Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: CC1(C)COB([C:8]2[CH:13]=[CH:12][C:11]([CH:14]3[CH2:18][CH2:17][N:16]([C:19]([O:21][CH3:22])=[O:20])[CH2:15]3)=[CH:10][CH:9]=2)OC1.Br[C:25]1[CH:26]=[C:27]2[C:31](=[CH:32][C:33]=1[Cl:34])[NH:30][CH:29]=[C:28]2[CH:35]=[O:36].C(=O)([O-])[O-].[K+].[K+]>C1(C)C=CC=CC=1.CCO.C1C=CC(P(C2C=CC=CC=2)[C-]2C=CC=C2)=CC=1.C1C=CC(P(C2C=CC=CC=2)[C-]2C=CC=C2)=CC=1.Cl[Pd]Cl.[Fe+2]>[Cl:34][C:33]1[CH:32]=[C:31]2[C:27]([C:28]([CH:35]=[O:36])=[CH:29][NH:30]2)=[CH:26][C:25]=1[C:8]1[CH:9]=[CH:10][C:11]([CH:14]2[CH2:18][CH2:17][N:16]([C:19]([O:21][CH3:22])=[O:20])[CH2:15]2)=[CH:12][CH:13]=1
Reactant: O=Cc1c[nH]c2cc(Cl)c(Br)cc12
Reactant: COC(=O)N1CCC(c2ccc(B3OCC(C)(C)CO3)cc2)C1
Agent: Cl[Pd]Cl
Agent: [Fe+2]
Agent: O=C([O-])[O-]
Solvent: Cc1ccccc1
Solvent: CCO
Product: COC(=O)N1CCC(c2ccc(-c3cc4c(C=O)c[nH]c4cc3Cl)cc2)C1
Temperature: 115 °C
Yield: 67.9 %

Procedure:
To a degassed mixture of methyl 3-[4-(5,5-dimethyl-1,3,2-dioxaborinan-2-yl)phenyl]pyrrolidine-1-carboxylate (0.158 g, 0.5 mmol), 5-bromo-6-chloro-1H-indole-3-carbaldehyde (142.5 mg, 0.55 mmol) and 2N aqueous potassium carbonate (1.0 mL, 2.0 mmol) in toluene (3 mL) and EtOH (1 mL) was added [1,1′-bis(diphenylphosphino)ferrocene]dichloropalladium(II) (36.6 mg, 0.05 mmol). The resulting mixture was heated to 115° C. in a microwave for 30 min. The reaction mixture was partitioned between water and EtOAc. The organic layer was washed with brine, dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash chromatography on silica gel eluting with EtOAc/petroleum ether (0:100 to 57:43) to give methyl 3-[4-(6-chloro-3-formyl-1H-indol-5-yl)phenyl]pyrrolidine-1-carboxylate (0.13 g, 68%) as a yellow solid, which was used in the next step without further purification.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:8]=[CH:7][CH:6]=[CH:5][C:4]=1[CH:9]([CH3:12])[CH2:10]O.[C:13]1(=[O:23])[NH:17][C:16](=[O:18])[C:15]2=[CH:19][CH:20]=[CH:21][CH:22]=[C:14]12.C1C=CC(P(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1.CC(OC(/N=N/C(OC(C)C)=O)=O)C>>[CH3:1][O:2][C:3]1[CH:8]=[CH:7][CH:6]=[CH:5][C:4]=1[CH:9]([CH3:12])[CH2:10][N:17]1[C:13](=[O:23])[C:14]2[C:15](=[CH:19][CH:20]=[CH:21][CH:22]=2)[C:16]1=[O:18]
Reactant: O=C1NC(=O)c2ccccc21
Reactant: COc1ccccc1C(C)CO
Agent: CC(C)OC(=O)/N=N/C(=O)OC(C)C
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Product: COc1ccccc1C(C)CN1C(=O)c2ccccc2C1=O
Temperature: 25 °C
Reaction time: 0.25 h

