Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [OH:1][CH2:2][CH2:3][O:4][C:5]1[CH:10]=[CH:9][C:8]([C:11]2[O:12][C:13]3[C:18]([C:19](=[O:25])[C:20]=2[O:21][CH2:22][O:23][CH3:24])=[CH:17][CH:16]=[C:15]([O:26][CH2:27][O:28][CH3:29])[CH:14]=3)=[CH:7][C:6]=1[O:30][CH2:31][O:32][CH3:33].CCN(C(C)C)C(C)C.[CH3:43][C:44]1[CH:49]=[CH:48][C:47]([S:50](Cl)(=[O:52])=[O:51])=[CH:46][CH:45]=1>CCOCC>[CH3:43][C:44]1[CH:49]=[CH:48][C:47]([S:50]([O:1][CH2:2][CH2:3][O:4][C:5]2[CH:10]=[CH:9][C:8]([C:11]3[O:12][C:13]4[C:18]([C:19](=[O:25])[C:20]=3[O:21][CH2:22][O:23][CH3:24])=[CH:17][CH:16]=[C:15]([O:26][CH2:27][O:28][CH3:29])[CH:14]=4)=[CH:7][C:6]=2[O:30][CH2:31][O:32][CH3:33])(=[O:52])=[O:51])=[CH:46][CH:45]=1
Reactant: Cc1ccc(S(=O)(=O)Cl)cc1
Reactant: COCOc1ccc2c(=O)c(OCOC)c(-c3ccc(OCCO)c(OCOC)c3)oc2c1
Solvent: CCN(C(C)C)C(C)C
Solvent: CCOCC
Product: COCOc1ccc2c(=O)c(OCOC)c(-c3ccc(OCCOS(=O)(=O)c4ccc(C)cc4)c(OCOC)c3)oc2c1
Temperature: 25 °C
Reaction time: 15 h

Procedure:
To 2-(4-(2-hydroxyethoxy)-3-(methoxymethoxy)phenyl)-3,7-bis(methoxymethoxy)-4H-chromen-4-one (18 mg, 0.039 mmol) and DIPEA (15 mg, 0.11 mmol) was added 4-methylbenzene-1-sulfonyl chloride (11 mg, 0.058 mmol). The mixture was stirred at rt for 15 h under Ar atmosphere and diluted with ether (30 mL). It was washed with 0.5 M HCl(2×30 mL) and water (50 mL), and dried over MgSO4 and concentrated. The crude product was chromatographed to afford 2-(4-(3,7-bis(methoxymethoxy)-4-oxo-4H-chromen-2-yl)-2-(methoxymethoxy)phenoxy)ethyl 4-methylbenzenesulfonate (AD-C-001P-WZ01079) as a yellow wax (20 mg, 83%). 1H NMR (400 MHz, CDCl3) δ 8.15 (dd, J=8.8, 2.0 Hz, 1H), 7.89 (d, J=2.0 Hz, 1H), 7.76 (dd, J=8.4 Hz, 2.0 Hz, 2H), 7.73 (dd, J=8.4, 2.0 Hz, 1H), 7.36 (d, J=6.8 Hz, 2H), 7.27 (d, J=2.0 Hz, 1H), 7.14 (d, J=2.4 Hz, 1H), 7.05 (dd, J=8.8, 2.0 Hz, 1H), 6.94 (dd, J=8.8, 2.0 Hz, 1H), 5.29 (d, J=1.6 Hz, 2H), 5.22 (d, J=2.0 Hz, 4H), 4.42 (t, J=3.0 Hz, 2H), 4.32 (t, J=3.0 Hz, 2H), 3.53 (d, J=2.4 Hz, 3H), 3.52 (d, J=2.0 Hz, 3H), 3.20 (d, J=2.4 Hz, 3H), 2.46 (s, 3H); MS (ESI) m/z 617 (M+H+).
Reaction SMILES: [NH2:1][C:2]1[C:3]([C:10](/[N:12]=[C:13]2/[NH:14][C:15]3([CH2:22][CH2:21][N:20]([C:23]([C:25]4[CH:26]=[C:27]([S:31]([NH:34][CH2:35][CH2:36][C:37]([OH:39])=[O:38])(=[O:33])=[O:32])[CH:28]=[CH:29][CH:30]=4)=[O:24])[CH2:19][CH2:18]3)[CH2:16][NH:17]/2)=[O:11])=[N:4][C:5]([Cl:9])=[C:6]([NH2:8])[N:7]=1.C(N(CC)C(C)C)(C)C.CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.O[CH2:74][C:75]([N:77]1[CH2:81][CH2:80][CH2:79][CH:78]1[C:82]([F:85])([F:84])[F:83])=[O:76]>CN(C=O)C>[O:76]=[C:75]([N:77]1[CH2:81][CH2:80][CH2:79][CH:78]1[C:82]([F:85])([F:83])[F:84])[CH2:74][O:38][C:37](=[O:39])[CH2:36][CH2:35][NH:34][S:31]([C:27]1[CH:28]=[CH:29][CH:30]=[C:25]([C:23]([N:20]2[CH2:21][CH2:22][C:15]3([NH:14]/[C:13](=[N:12]/[C:10]([C:3]4[C:2]([NH2:1])=[N:7][C:6]([NH2:8])=[C:5]([Cl:9])[N:4]=4)=[O:11])/[NH:17][CH2:16]3)[CH2:18][CH2:19]2)=[O:24])[CH:26]=1)(=[O:32])=[O:33]
Reactant: O=C(CO)N1CCCC1C(F)(F)F
Reactant: Nc1nc(N)c(C(=O)/N=C2\NCC3(CCN(C(=O)c4cccc(S(=O)(=O)NCCC(=O)O)c4)CC3)N2)nc1Cl
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: Nc1nc(N)c(C(=O)/N=C2\NCC3(CCN(C(=O)c4cccc(S(=O)(=O)NCCC(=O)OCC(=O)N5CCCC5C(F)(F)F)c4)CC3)N2)nc1Cl
Temperature: 25 °C
Reaction time: 0.25 h

