cook2021_corrected.pb.gz · Review evidence

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HTE Buchwald-Hartwig amidation of 2-pyrrolidone with 2-halopyrimidines in 96-well plates (Cook, Clement, Newman, Nat. Protoc. 2021)

Dataset description

Reactions from Cook, Clement & Newman, 'Reaction screening in multiwell plates: high-throughput optimization of a Buchwald-Hartwig amination', Nat. Protoc. 2021, 16, 1152 (doi 10.1038/s41596-020-00452-7). [Pd(cinnamyl)Cl]2-catalysed N-arylation of 2-pyrrolidone with 2-chloro- or 2-bromopyrimidine in toluene (0.17 M) at 100 C for 16 h, screening 12 ligands x 4 bases x 2 halides in a 96-well plate. The same plate was run three times: plates A and B on a magnetic stirrer/hotplate with gravity filtration, plate C on a heated tumble stirrer with pressurised parallel filtration. One Reaction per well per plate (288) with the calibrated GC yield of that plate (SI Supporting Table 1), plus the 1.0 mmol round-bottom-flask scale-up with isolated yield (289 reactions). Wells follow the article's Fig. 7 layout (columns 1-12 = ligands L1-L12; rows A-D = 2-chloropyrimidine with bases B1-B4, rows E-H = 2-bromopyrimidine with B1-B4); the 'experiment' labels of Supporting Table 1 enumerate the plate column-major and are kept in each reaction identifier. Per-well absolute amounts are not in the open SI, so HTE amounts are recorded as stoichiometry relative to 2-pyrrolidone (unmeasured CUSTOM amounts). Halide labels follow Fig. 7 and SI Figs. 3-5 as printed; note that the halide averages in SI Fig. 12 are not reproduced exactly by the per-well data under either assignment.

Decoded from the bound file. This is a read-only preview, not schema validation or scientific verification. Missing values remain unreported; AREA is not relabeled as YIELD.

Location	Record	Inputs and roles	Temperature	Reported measurements	Source
reactions[0]	Record 1	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: RuPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 21% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[0] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A1, Table 1 experiment A1" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "RuPhos" }, { "type": "SMILES", "value": "CC(C)Oc1cccc(OC(C)C)c1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "787618-22-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A1", "row": "A", "col": "1" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A1: ligand L1 (RuPhos), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 21, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[1]	Record 2	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: Xantphos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 71% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[1] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A2, Table 1 experiment A9" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Xantphos" }, { "type": "SMILES", "value": "CC1(C)c2cccc(P(c3ccccc3)c3ccccc3)c2Oc2c(P(c3ccccc3)c3ccccc3)cccc21" }, { "type": "CAS_NUMBER", "value": "161265-03-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A2", "row": "A", "col": "2" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A2: ligand L2 (Xantphos), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 71, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[2]	Record 3	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: DPEPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 59% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[2] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A3, Table 1 experiment B5" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DPEPhos" }, { "type": "SMILES", "value": "c1ccc(P(c2ccccc2)c2ccccc2Oc2ccccc2P(c2ccccc2)c2ccccc2)cc1" }, { "type": "CAS_NUMBER", "value": "166330-10-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A3", "row": "A", "col": "3" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A3: ligand L3 (DPEPhos), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 59, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[3]	Record 4	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: IPr SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 18% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[3] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A4, Table 1 experiment C1" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "IPr" }, { "type": "SMILES", "value": "CC(C)c1cccc(C(C)C)c1N1[C]N(c2c(C(C)C)cccc2C(C)C)C=C1" }, { "type": "CAS_NUMBER", "value": "244187-81-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A4", "row": "A", "col": "4" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A4: ligand L4 (IPr), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 18, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[4]	Record 5	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: PCy3 SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 11% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[4] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A5, Table 1 experiment C9" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "PCy3" }, { "type": "SMILES", "value": "C1CCC(P(C2CCCCC2)C2CCCCC2)CC1" }, { "type": "CAS_NUMBER", "value": "2622-14-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A5", "row": "A", "col": "5" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A5: ligand L5 (PCy3), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 11, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[5]	Record 6	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: dppf SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 65% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[5] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A6, Table 1 experiment D5" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "dppf" }, { "type": "SMILES", "value": "[Fe+2].c1ccc(P(c2ccccc2)c2ccc[cH-]2)cc1.c1ccc(P(c2ccccc2)c2ccc[cH-]2)cc1" }, { "type": "CAS_NUMBER", "value": "12150-46-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A6", "row": "A", "col": "6" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A6: ligand L6 (dppf), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 65, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[6]	Record 7	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: BINAP SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 68% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[6] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A7, Table 1 experiment E1" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "BINAP" }, { "type": "SMILES", "value": "c1ccc(P(c2ccccc2)c2ccc3ccccc3c2-c2c(P(c3ccccc3)c3ccccc3)ccc3ccccc23)cc1" }, { "type": "CAS_NUMBER", "value": "98327-87-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A7", "row": "A", "col": "7" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A7: ligand L7 (BINAP), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 68, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[7]	Record 8	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: dcype SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 64% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[7] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A8, Table 1 experiment E9" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "dcype" }, { "type": "SMILES", "value": "C1CCC(P(CCP(C2CCCCC2)C2CCCCC2)C2CCCCC2)CC1" }, { "type": "CAS_NUMBER", "value": "23743-26-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A8", "row": "A", "col": "8" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A8: ligand L8 (dcype), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 64, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[8]	Record 9	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: DavePhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 17% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[8] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A9, Table 1 experiment F5" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DavePhos" }, { "type": "SMILES", "value": "CN(C)c1ccccc1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "213697-53-1" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A9", "row": "A", "col": "9" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A9: ligand L9 (DavePhos), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 17, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[9]	Record 10	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: tBuXPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 31% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[9] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A10, Table 1 experiment G1" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "tBuXPhos" }, { "type": "SMILES", "value": "CC(C)c1cc(C(C)C)c(-c2ccccc2P(C(C)(C)C)C(C)(C)C)c(C(C)C)c1" }, { "type": "CAS_NUMBER", "value": "564483-19-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A10", "row": "A", "col": "10" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A10: ligand L10 (tBuXPhos), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 31, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[10]	Record 11	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: SPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 18% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[10] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A11, Table 1 experiment G9" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "SPhos" }, { "type": "SMILES", "value": "COc1cccc(OC)c1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "657408-07-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A11", "row": "A", "col": "11" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A11: ligand L11 (SPhos), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 18, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[11]	Record 12	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: P(o-tolyl)3 SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 4% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[11] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well A12, Table 1 experiment H5" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "P(o-tolyl)3" }, { "type": "SMILES", "value": "Cc1ccccc1P(c1ccccc1C)c1ccccc1C" }, { "type": "CAS_NUMBER", "value": "6163-58-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "A12", "row": "A", "col": "12" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well A12: ligand L12 (P(o-tolyl)3), base B1 (NaOtBu), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 4, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[12]	Record 13	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: RuPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 23% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[12] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B1, Table 1 experiment A2" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "RuPhos" }, { "type": "SMILES", "value": "CC(C)Oc1cccc(OC(C)C)c1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "787618-22-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B1", "row": "B", "col": "1" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B1: ligand L1 (RuPhos), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 23, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[13]	Record 14	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: Xantphos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 83% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[13] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B2, Table 1 experiment A10" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Xantphos" }, { "type": "SMILES", "value": "CC1(C)c2cccc(P(c3ccccc3)c3ccccc3)c2Oc2c(P(c3ccccc3)c3ccccc3)cccc21" }, { "type": "CAS_NUMBER", "value": "161265-03-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B2", "row": "B", "col": "2" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B2: ligand L2 (Xantphos), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 83, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[14]	Record 15	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: DPEPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 67% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[14] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B3, Table 1 experiment B6" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DPEPhos" }, { "type": "SMILES", "value": "c1ccc(P(c2ccccc2)c2ccccc2Oc2ccccc2P(c2ccccc2)c2ccccc2)cc1" }, { "type": "CAS_NUMBER", "value": "166330-10-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B3", "row": "B", "col": "3" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B3: ligand L3 (DPEPhos), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 67, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[15]	Record 16	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: IPr SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 14% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[15] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B4, Table 1 experiment C2" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "IPr" }, { "type": "SMILES", "value": "CC(C)c1cccc(C(C)C)c1N1[C]N(c2c(C(C)C)cccc2C(C)C)C=C1" }, { "type": "CAS_NUMBER", "value": "244187-81-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B4", "row": "B", "col": "4" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B4: ligand L4 (IPr), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 14, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[16]	Record 17	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: PCy3 SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 17% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[16] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B5, Table 1 experiment C10" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "PCy3" }, { "type": "SMILES", "value": "C1CCC(P(C2CCCCC2)C2CCCCC2)CC1" }, { "type": "CAS_NUMBER", "value": "2622-14-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B5", "row": "B", "col": "5" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B5: ligand L5 (PCy3), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 17, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[17]	Record 18	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: dppf SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 69% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[17] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B6, Table 1 experiment D6" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "dppf" }, { "type": "SMILES", "value": "[Fe+2].c1ccc(P(c2ccccc2)c2ccc[cH-]2)cc1.c1ccc(P(c2ccccc2)c2ccc[cH-]2)cc1" }, { "type": "CAS_NUMBER", "value": "12150-46-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B6", "row": "B", "col": "6" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B6: ligand L6 (dppf), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 69, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[18]	Record 19	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: BINAP SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 73% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[18] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B7, Table 1 experiment E2" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "BINAP" }, { "type": "SMILES", "value": "c1ccc(P(c2ccccc2)c2ccc3ccccc3c2-c2c(P(c3ccccc3)c3ccccc3)ccc3ccccc23)cc1" }, { "type": "CAS_NUMBER", "value": "98327-87-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B7", "row": "B", "col": "7" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B7: ligand L7 (BINAP), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 73, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[19]	Record 20	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: dcype SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 71% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[19] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B8, Table 1 experiment E10" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "dcype" }, { "type": "SMILES", "value": "C1CCC(P(CCP(C2CCCCC2)C2CCCCC2)C2CCCCC2)CC1" }, { "type": "CAS_NUMBER", "value": "23743-26-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B8", "row": "B", "col": "8" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B8: ligand L8 (dcype), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 71, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[20]	Record 21	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: DavePhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 13% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[20] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B9, Table 1 experiment F6" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DavePhos" }, { "type": "SMILES", "value": "CN(C)c1ccccc1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "213697-53-1" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B9", "row": "B", "col": "9" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B9: ligand L9 (DavePhos), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 13, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[21]	Record 22	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: tBuXPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 33% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[21] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B10, Table 1 experiment G2" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "tBuXPhos" }, { "type": "SMILES", "value": "CC(C)c1cc(C(C)C)c(-c2ccccc2P(C(C)(C)C)C(C)(C)C)c(C(C)C)c1" }, { "type": "CAS_NUMBER", "value": "564483-19-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B10", "row": "B", "col": "10" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B10: ligand L10 (tBuXPhos), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 33, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[22]	Record 23	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: SPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 27% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[22] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B11, Table 1 experiment G10" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "SPhos" }, { "type": "SMILES", "value": "COc1cccc(OC)c1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "657408-07-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B11", "row": "B", "col": "11" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B11: ligand L11 (SPhos), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 27, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[23]	Record 24	REACTANT: 2-pyrrolidone REAGENT: Cs2CO3 CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: P(o-tolyl)3 SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 6% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[23] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well B12, Table 1 experiment H6" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Cs2CO3" }, { "type": "SMILES", "value": "O=C([O-])[O-].[Cs+].[Cs+]" }, { "type": "CAS_NUMBER", "value": "534-17-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 15 extra-large scoop, 12.9 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "P(o-tolyl)3" }, { "type": "SMILES", "value": "Cc1ccccc1P(c1ccccc1C)c1ccccc1C" }, { "type": "CAS_NUMBER", "value": "6163-58-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "B12", "row": "B", "col": "12" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well B12: ligand L12 (P(o-tolyl)3), base B2 (Cs2CO3), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 6, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[24]	Record 25	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: RuPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 6% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[24] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C1, Table 1 experiment A3" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "RuPhos" }, { "type": "SMILES", "value": "CC(C)Oc1cccc(OC(C)C)c1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "787618-22-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C1", "row": "C", "col": "1" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C1: ligand L1 (RuPhos), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 6, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[25]	Record 26	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: Xantphos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 29% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[25] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C2, Table 1 experiment A11" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Xantphos" }, { "type": "SMILES", "value": "CC1(C)c2cccc(P(c3ccccc3)c3ccccc3)c2Oc2c(P(c3ccccc3)c3ccccc3)cccc21" }, { "type": "CAS_NUMBER", "value": "161265-03-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C2", "row": "C", "col": "2" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C2: ligand L2 (Xantphos), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 29, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[26]	Record 27	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: DPEPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 21% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[26] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C3, Table 1 experiment B7" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DPEPhos" }, { "type": "SMILES", "value": "c1ccc(P(c2ccccc2)c2ccccc2Oc2ccccc2P(c2ccccc2)c2ccccc2)cc1" }, { "type": "CAS_NUMBER", "value": "166330-10-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C3", "row": "C", "col": "3" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C3: ligand L3 (DPEPhos), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 21, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[27]	Record 28	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: IPr SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 0% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[27] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C4, Table 1 experiment C3" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "IPr" }, { "type": "SMILES", "value": "CC(C)c1cccc(C(C)C)c1N1[C]N(c2c(C(C)C)cccc2C(C)C)C=C1" }, { "type": "CAS_NUMBER", "value": "244187-81-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C4", "row": "C", "col": "4" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C4: ligand L4 (IPr), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i). Reported as 0%.", "uses_internal_standard": true, "percentage": { "value": 0, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[28]	Record 29	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: PCy3 SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 4% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[28] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C5, Table 1 experiment C11" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "PCy3" }, { "type": "SMILES", "value": "C1CCC(P(C2CCCCC2)C2CCCCC2)CC1" }, { "type": "CAS_NUMBER", "value": "2622-14-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C5", "row": "C", "col": "5" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C5: ligand L5 (PCy3), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 4, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[29]	Record 30	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: dppf SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 18% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[29] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C6, Table 1 experiment D7" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "dppf" }, { "type": "SMILES", "value": "[Fe+2].c1ccc(P(c2ccccc2)c2ccc[cH-]2)cc1.c1ccc(P(c2ccccc2)c2ccc[cH-]2)cc1" }, { "type": "CAS_NUMBER", "value": "12150-46-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C6", "row": "C", "col": "6" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C6: ligand L6 (dppf), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 18, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[30]	Record 31	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: BINAP SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 37% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[30] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C7, Table 1 experiment E3" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "BINAP" }, { "type": "SMILES", "value": "c1ccc(P(c2ccccc2)c2ccc3ccccc3c2-c2c(P(c3ccccc3)c3ccccc3)ccc3ccccc23)cc1" }, { "type": "CAS_NUMBER", "value": "98327-87-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C7", "row": "C", "col": "7" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C7: ligand L7 (BINAP), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 37, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[31]	Record 32	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: dcype SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 20% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[31] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C8, Table 1 experiment E11" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "dcype" }, { "type": "SMILES", "value": "C1CCC(P(CCP(C2CCCCC2)C2CCCCC2)C2CCCCC2)CC1" }, { "type": "CAS_NUMBER", "value": "23743-26-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C8", "row": "C", "col": "8" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C8: ligand L8 (dcype), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 20, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[32]	Record 33	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: DavePhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 0% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[32] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C9, Table 1 experiment F7" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DavePhos" }, { "type": "SMILES", "value": "CN(C)c1ccccc1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "213697-53-1" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C9", "row": "C", "col": "9" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C9: ligand L9 (DavePhos), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i). Reported as 0%.", "uses_internal_standard": true, "percentage": { "value": 0, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[33]	Record 34	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: tBuXPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 4% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[33] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C10, Table 1 experiment G3" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "tBuXPhos" }, { "type": "SMILES", "value": "CC(C)c1cc(C(C)C)c(-c2ccccc2P(C(C)(C)C)C(C)(C)C)c(C(C)C)c1" }, { "type": "CAS_NUMBER", "value": "564483-19-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C10", "row": "C", "col": "10" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C10: ligand L10 (tBuXPhos), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 4, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[34]	Record 35	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: SPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 8% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[34] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C11, Table 1 experiment G11" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "SPhos" }, { "type": "SMILES", "value": "COc1cccc(OC)c1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "657408-07-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C11", "row": "C", "col": "11" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C11: ligand L11 (SPhos), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 8, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[35]	Record 36	REACTANT: 2-pyrrolidone REAGENT: KHMDS CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: P(o-tolyl)3 SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 0% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[35] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well C12, Table 1 experiment H7" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "KHMDS" }, { "type": "SMILES", "value": "C[Si](C)(C)[N-][Si](C)(C)C.[K+]" }, { "type": "CAS_NUMBER", "value": "40949-94-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 16 large scoop, 8.9 +/- 0.7 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "P(o-tolyl)3" }, { "type": "SMILES", "value": "Cc1ccccc1P(c1ccccc1C)c1ccccc1C" }, { "type": "CAS_NUMBER", "value": "6163-58-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "C12", "row": "C", "col": "12" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well C12: ligand L12 (P(o-tolyl)3), base B3 (KHMDS), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i). Reported as 0%.", "uses_internal_standard": true, "percentage": { "value": 0, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[36]	Record 37	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: RuPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 0% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[36] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D1, Table 1 experiment A4" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "RuPhos" }, { "type": "SMILES", "value": "CC(C)Oc1cccc(OC(C)C)c1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "787618-22-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D1", "row": "D", "col": "1" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D1: ligand L1 (RuPhos), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i). Reported as 0%.", "uses_internal_standard": true, "percentage": { "value": 0, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[37]	Record 38	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: Xantphos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 2% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[37] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D2, Table 1 experiment