Procedure:
As shown in step 4-iii of Scheme 4, a mixture of 2-(2-methoxyphenyl)-1-propanol (1.31 g, 7.08 mmol), phthalimide (1.09 g, 7.44 mmol), and PPh3 resin (3.43 g, 10.6 mmol) was stirred at room temperature for 15 minutes to allow the resin to swell. Diisopropylazodicarboxylate (2.29 g, 2.24 mL, 10.6 mmol) was added and the reaction was stirred for 18 hours. The reaction mixture was filtered through diatomaceous earth, which was subsequently washed with EtOAc and DCM. The filtrate was concentrated under reduced pressure and purified by medium pressure chromatography on silica gel (10 to 20% EtOAc in hexanes) to give 2-(2-(2-methoxyphenyl)propyl)isoindoline-1,3-dione as a clear, colorless oil (Compound 2010, 2.15 g, quantitative yield): 1H NMR (CDCl3) δ 7.81 (dd, J=5.5, 3.0 Hz, 2H), 7.69 (dd, J=5.5, 3.0 Hz, 2H), 7.34-7.24 (m, 1H), 7.19 (ddd, J=8.1, 7.5, 1.7 Hz, 1H), 6.94 (td, J=7.5, 1.1 Hz, 1H), 6.76 (dd, J=8.2, 0.9 Hz, 1H), 4.03-3.69 (m, 3H), 3.66 (s, 3H), 1.32 (d, J=6.8 Hz, 3H).
Reaction SMILES: C(O)=O.[NH2:4][CH2:5][CH2:6][C:7]1[CH:31]=[CH:30][C:10]([NH:11][CH:12]2[CH2:17][CH2:16][N:15]([C:18]([NH:20][CH2:21][C:22]3[CH:27]=[C:26]([F:28])[CH:25]=[CH:24][C:23]=3[F:29])=[O:19])[CH2:14][CH2:13]2)=[CH:9][CH:8]=1.C([Si]([O:49][C:50]1[CH:55]=[CH:54][C:53]([O:56][CH2:57][CH:58]2[CH2:60][O:59]2)=[CH:52][CH:51]=1)(C1C=CC=CC=1)C1C=CC=CC=1)(C)(C)C>C(Cl)(Cl)Cl.CO>[F:29][C:23]1[CH:24]=[CH:25][C:26]([F:28])=[CH:27][C:22]=1[CH2:21][NH:20][C:18]([N:15]1[CH2:16][CH2:17][CH:12]([NH:11][C:10]2[CH:9]=[CH:8][C:7]([CH2:6][CH2:5][NH:4][CH2:60][C@H:58]([OH:59])[CH2:57][O:56][C:53]3[CH:54]=[CH:55][C:50]([OH:49])=[CH:51][CH:52]=3)=[CH:31][CH:30]=2)[CH2:13][CH2:14]1)=[O:19]
Reactant: CC(C)(C)[Si](Oc1ccc(OCC2CO2)cc1)(c1ccccc1)c1ccccc1
Reactant: NCCc1ccc(NC2CCN(C(=O)NCc3cc(F)ccc3F)CC2)cc1
Solvent: CO
Solvent: ClC(Cl)Cl
Solvent: O=CO
Product: O=C(NCc1cc(F)ccc1F)N1CCC(Nc2ccc(CCNC[C@H](O)COc3ccc(O)cc3)cc2)CC1
Yield: 25.2 %

Procedure:
4-[4-(2-Aminoethyl)anilino]-N-(2,5-difluorobenzyl)-1-piperidinecarboxamide formate (0.50 g, 1.15 mmol) was reacted with tert-butyl-(4-oxiranylmethoxy-phenoxy)-diphenyl-silane (0.465 g, 1.15 mmol) according to Procedure G (eluant: 20:1 chloroform-methanol) to give the title compound (0.238 g, 0.29 mmol).
Reaction SMILES: Br[C:2]1[CH:7]=[CH:6][N:5]2[C:8]([C:11]([NH:13][C:14]3[CH:19]=[C:18]([C:20](=[O:36])[NH:21][CH2:22][C:23]4[CH:28]=[CH:27][CH:26]=[CH:25][C:24]=4[N:29]4[CH2:34][CH2:33][N:32]([CH3:35])[CH2:31][CH2:30]4)[CH:17]=[CH:16][C:15]=3[F:37])=[O:12])=[CH:9][N:10]=[C:4]2[CH:3]=1.[F:38][C:39]1[CH:40]=[C:41](B(O)O)[CH:42]=[CH:43][C:44]=1[C:45](=[O:50])[NH:46][CH2:47][CH2:48][OH:49].C(=O)([O-])[O-].[Cs+].[Cs+].C(Cl)Cl>CN(C=O)C.CCOC(C)=O.O.C1C=CC(P(C2C=CC=CC=2)[C-]2C=CC=C2)=CC=1.C1C=CC(P(C2C=CC=CC=2)[C-]2C=CC=C2)=CC=1.Cl[Pd]Cl.[Fe+2]>[F:38][C:39]1[CH:40]=[C:41]([C:2]2[CH:7]=[CH:6][N:5]3[C:8]([C:11]([NH:13][C:14]4[CH:19]=[C:18]([C:20](=[O:36])[NH:21][CH2:22][C:23]5[CH:28]=[CH:27][CH:26]=[CH:25][C:24]=5[N:29]5[CH2:34][CH2:33][N:32]([CH3:35])[CH2:31][CH2:30]5)[CH:17]=[CH:16][C:15]=4[F:37])=[O:12])=[CH:9][N:10]=[C:4]3[CH:3]=2)[CH:42]=[CH:43][C:44]=1[C:45](=[O:50])[NH:46][CH2:47][CH2:48][OH:49]
Reactant: O=C(NCCO)c1ccc(B(O)O)cc1F
Reactant: CN1CCN(c2ccccc2CNC(=O)c2ccc(F)c(NC(=O)c3cnc4cc(Br)ccn34)c2)CC1
Agent: Cl[Pd]Cl
Agent: [Fe+2]
Agent: O=C([O-])[O-]
Solvent: ClCCl
Solvent: CCOC(C)=O
Solvent: CN(C)C=O
Product: CN1CCN(c2ccccc2CNC(=O)c2ccc(F)c(NC(=O)c3cnc4cc(-c5ccc(C(=O)NCCO)c(F)c5)ccn34)c2)CC1
Reaction time: 8 h

