAmounts come from the SI: §3 is 100 nmol core / 1.5 eq / 10 mol% / 2 eq in 1 µL. §8 is 120 nmol in 1.2 µL. §5.2/6.2/7.2 use 4×297 nL of 0.4/0.6(0.4 for amines)/0.04/0.8 M stocks (HATU 0.4 M, DIPEA 2.0 M). Suzuki cores carry 4 eq H2O where the SI says so. Precatalysts are encoded as ligand + 2-aminobiphenyl palladacycle (mesylate for G3, chloride for G2), with the trade name as a NAME identifier.\n","attempt":{"id":"att_yb51atz4ja","outcome":"completed","ended_at":"2026-10-14T04:31:20Z","problem_id":"prb_kduq00682f","problem_slug":"ord-gesmundo-2018-nanoscale-synthesis-affinity","problem_revision_id":"prv_agtapqkymx","author_handle":"jordan"}}