A12" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Xantphos" }, { "type": "SMILES", "value": "CC1(C)c2cccc(P(c3ccccc3)c3ccccc3)c2Oc2c(P(c3ccccc3)c3ccccc3)cccc21" }, { "type": "CAS_NUMBER", "value": "161265-03-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D2", "row": "D", "col": "2" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D2: ligand L2 (Xantphos), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 2, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[38]	Record 39	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: DPEPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 5% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[38] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D3, Table 1 experiment B8" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DPEPhos" }, { "type": "SMILES", "value": "c1ccc(P(c2ccccc2)c2ccccc2Oc2ccccc2P(c2ccccc2)c2ccccc2)cc1" }, { "type": "CAS_NUMBER", "value": "166330-10-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D3", "row": "D", "col": "3" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D3: ligand L3 (DPEPhos), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 5, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[39]	Record 40	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: IPr SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 0% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[39] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D4, Table 1 experiment C4" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "IPr" }, { "type": "SMILES", "value": "CC(C)c1cccc(C(C)C)c1N1[C]N(c2c(C(C)C)cccc2C(C)C)C=C1" }, { "type": "CAS_NUMBER", "value": "244187-81-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D4", "row": "D", "col": "4" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D4: ligand L4 (IPr), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i). Reported as 0%.", "uses_internal_standard": true, "percentage": { "value": 0, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[40]	Record 41	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: PCy3 SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 0% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[40] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D5, Table 1 experiment C12" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "PCy3" }, { "type": "SMILES", "value": "C1CCC(P(C2CCCCC2)C2CCCCC2)CC1" }, { "type": "CAS_NUMBER", "value": "2622-14-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D5", "row": "D", "col": "5" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D5: ligand L5 (PCy3), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i). Reported as 0%.", "uses_internal_standard": true, "percentage": { "value": 0, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[41]	Record 42	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: dppf SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 7% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[41] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D6, Table 1 experiment D8" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "dppf" }, { "type": "SMILES", "value": "[Fe+2].c1ccc(P(c2ccccc2)c2ccc[cH-]2)cc1.c1ccc(P(c2ccccc2)c2ccc[cH-]2)cc1" }, { "type": "CAS_NUMBER", "value": "12150-46-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D6", "row": "D", "col": "6" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D6: ligand L6 (dppf), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 7, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[42]	Record 43	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: BINAP SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 3% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[42] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D7, Table 1 experiment E4" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "BINAP" }, { "type": "SMILES", "value": "c1ccc(P(c2ccccc2)c2ccc3ccccc3c2-c2c(P(c3ccccc3)c3ccccc3)ccc3ccccc23)cc1" }, { "type": "CAS_NUMBER", "value": "98327-87-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D7", "row": "D", "col": "7" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D7: ligand L7 (BINAP), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 3, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[43]	Record 44	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: dcype SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 4% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[43] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D8, Table 1 experiment E12" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "dcype" }, { "type": "SMILES", "value": "C1CCC(P(CCP(C2CCCCC2)C2CCCCC2)C2CCCCC2)CC1" }, { "type": "CAS_NUMBER", "value": "23743-26-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D8", "row": "D", "col": "8" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D8: ligand L8 (dcype), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 4, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[44]	Record 45	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: DavePhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 0% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[44] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D9, Table 1 experiment F8" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DavePhos" }, { "type": "SMILES", "value": "CN(C)c1ccccc1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "213697-53-1" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D9", "row": "D", "col": "9" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D9: ligand L9 (DavePhos), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i). Reported as 0%.", "uses_internal_standard": true, "percentage": { "value": 0, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[45]	Record 46	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: tBuXPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 0% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[45] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D10, Table 