Procedure:
A mixture comprising 7-bromo-N-(2-fluoro-5-(2-(4-methylpiperazin-1-yl)benzylcarbamoyl)phenyl)imidazo[1,2-a]pyridine-3-carboxamide (Ex 1.1, step 1) (120 mg, 0.212 mmol), 3-fluoro-4-(2-hydroxyethylcarbamoyl)phenylboronic acid (48.2 mg, 0.212 mmol), cesium carbonate (69.1 mg, 0.212 mmol) and PdCl2(dppf).CH2Cl2 adduct (17.33 mg, 0.021 mmol) in DMF (3 ml) under N2 was heated at 85° C. for 2 hrs. Further portions of 3-fluoro-4-(2-hydroxyethylcarbamoyl)phenylboronic acid (48.2 mg, 0.212 mmol), cesium carbonate (69.1 mg, 0.212 mmol) and PdCl2(dppf).CH2Cl2 adduct (17.33 mg, 0.021 mmol) were added and heating continued at 100° C. overnight. The reaction mixture was diluted with EtOAc and water and the biphasic mixture was filtered. The filtercake was washed with MeOH and the filtrate was concentrated under vacuum. Purification of the crude residue by chromatography on silica eluting with 0-20% NH3MeOH/DCM afforded a beige solid. The solid was triturated with THF/ether and dried in vacuo at 45° C. overnight to afford the title compound;
Reaction SMILES: [C:1]1([C:43]2[CH:48]=[CH:47][CH:46]=[CH:45][CH:44]=2)[CH:6]=[CH:5][C:4]([C@@:7]2([O:41][CH3:42])[CH2:40][N:10]3[C:11](=[O:39])[C@@H:12]([NH:31][C:32]([O:34][C:35]([CH3:38])([CH3:37])[CH3:36])=[O:33])[CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH:18]=[CH:19][C@@H:20]4[CH2:25][C@@:21]4([C:26]([O:28]CC)=[O:27])[NH:22][C:23](=[O:24])[C@@H:9]3[CH2:8]2)=[CH:3][CH:2]=1.O.CO>O1CCCC1>[C:1]1([C:43]2[CH:48]=[CH:47][CH:46]=[CH:45][CH:44]=2)[CH:2]=[CH:3][C:4]([C@@:7]2([O:41][CH3:42])[CH2:40][N:10]3[C:11](=[O:39])[C@@H:12]([NH:31][C:32]([O:34][C:35]([CH3:37])([CH3:38])[CH3:36])=[O:33])[CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH:18]=[CH:19][C@@H:20]4[CH2:25][C@@:21]4([C:26]([OH:28])=[O:27])[NH:22][C:23](=[O:24])[C@@H:9]3[CH2:8]2)=[CH:5][CH:6]=1
Reactant: CCOC(=O)[C@@]12C[C@H]1C=CCCCCC[C@H](NC(=O)OC(C)(C)C)C(=O)N1C[C@](OC)(c3ccc(-c4ccccc4)cc3)C[C@H]1C(=O)N2
Agent: CCOC(=O)[C@@]12C[C@H]1/C=C\CCCCC[C@H](NC(=O)OC(C)(C)C)C(=O)N1C[C@](OC)(c3ccc(-c4ccccc4)cc3)C[C@H]1C(=O)N2
Agent: CO[C@@]1(c2ccc(-c3ccccc3)cc2)C[C@H]2C(=O)N[C@]3(C(=O)O)C[C@H]3/C=C\CCCCC[C@H](NC(=O)OC(C)(C)C)C(=O)N2C1
Solvent: C1CCOC1
Solvent: O
Solvent: CO
Product: CO[C@@]1(c2ccc(-c3ccccc3)cc2)C[C@H]2C(=O)N[C@]3(C(=O)O)C[C@H]3C=CCCCCC[C@H](NC(=O)OC(C)(C)C)C(=O)N2C1
Temperature: 25 °C
Reaction time: 18 h