Procedure:
To a stirred solution of 3-(3-{2-[(E)-3,5-Diamino-6-chloro-pyrazine-2-carbonylimino]-1,3,8-triaza-spiro[4.5]decane-8-carbonyl}-benzenesulfonylamino)-propionic acid (step 2) (400 mg, 0.690 mmol) and N,N-diisopropylethylamine (357 mg, 2.76 mmol) in DMF (4 ml) was added HATU (262 mg, 0.690 mmol). The solution was stirred at RT for 15 min, after which time 2-hydroxy-1-(2-(trifluoromethyl)pyrrolidin-1-yl)ethanone (Int. D) (262 mg, 0.690 mmol) in DMF (2 ml) was added. The resulting solution was stirred at RT for 6 days, after which time it was poured onto water (10 ml). A white precipitate formed which was collected by filtration, and washed with iso-hexane (20 ml), and purified by C18 reverse phase chromatography eluting with MeCN/water/0.1% TFA to afford the title product; 1H NMR (400 MHz, DMSO-d6) δ 11.03 (1H, s), 9.37 (1H, s), 9.02 (1H, s), 7.92-7.29 (4H, m), 7.24 (14N, s) 7.12 (14N,s), 6.96 (14N,s), 4.95-3.90 (11H, m), 3.66 (2H, t), 3.41 (2H, t), 3.35 (2H, m), 3.07 (2H, t) 2.20-1.61 (7H, m); LC-MS Rt 0.91 mins; 759.0 [M+H]+, Method 2minLC_v003.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[S:8]([C@H:11]1[CH2:15][NH:14][C@H:13]([C:16]([NH:18][C:19]2([C:22]#[N:23])[CH2:21][CH2:20]2)=[O:17])[CH2:12]1)(=[O:10])=[O:9].[S:24]1[CH2:29][CH2:28][CH:27]([N:30]2[CH2:33][CH2:32][CH:31]2[C:34]([O-])=[O:35])[CH2:26][CH2:25]1.[Li+]>>[Cl:1][C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[S:8]([C@H:11]1[CH2:15][N:14]([C:34]([CH:31]2[CH2:32][CH2:33][N:30]2[CH:27]2[CH2:26][CH2:25][S:24][CH2:29][CH2:28]2)=[O:35])[C@H:13]([C:16]([NH:18][C:19]2([C:22]#[N:23])[CH2:21][CH2:20]2)=[O:17])[CH2:12]1)(=[O:10])=[O:9]
Reactant: N#CC1(NC(=O)[C@@H]2C[C@@H](S(=O)(=O)c3ccccc3Cl)CN2)CC1
Reactant: O=C([O-])C1CCN1C1CCSCC1
Agent: [Li+]
Product: N#CC1(NC(=O)[C@@H]2C[C@@H](S(=O)(=O)c3ccccc3Cl)CN2C(=O)C2CCN2C2CCSCC2)CC1

Procedure:
The reaction of (2S,4R)-4-(2-chlorophenylsulfonyl)-N-(1-cyanocyclopropyl)pyrrolidine-2-carboxamide 7H and lithium 1-(tetrahydro-2H-thiopyran-4-yl)azetidine-2-carboxylate 20J carried out according to the general procedure L yielded (2S,4R)-4-(2-chlorophenylsulfonyl)-N-(1-cyanocyclopropyl)-1-(1-(tetrahydro-2H-thiopyran-4-yl)azetidine-2-carbonyl)pyrrolidine-2-carboxamide 1:1 epimers as a light brown solid (quant.). MS ISP (m/e): 537.3 (100) [(M+H)]]+.
Reaction SMILES: [OH:1][C:2]1[CH:9]=[CH:8][C:7]([O:10][CH3:11])=[CH:6][C:3]=1[CH:4]=[O:5].C([O-])(=O)C.[Na+].[Br:17]Br.S([O-])([O-])(=O)=S.[Na+].[Na+]>C(O)(=O)C>[Br:17][C:9]1[C:2]([OH:1])=[C:3]([CH:6]=[C:7]([O:10][CH3:11])[CH:8]=1)[CH:4]=[O:5]
Reactant: BrBr
Reactant: COc1ccc(O)c(C=O)c1
Agent: CC(=O)[O-]
Agent: O=S([O-])([O-])=S
Agent: [Na+]
Solvent: CC(=O)O
Product: COc1cc(Br)c(O)c(C=O)c1
Temperature: 25 °C
Reaction time: 2 h
Yield: 59.9 %