1 experiment G4" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "tBuXPhos" }, { "type": "SMILES", "value": "CC(C)c1cc(C(C)C)c(-c2ccccc2P(C(C)(C)C)C(C)(C)C)c(C(C)C)c1" }, { "type": "CAS_NUMBER", "value": "564483-19-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D10", "row": "D", "col": "10" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D10: ligand L10 (tBuXPhos), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i). Reported as 0%.", "uses_internal_standard": true, "percentage": { "value": 0, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[46]	Record 47	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: SPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 0% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[46] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D11, Table 1 experiment G12" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "SPhos" }, { "type": "SMILES", "value": "COc1cccc(OC)c1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "657408-07-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D11", "row": "D", "col": "11" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D11: ligand L11 (SPhos), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i). Reported as 0%.", "uses_internal_standard": true, "percentage": { "value": 0, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[47]	Record 48	REACTANT: 2-pyrrolidone REAGENT: DBU CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-chloropyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: P(o-tolyl)3 SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 0% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[47] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well D12, Table 1 experiment H8" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "DBU" }, { "type": "SMILES", "value": "C1CCC2=NCCCN2CC1" }, { "type": "CAS_NUMBER", "value": "6674-22-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-chloropyrimidine" }, { "type": "SMILES", "value": "Clc1ncccn1" }, { "type": "CAS_NUMBER", "value": "1722-12-9" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "P(o-tolyl)3" }, { "type": "SMILES", "value": "Cc1ccccc1P(c1ccccc1C)c1ccccc1C" }, { "type": "CAS_NUMBER", "value": "6163-58-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "D12", "row": "D", "col": "12" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well D12: ligand L12 (P(o-tolyl)3), base B4 (DBU), 2-chloropyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i). Reported as 0%.", "uses_internal_standard": true, "percentage": { "value": 0, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[48]	Record 49	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-bromopyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: RuPhos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 17% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[48] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well E1, Table 1 experiment A5" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-bromopyrimidine" }, { "type": "SMILES", "value": "Brc1ncccn1" }, { "type": "CAS_NUMBER", "value": "4595-60-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "RuPhos" }, { "type": "SMILES", "value": "CC(C)Oc1cccc(OC(C)C)c1-c1ccccc1P(C1CCCCC1)C1CCCCC1" }, { "type": "CAS_NUMBER", "value": "787618-22-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "E1", "row": "E", "col": "1" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well E1: ligand L1 (RuPhos), base B1 (NaOtBu), 2-bromopyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 17, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }
reactions[49]	Record 50	REACTANT: 2-pyrrolidone REAGENT: NaOtBu CATALYST: [Pd(cinnamyl)Cl]2 REACTANT: 2-bromopyrimidine INTERNAL_STANDARD: 1,3,5-trimethoxybenzene CATALYST: Xantphos SOLVENT: toluene	100 CELSIUS	1-(pyrimidin-2-yl)pyrrolidin-2-one · YIELD: 73% [GC]	10.1038/s41596-020-00452-7
Decoded fields · reactions[49] Only fields present in the bytes are shown. Unrecognized fields and binary payloads are marked as omitted. { "identifiers": [ { "type": "REACTION_TYPE", "value": "Buchwald-Hartwig amidation (N-arylation of a lactam)" }, { "type": "CUSTOM", "details": "plate / well (Fig. 7 layout) / Supporting Table 1 experiment label", "value": "plate A, well E2, Table 1 experiment B1" } ], "inputs": { "2-pyrrolidone": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-pyrrolidone" }, { "type": "SMILES", "value": "O=C1CCCN1" }, { "type": "CAS_NUMBER", "value": "616-45-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1 equiv; absolute per-well amount not given in the open SI" } }, "reaction_role": "REACTANT", "is_limiting": true } ] }, "base": { "components": [ { "identifiers": [ { "type": "NAME", "value": "NaOtBu" }, { "type": "SMILES", "value": "CC(C)(C)[O-].[Na+]" }, { "type": "CAS_NUMBER", "value": "865-48-5" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "1.2 equiv relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (SI Fig. 14 extra-large scoop, 13.1 +/- 0.8 mg per dose)" } }, "reaction_role": "REAGENT" } ] }, "catalyst": { "components": [ { "identifiers": [ { "type": "NAME", "value": "[Pd(cinnamyl)Cl]2" }, { "type": "SMILES", "value": "[Cl-].[Cl-].[Pd+2].[Pd+2].[CH2-]/C=C/c1ccccc1.