Procedure:
A mixture of (2R,6S,13aS,14aR,16aS,Z)-ethyl 2-(biphenyl-4-yl)-6-(tert-butoxycarbonylamino)-2-methoxy-5,16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecine-14a-carboxylate (56 mg, 0.085 mmol), LiOH monohydrate (40.7 mg, 1.70 mmol) in tetrahydrofuran (2 mL)/water (0.5 mL)/MeOH (1 mL) was stirred at rt for 18 h. It was then concentrated in vacuo, and washed with ether. The aqueous phase was adjusted to pH=4 using 1N HCl and extracted with EtOAc. The EtOAc extract was dried over MgSO4, filtered and concentrated in vacuo to give 52 mg (97%) of (2R,6S,13aS,14aR,16aS,Z)-2-(biphenyl-4-yl)-6-(tert-butoxycarbonylamino)-2-methoxy-5,16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecine-14a-carboxylic acid as an off-white solid.
Reaction SMILES: C([O:8][C:9]1[CH:14]=[CH:13][N:12]([CH2:15][CH:16]([NH:31][C:32]([N:34]2[CH2:39][CH2:38][CH:37]([N:40]3[CH2:49][C:48]4[C:43](=[CH:44][CH:45]=[CH:46][CH:47]=4)[NH:42][C:41]3=[O:50])[CH2:36][CH2:35]2)=[O:33])[C:17]([N:19]2[CH2:24][CH2:23][CH:22]([N:25]3[CH2:30][CH2:29][CH2:28][CH2:27][CH2:26]3)[CH2:21][CH2:20]2)=[O:18])[C:11](=[O:51])[CH:10]=1)C1C=CC=CC=1>[Pd].CO>[N:25]1([CH:22]2[CH2:23][CH2:24][N:19]([C:17](=[O:18])[CH:16]([NH:31][C:32]([N:34]3[CH2:35][CH2:36][CH:37]([N:40]4[CH2:49][C:48]5[C:43](=[CH:44][CH:45]=[CH:46][CH:47]=5)[NH:42][C:41]4=[O:50])[CH2:38][CH2:39]3)=[O:33])[CH2:15][N:12]3[CH:13]=[CH:14][C:9]([OH:8])=[CH:10][C:11]3=[O:51])[CH2:20][CH2:21]2)[CH2:26][CH2:27][CH2:28][CH2:29][CH2:30]1
Reactant: O=C(NC(Cn1ccc(OCc2ccccc2)cc1=O)C(=O)N1CCC(N2CCCCC2)CC1)N1CCC(N2Cc3ccccc3NC2=O)CC1
Agent: [Pd]
Solvent: CO
Product: O=C(NC(Cn1ccc(O)cc1=O)C(=O)N1CCC(N2CCCCC2)CC1)N1CCC(N2Cc3ccccc3NC2=O)CC1
Reaction time: 1 h

Procedure:
A stirred solution of 4-(2-oxo-1,4-dihydro-2H-quinazolin-3-yl)-piperidine-1-carboxylic acid [1-(4-benzyloxy-2-oxo-2H-pyridin-1-ylmethyl)-2-[1,4′]bipiperidinyl-1′-yl-2-oxo-ethyl]-amide (29 mg) and 10% palladium on charcoal (5 mg) in methanol (1 mL) was placed under an atmosphere of hydrogen. After 1 h at room temperature, the reaction was flushed with nitrogen, filtered through celite, and concentrated to give the product. 1H-NMR (CD3OD, 500 MHz) δ 1.40-1.85 (m, 12H), 2.04 (dd, J=27.4, 17.0, 2H), 2.66 (dd, J=21.1, 11.0, 1H), 2.80-3.19 (m, 8H), 3.95 (ddd, J=49.8, 12.5, 7.9, 1H), 4.07-4.28 (m, 3H), 4.34 (bs, 2H), 4.36-4.59 (m, 2H), 4.63 (bd, J=12.8, 1H), 5.20 (m, 1H), 5.75 (dd, J=7.3, 2.1, 1H), 5.97 (dd, J=8.9, 7.6, 1H), 6.78 (d, J=7.6, 1H), 6.93 (dd, J=7.6, 7.3, 1H), 7.08-7.18 (m, 2H), 7.33 (dd, J=18.3, 11.0, 1H). Mass spec.: 606.32 (MH)+.
Reaction SMILES: CS(O[CH2:6][CH2:7][CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][CH2:13][CH:14]1[CH2:22][C:21]2[C:16](=[C:17]([O:29][CH3:30])[C:18]([O:27][CH3:28])=[C:19]([O:25][CH3:26])[C:20]=2[O:23][CH3:24])[CH2:15]1)(=O)=O.[I-:31].[Na+].O>CC(C)=O>[I:31][CH2:6][CH2:7][CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][CH2:13][CH:14]1[CH2:22][C:21]2[C:16](=[C:17]([O:29][CH3:30])[C:18]([O:27][CH3:28])=[C:19]([O:25][CH3:26])[C:20]=2[O:23][CH3:24])[CH2:15]1
Reactant: COc1c2c(c(OC)c(OC)c1OC)CC(CCCCCCCCOS(C)(=O)=O)C2
Reactant: [I-]
Agent: [Na+]
Solvent: O
Solvent: CC(C)=O
Product: COc1c2c(c(OC)c(OC)c1OC)CC(CCCCCCCCI)C2
Yield: 96.5 %

Procedure:
The mixture of 8-(4,5,6,7-tetramethoxyindan-2-yl)octyl methanesulfonate (2.36 g), sodium iodide (2.38 g) in acetone (20 ml) was heated under reflux for 3 hr. Water was added to the reaction mixture, which was then extracted with ethyl acetate. The organic layer was washed with 5% aqueous sodium sulfite, water, and saturated aqueous sodium chloride, and dried. The solvent was removed in vacuo to yield the entitled compound (2.44 g) as an oil.
Reaction SMILES: [F:1][C:2]1[CH:3]=[C:4]([CH:22]=[C:23]([F:25])[CH:24]=1)[CH2:5][C@@H:6]1[CH2:11][C@@H:10]([C:12]2[O:16][NH:15][C:14](=[O:17])[CH:13]=2)[CH2:9][CH2:8][N:7]1C(OC)=O.Br>>[F:25][C:23]1[CH:22]=[C:4]([CH:3]=[C:2]([F:1])[CH:24]=1)[CH2:5][C@@H:6]1[CH2:11][C@@H:10]([C:12]2[O:16][NH:15][C:14](=[O:17])[CH:13]=2)[CH2:9][CH2:8][NH:7]1
Reactant: COC(=O)N1CC[C@H](c2cc(=O)[nH]o2)C[C@H]1Cc1cc(F)cc(F)c1
Agent: Br
Product: O=c1cc([C@H]2CCN[C@H](Cc3cc(F)cc(F)c3)C2)o[nH]1
Temperature: 25 °C
Reaction time: 8 h
Yield: 16.3 %

Procedure:
(2S,4S)-Methyl 2-(3,5-difluorobenzyl)-4-(3-oxo-2,3-dihydroisoxazol-5-yl)piperidine-1-carboxylate (0.249 g, 0.71 mmol) was dissolved in hydrogen bromide (33% in acetic acid, 5.57 mL, 31.80 mmol) and the mixture was stirred at room temperature overnight. The solvent was evaporated and the residue purified by preparative HPLC (Instrument: FractionLynx II, Mobilphase: gradient 5-95% MeCN in 0.2% NH3, pH 10, Column: Xbridge Prep C18 5 μm OBD 19*150 mm) to yield 5-((2S,4S)-2-(3,5-difluorobenzyl)piperidin-4-yl)isoxazol-3(2H)-one (34 mg, 16%). 1H NMR (400 MHz, cd3od) δ 1.70-2.16 (m, 4H), 2.84-3.43 (m, 6H), 5.57 (s, 1H), 6.81-7.02 (m, 3H). HRMS Calculated for [C15H16F2N2O2+H]+: 295.1258. Found: 295.1254
Reaction SMILES: Cl[C:2]1[CH:10]=[C:9]2[C:5]([CH:6]=[N:7][N:8]2[S:11]([C:14]2[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=2)(=[O:13])=[O:12])=[C:4]([C:20]2[O:21][C:22]([C:25]([O:27][CH2:28][CH3:29])=[O:26])=[CH:23][N:24]=2)[CH:3]=1.[CH3:30][C:31]([Si:34]([CH3:48])([CH3:47])[N:35]1[C:43]2[C:38](=[C:39](B(O)O)[CH:40]=[CH:41][CH:42]=2)[CH:37]=[CH:36]1)([CH3:33])[CH3:32].[O-]P([O-])([O-])=O.[K+].[K+].[K+]>O1CCOCC1.O.Cl[Pd]C1C=CC=CC=1C1C=CC=CC=1N(C)C.[C@H]12C[C@H](CC1)CC2PC1C[C@H]2C[C@@H]1CC2>[CH3:33][C:31]([Si:34]([CH3:48])([CH3:47])[N:35]1[C:43]2[C:38](=[C:39]([C:2]3[CH:10]=[C:9]4[C:5]([CH:6]=[N:7][N:8]4[S:11]([C:14]4[CH:15]=[CH:16][CH:17]=[CH:18][CH:19]=4)(=[O:13])=[O:12])=[C:4]([C:20]4[O:21][C:22]([C:25]([O:27][CH2:28][CH3:29])=[O:26])=[CH:23][N:24]=4)[CH:3]=3)[CH:40]=[CH:41][CH:42]=2)[CH:37]=[CH:36]1)([CH3:30])[CH3:32]
Reactant: CCOC(=O)c1cnc(-c2cc(Cl)cc3c2cnn3S(=O)(=O)c2ccccc2)o1
Reactant: CC(C)(C)[Si](C)(C)n1ccc2c(B(O)O)cccc21
Agent: CN(C)c1ccccc1-c1ccccc1[Pd]Cl
Agent: C1C[C@@H]2C[C@H]1CC2PC1C[C@@H]2CC[C@H]1C2
Agent: O=P([O-])([O-])[O-]
Solvent: O
Solvent: C1COCCO1
Product: CCOC(=O)c1cnc(-c2cc(-c3cccc4c3ccn4[Si](C)(C)C(C)(C)C)cc3c2cnn3S(=O)(=O)c2ccccc2)o1
Temperature: 100 °C
Yield: 38.9 %