[CH2-]/C=C/c1ccccc1" }, { "type": "CAS_NUMBER", "value": "12131-44-6" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "5 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI" } }, "reaction_role": "CATALYST", "preparations": [ { "type": "NONE", "details": "dosed as a solid with a small polypropylene transfer scoop (SI Fig. 13: 2.55 +/- 0.32 mg per dose)" } ] } ] }, "halopyrimidine": { "components": [ { "identifiers": [ { "type": "NAME", "value": "2-bromopyrimidine" }, { "type": "SMILES", "value": "Brc1ncccn1" }, { "type": "CAS_NUMBER", "value": "4595-60-2" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI (1.2 equiv in the scale-up procedure)" } }, "reaction_role": "REACTANT" } ] }, "internal_standard_timing_unspecified": { "components": [ { "identifiers": [ { "type": "NAME", "value": "1,3,5-trimethoxybenzene" }, { "type": "SMILES", "value": "COc1cc(OC)cc(OC)c1" }, { "type": "CAS_NUMBER", "value": "621-23-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "amount not given in the open SI" } }, "reaction_role": "INTERNAL_STANDARD" } ] }, "ligand": { "components": [ { "identifiers": [ { "type": "NAME", "value": "Xantphos" }, { "type": "SMILES", "value": "CC1(C)c2cccc(P(c3ccccc3)c3ccccc3)c2Oc2c(P(c3ccccc3)c3ccccc3)cccc21" }, { "type": "CAS_NUMBER", "value": "161265-03-8" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "10-20 mol% relative to 2-pyrrolidone (limiting reagent, 0.17 M); per-well scale not given in the open SI (the scheme gives the range 10-20 mol% without per-ligand loading)" } }, "reaction_role": "CATALYST" } ] }, "solvent": { "components": [ { "identifiers": [ { "type": "NAME", "value": "toluene" }, { "type": "SMILES", "value": "Cc1ccccc1" }, { "type": "CAS_NUMBER", "value": "108-88-3" } ], "amount": { "unmeasured": { "type": "CUSTOM", "details": "volume giving 0.17 M in 2-pyrrolidone; anhydrous (PureSolv, <20 ppm water by Karl Fischer), degassed with N2" } }, "reaction_role": "SOLVENT" } ] } }, "setup": { "vessel": { "type": "VIAL", "details": "8 x 40 mm glass vial in a machined aluminium 96-well plate (PFA sheet and rubber gasket seal)", "material": { "type": "GLASS" }, "volume": { "value": 1.2000000476837158, "units": "MILLILITER" }, "vessel_id": "plate A", "position": "E2", "row": "E", "col": "2" }, "is_automated": false }, "conditions": { "temperature": { "control": { "type": "DRY_ALUMINUM_PLATE", "details": "aluminium 96-well plate on a Heidolph magnetic stirrer/hotplate" }, "setpoint": { "value": 100, "units": "CELSIUS" } }, "pressure": { "control": { "type": "SEALED" }, "atmosphere": { "type": "NITROGEN" } }, "stirring": { "type": "STIR_BAR", "details": "magnetic stirring on a Heidolph stirrer/hotplate" }, "conditions_are_dynamic": false }, "notes": { "procedure_details": "Plate A of three replicate 96-well plates (A, B, C) run by protocol steps 1-63. Well E2: ligand L2 (Xantphos), base B1 (NaOtBu), 2-bromopyrimidine. Vials charged under N2 with 2-pyrrolidone, the 2-halopyrimidine, [Pd(cinnamyl)Cl]2 (5 mol%), ligand (10-20 mol%), base (1.2 equiv) and toluene (0.17 M); plate sealed and heated at 100 C for 16 h; 15 uL aliquots filtered through silica and analysed by GC. Solids were dosed with polypropylene transfer scoops and liquids with micropipettes. Plates A and B: Heidolph stirrer/hotplate and gravity filtration. The source establishes 1,3,5-trimethoxybenzene as the GC internal standard, but the accessible SI does not specify its amount or addition timing. Nitrogen/anhydrous handling is reported; oxygen/moisture sensitivity is not independently established, so these flags are left unset." }, "workups": [ { "type": "TEMPERATURE", "details": "cooled to room temperature", "temperature": { "control": { "type": "AMBIENT" } } }, { "type": "ALIQUOT", "details": "15 uL aliquot of each reaction mixture taken for filtration", "amount": { "volume": { "value": 15, "units": "MICROLITER" } } }, { "type": "FILTRATION", "details": "gravity filtration through a short plug of Silicycle F60 40-63 um silica gel in a chemically resistant 96-well filter plate into a second 96-well plate", "keep_phase": "filtrate" } ], "outcomes": [ { "reaction_time": { "value": 16, "units": "HOUR" }, "products": [ { "identifiers": [ { "type": "NAME", "value": "1-(pyrimidin-2-yl)pyrrolidin-2-one" }, { "type": "SMILES", "value": "O=C1CCCN1c1ncccn1" } ], "is_desired_product": true, "measurements": [ { "analysis_key": "GC", "type": "YIELD", "details": "Calibrated GC yield for this single plate (Supporting Table 1). Precision = pooled standard deviation of the triplicate plates A/B/C (+/- 3.0%, SI section 3.2.i).", "uses_internal_standard": true, "percentage": { "value": 73, "precision": 3 } } ], "reaction_role": "PRODUCT" } ], "analyses": { "GC": { "type": "GC", "details": "GC-FID, Agilent 7890B, 30 m x 0.25 mm HP-5 column, XYZ autosampler for multiwell plates; 5-point calibration curve with 1,3,5-trimethoxybenzene internal standard", "instrument_manufacturer": "Agilent Technologies" } } } ], "provenance": { "experimenter": { "name": "Adam Cook; Roxanne Clément (University of Ottawa, Newman group)", "organization": "University of Ottawa" }, "city": "Ottawa, ON, Canada", "doi": "10.1038/s41596-020-00452-7", "publication_url": "https://doi.org/10.1038/s41596-020-00452-7", "record_created": { "time": { "value": "2026-10-14T00:00:00Z" }, "person": { "name": "Jordan (Tokens for Progress @jordan)", "email": "hello@tokensforprogress.org" }, "details": "Curated from the open Supplementary Information PDF (https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41596-020-00452-7/MediaObjects/41596_2020_452_MOESM1_ESM.pdf) and the open Fig. 7 plate layout of the article, with AI assistance (Tokens for Progress). Email is a placeholder (example.org) to be replaced by the submitter's address on ORD submission." }, "record_modified": [ { "time": { "value": "2026-10-16T21:50:17Z" }, "person": { "name": "Tokens for Progress", "email": "hello@tokensforprogress.org" }, "details": "Authorized public contact correction for Tokens for Progress-commissioned work: record_created.person.email changed from ord-curation-placeholder@example.org to hello@tokensforprogress.org. Original creator name, username, creation timestamp and details retained; no original numerical result, molecular structure, or source uncertainty changed. Original artifact sha256:cd8989ef0c7566898b08e67812ad3065e8dabd90bdd251a2705f9b532d5364fa. Cleared unsupported oxygen/moisture sensitivity flags and removed the unknown-time internal-standard ADDITION workup; the identical internal-standard compound is preserved as an input with addition timing/order/temperature unset, the GC analysis remains unchanged, and uncertainty is explicit in procedure notes." } ] } }