Procedure:
To a solution of ethyl 2-[6-chloro-1-(phenylsulfonyl)-1H-indazol-4-yl]-1,3-oxazole-5-carboxylate (1.5 g, 3.47 mmol) in 1,4-dioxane (15 ml) and water (1.5 ml) was added {1-[(1,1-dimethylethyl)(dimethyl)silyl]-1H-indol-4-yl}boronic acid (1.243 g, 4.52 mmol, available from Combi-Blocks Inc.), chloro[2′-(dimethylamino)-2-biphenylyl]palladium-1(1R,4S)-bicyclo[2.2.1]hept-2-yl[(1S,4R)-bicyclo[2.2.1]hept-2-yl]phosphane (0.097 g, 0.174 mmol) and potassium phosphate tribasic (2.212 g, 10.42 mmol). The reaction mixture was heated to 100° C. for 3 h, the solvent removed in vacuo and the residue partitioned between dichloromethane (20 ml) and water (10 ml). Saturated sodium chloride solution (100 ml) was added and the organic phase separated and dried over anhydrous sodium sulphate. The crude product was purified by silica gel chromatography, eluting with a gradient of cyclohexane and ethyl acetate. The desired fractions were concentrated to give the title compound as a white solid (0.846 g), which by LCMS contained some unreacted starting material.
Reaction SMILES: [OH:1][CH:2]([CH:7]([CH3:9])[CH3:8])[C:3](=[CH2:6])[C:4]#[N:5].N1C=CC=CC=1.Cl[C:17]([O:19][CH2:20][CH3:21])=[O:18].Cl>O.C(Cl)Cl>[CH2:20]([O:19][C:17](=[O:18])[O:1][CH:2]([CH:7]([CH3:9])[CH3:8])[C:3]([C:4]#[N:5])=[CH2:6])[CH3:21]
Reactant: C=C(C#N)C(O)C(C)C
Reactant: CCOC(=O)Cl
Agent: Cl
Solvent: O
Solvent: c1ccncc1
Solvent: ClCCl
Product: C=C(C#N)C(OC(=O)OCC)C(C)C
Yield: 95.5 %

Procedure:
A nitrogen-purged 5 L, three-necked, round-bottom flask with overhead stirring is charged with 150 g (1.2 mol) of 3-hydroxy-4-methyl-2-methylenepentanenitrile, 1.0 L of methylene chloride, and 170 mL (2.1 mol) of pyridine. The solution is cooled at 10° C. to 15° C. in an ice bath. Using a 1 L graduated addition funnel, a mixture of 0.5 L of methylene chloride and 200 mL (2.1 mol) of ethyl chloroformate is added slowly while maintaining the reaction temperature at 20° C.±5° C. The reaction is stirred at 22° C.±3° C. for about two additional hours. The reaction solution is poured into a 6 L separatory funnel containing 200 mL (2.3 mol) of hydrochloric acid and 1.25 L of water. The lower organic layer is washed again with a solution of 60 mL (0.7 mol) of HCl and 0.5 L of water. The organic layer is dried over anhydrous magnesium sulfate (30 g), filtered, and concentrated by rotary evaporation to provide 226 g of carbonic acid 2-cyano-1-isopropyl-allyl ester ethyl ester as a yellow oil which may be used in the next step without further purification. Acetic acid 2-cyano-1-isopropyl-allyl ester (using acetyl chloride)
Reaction SMILES: Cl[C:2]1[C:3]([C:16]2[CH:21]=[CH:20][C:19]([F:22])=[CH:18][CH:17]=2)=[N:4][C:5]2[C:10]([N:11]=1)=[CH:9][C:8]([C:12]([O:14][CH3:15])=[O:13])=[CH:7][CH:6]=2.CCN(C(C)C)C(C)C.[CH:32]1([NH2:38])[CH2:37][CH2:36][CH2:35][CH2:34][CH2:33]1>CS(C)=O.O>[CH:32]1([NH:38][C:2]2[C:3]([C:16]3[CH:21]=[CH:20][C:19]([F:22])=[CH:18][CH:17]=3)=[N:4][C:5]3[C:10]([N:11]=2)=[CH:9][C:8]([C:12]([O:14][CH3:15])=[O:13])=[CH:7][CH:6]=3)[CH2:37][CH2:36][CH2:35][CH2:34][CH2:33]1
Reactant: NC1CCCCC1
Reactant: COC(=O)c1ccc2nc(-c3ccc(F)cc3)c(Cl)nc2c1
Solvent: CCN(C(C)C)C(C)C
Solvent: O
Solvent: CS(C)=O
Product: COC(=O)c1ccc2nc(-c3ccc(F)cc3)c(NC3CCCCC3)nc2c1
Temperature: 90 °C
Reaction time: 8 h
Yield: 83.7 %

Procedure:
To a solution of methyl 3-chloro-2-(4-fluorophenyl)quinoxaline-6-carboxylate (200 mg, 0.63 mmol) in DMSO (10 mL) was added DIEA (163.3 mg, 1.27 mmol) and cyclohexanamine (250.7 mg, 2.53 mmol), and the reaction was allowed to proceed with stirring overnight at 90° C. in an oil bath. The reaction mixture was cooled down to room temperature and diluted with water (150 mL). The mixture was extracted with ethyl acetate (3×80 mL), the organic layers combined and dried over magnesium sulfate, concentrated in vacuo to give the residue, which was purified by a silica gel column chromatography (1% ethyl acetate in petroleum ether) to afford methyl 3-(cyclohexylamino)-2-(4-fluorophenyl)quinoxaline-6-carboxylate as a light yellow solid (200 mg, 83%).
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([C:9]([C:12]2[N:16]([C:17]3[CH:22]=[CH:21][C:20]([F:23])=[CH:19][CH:18]=3)[C:15](=[S:24])[NH:14][CH:13]=2)([CH3:11])[CH3:10])[CH:5]=[CH:6][C:7]=1[Cl:8].C([O-])([O-])=O.[K+].[K+].[Cl:31][C:32]1[CH:39]=[CH:38][CH:37]=[C:36]([F:40])[C:33]=1[CH2:34]Cl>CC(C)=O>[Cl:31][C:32]1[CH:39]=[CH:38][CH:37]=[C:36]([F:40])[C:33]=1[CH2:34][S:24][C:15]1[N:16]([C:17]2[CH:18]=[CH:19][C:20]([F:23])=[CH:21][CH:22]=2)[C:12]([C:9]([C:4]2[CH:5]=[CH:6][C:7]([Cl:8])=[C:2]([Cl:1])[CH:3]=2)([CH3:11])[CH3:10])=[CH:13][N:14]=1
Reactant: Fc1cccc(Cl)c1CCl
Reactant: CC(C)(c1ccc(Cl)c(Cl)c1)c1c[nH]c(=S)n1-c1ccc(F)cc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC(C)=O
Product: CC(C)(c1ccc(Cl)c(Cl)c1)c1cnc(SCc2c(F)cccc2Cl)n1-c1ccc(F)cc1
Reaction time: 2 h
Yield: 40.6 %

Procedure:
To a mixture of 5-(2-(3,4-dichlorophenyl)propan-2-yl)-1-(4-fluorophenyl)-1H-imidazole-2(3H)-thione (138 mg, 0.362 mmol) and K2CO3 (76 mg, 0.543 mmol) in acetone (6 mL) was added 2-chloro-6-fluorobenzyl chloride (79 mg, 0.434 mmol). After stirring 2 h, the reaction mixture was filtered, concentrated and purified by flash chromatography to provide the title product (77 mg, 33%). 1H NMR (400 MHz, CDCl3) δ 7.25 (m, 1H), 7.22 (s, 1H), 7.16-7.11 (m, 2H), 7.03 (d, 1H), 6.91 (m, 1H), 6.83 (dd, 1H), 6.78 (t, 2H), 6.34 (m, 2H), 4.25 (s, 2H), 1.49 (s, 6H); MS (EI) m/z 523, 525 (MH+).
Reaction SMILES: [F:1][C:2]1[CH:9]=[CH:8][C:5]([NH:6][CH3:7])=[CH:4][CH:3]=1.FC(F)(F)S(O[C:16]1[C:17]2[CH2:37][N:36]([C:38](=[O:40])[CH3:39])[CH2:35][CH2:34][C:18]=2[N:19]=[C:20]([NH:22][C:23]2[CH:28]=[CH:27][C:26]([C:29]3[O:33][CH:32]=[N:31][CH:30]=3)=[CH:25][CH:24]=2)[N:21]=1)(=O)=O.S(C1C=CC(C)=CC=1)([O-])(=O)=O>>[F:1][C:2]1[CH:9]=[CH:8][C:5]([N:6]([CH3:7])[C:16]2[C:17]3[CH2:37][N:36]([C:38](=[O:40])[CH3:39])[CH2:35][CH2:34][C:18]=3[N:19]=[C:20]([NH:22][C:23]3[CH:28]=[CH:27][C:26]([C:29]4[O:33][CH:32]=[N:31][CH:30]=4)=[CH:25][CH:24]=3)[N:21]=2)=[CH:4][CH:3]=1
Reactant: CC(=O)N1CCc2nc(Nc3ccc(-c4cnco4)cc3)nc(OS(=O)(=O)C(F)(F)F)c2C1
Reactant: CNc1ccc(F)cc1
Agent: Cc1ccc(S(=O)(=O)[O-])cc1
Product: CC(=O)N1CCc2nc(Nc3ccc(-c4cnco4)cc3)nc(N(C)c3ccc(F)cc3)c2C1
Yield: 18 %

Procedure:
1-(4-((4-fluorophenyl)(methyl)amino)-2-(4-(oxazol-5-yl)phenylamino)-7,8-dihydropyrido[4,3-d]pyrimidin-6(5H)-yl)ethanone (15 mg, 18%) was prepared from 4-fluoro-N-methylaniline and 6-acetyl-2-(4-(oxazol-5-yl)phenylamino)-5,6,7,8-tetrahydropyrido[4,3-d]pyrimidin-4-yl trifluoromethanesulfonate (example 88a) according to the general procedure for amine substitution of tosylate on pyrimidines.
Reaction SMILES: [C:1]([CH2:3][CH2:4][C:5]1[C:6](OS(C(F)(F)F)(=O)=O)=[N:7][CH:8]=[C:9]([CH:14]=1)[C:10]([O:12][CH3:13])=[O:11])#[N:2].[F:23][C:24]1[CH:29]=[CH:28][C:27]([O:30][CH3:31])=[CH:26][C:25]=1B(O)O.C(=O)([O-])[O-].[Na+].[Na+]>C1C=CC([P]([Pd]([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)[P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1.C1(C)C=CC=CC=1>[C:1]([CH2:3][CH2:4][C:5]1[C:6]([C:25]2[CH:26]=[C:27]([O:30][CH3:31])[CH:28]=[CH:29][C:24]=2[F:23])=[N:7][CH:8]=[C:9]([CH:14]=1)[C:10]([O:12][CH3:13])=[O:11])#[N:2]
Reactant: COc1ccc(F)c(B(O)O)c1
Reactant: COC(=O)c1cnc(OS(=O)(=O)C(F)(F)F)c(CCC#N)c1
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: Cc1ccccc1
Product: COC(=O)c1cnc(-c2cc(OC)ccc2F)c(CCC#N)c1
Temperature: 90 °C
Reaction time: 1 h
Yield: 97.6 %

Procedure:
Under a nitrogen atmosphere, to a mixture of methyl 5-(2-cyanoethyl)-6-(((trifluoromethyl)sulfonyl)oxy)nicotinate (700 mg), 2-fluoro-5-methoxyphenylboronic acid (700 mg), tetrakis(triphenylphosphine)palladium (237 mg) and toluene (10 mL) was added 2 M aqueous sodium carbonate solution (3.1 mL), and the mixture was stirred at 90° C. for 1 hr. The reaction mixture was filtered, and the filtrate was diluted with ethyl acetate and THF. The diluted solution was washed with water and saturated brine, and dried over anhydrous sodium sulfate. The solvent was evaporated under reduced pressure and the residue was purified by silica gel column chromatography (ethyl acetate/hexane) to give the title compound (635 mg) as a colorless oil.
Reaction SMILES: [H-].[Al+3].[Li+].[H-].[H-].[H-].[CH3:7][O:8][C:9]1[CH:10]=[C:11]([CH:16]=[C:17]([N+:19]([O-:21])=[O:20])[CH:18]=1)[C:12](OC)=[O:13]>CCOCC>[CH3:7][O:8][C:9]1[CH:10]=[C:11]([CH2:12][OH:13])[CH:16]=[C:17]([N+:19]([O-:21])=[O:20])[CH:18]=1
Reactant: COC(=O)c1cc(OC)cc([N+](=O)[O-])c1
Agent: [Al+3]
Agent: [H-]
Agent: [Li+]
Solvent: CCOCC
Product: COc1cc(CO)cc([N+](=O)[O-])c1
Reaction time: 8 h
Yield: 67.9 %

Procedure:
Lithium aluminum hydride (0.1116 g, 2.94 mmol, 1.5 eq) was added to a stirred solution of methyl 3-methoxy-5-nitrobenzoate (0.408 g, 1.96 mmol, 1 eq) in 10 ml anhydrous Et2O at 0° C. under Ar. The reaction was stirred at 0° C. to room temperature overnight. Starting material was still present after stirring overnight. Additional LAH (0.1116 g, 2.94 mmol, 1.5 eq) was added. After 2 h the reaction was quenched with water. The reaction was diluted with saturated aqueous NaHCO3 and extracted with EtOAc (×2). The combined organics were washed with brine (×1) and dried over Na2SO4. The inorganics were filtered off, and the solvent was removed in vacuo. Purification via flash chromatography yielded 0.2463 g (1.33 mmol, 68% yield) of (3-methoxy-5-nitrophenyl)methanol.