Procedure:
To 2-hydroxy-5-methoxybenzaldehyde (4.1 mL, 32.86 mmol) in acetic acid (150 mL) were added sodium acetate (4.0 g, 49.3 mmol) and bromine (2.2 mL, 42.7 mmol) and the mixture was stirred at rt for 2 h. Aqueous sodium thiosulfate was added and the mixture was concentrated by rotary evaporation. The solid was dissolved in dichloromethane and washed with water. The organic phase was separated, dried over MgSO4, filtered and the solvent removed by rotary evaporation. The solid residue was recrystallized from ethanol to yield 3-bromo-2-hydroxy-5-methoxybenzaldehyde (4.55 g, 60%).
Reaction SMILES: [ClH:1].C([O:9][C:10]1[CH:15]=[CH:14][C:13]([CH:16]([OH:24])[CH2:17][O:18][CH2:19][CH2:20][N:21]([CH3:23])[CH3:22])=[CH:12][CH:11]=1)C1C=CC=CC=1>[C].[Pd].CO>[ClH:1].[OH:9][C:10]1[CH:11]=[CH:12][C:13]([CH:16]([OH:24])[CH2:17][O:18][CH2:19][CH2:20][N:21]([CH3:22])[CH3:23])=[CH:14][CH:15]=1
Reactant: CN(C)CCOCC(O)c1ccc(OCc2ccccc2)cc1
Agent: [Pd]
Agent: Cl
Solvent: CO
Product: CN(C)CCOCC(O)c1ccc(O)cc1
Reaction time: 2 h
Yield: 94.1 %

Procedure:
A mixture of 2.0 g of 1-(4-benzyloxyphenyl)-2-[2-(N,N-dimethylamino)ethoxy]ethanol hydrochloride, 500 mg of 10% palladium-carbon and 10 ml of methanol was subjected to hydrogenation for 2 hours at room temperature under atmospheric pressure. After the completion of the reaction, palladium-carbon was removed by filtration. The solvent was removed by distillation under reduced pressure to obtain 1.4 g of 1-(4-hydroxyphenyl)-2-[2-(N,N-dimethylamino)ethoxy]ethanol hydrochloride (Compound No. 170).
Reaction SMILES: C([N:8]1[CH2:13][CH2:12][C:11]([CH2:15][C:16]2[CH:21]=[CH:20][CH:19]=[CH:18][C:17]=2[F:22])([OH:14])[CH2:10][CH2:9]1)C1C=CC=CC=1>C(OCC)(=O)C.[Pd]>[F:22][C:17]1[CH:18]=[CH:19][CH:20]=[CH:21][C:16]=1[CH2:15][C:11]1([OH:14])[CH2:10][CH2:9][NH:8][CH2:13][CH2:12]1
Reactant: OC1(Cc2ccccc2F)CCN(Cc2ccccc2)CC1
Agent: [Pd]
Solvent: CCOC(C)=O
Product: OC1(Cc2ccccc2F)CCNCC1

Procedure:
A solution of EXAMPLE 1A (39.0 g, 131 mmol) in ethyl acetate (500 mL) was treated with Pd/C (3.90 g), stirred under hydrogen atmosphere (60 psi) until the reaction was complete by TLC analysis, and filtered. The filtrate was concentrated to give a residue that was used without further purification. MS (ESI) m/e 210 (M+H)+.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[CH:4][C:5]([N:17]([CH2:30][C:31]([O:33][CH3:34])=[O:32])[S:18]([C:21]2[CH:26]=[CH:25][C:24]([N+:27]([O-])=O)=[CH:23][CH:22]=2)(=[O:20])=[O:19])=[C:6]([CH:16]=1)[C:7]([C:9]1[CH:14]=[CH:13][CH:12]=[CH:11][C:10]=1[F:15])=[O:8].CO>C(OCC)(=O)C.[Pd]>[Cl:1][C:2]1[CH:3]=[CH:4][C:5]([N:17]([CH2:30][C:31]([O:33][CH3:34])=[O:32])[S:18]([C:21]2[CH:26]=[CH:25][C:24]([NH2:27])=[CH:23][CH:22]=2)(=[O:19])=[O:20])=[C:6]([CH:16]=1)[C:7]([C:9]1[CH:14]=[CH:13][CH:12]=[CH:11][C:10]=1[F:15])=[O:8]
Reactant: COC(=O)CN(c1ccc(Cl)cc1C(=O)c1ccccc1F)S(=O)(=O)c1ccc([N+](=O)[O-])cc1
Agent: [Pd]
Solvent: CO
Solvent: CCOC(C)=O
Product: COC(=O)CN(c1ccc(Cl)cc1C(=O)c1ccccc1F)S(=O)(=O)c1ccc(N)cc1

Procedure:
The 5-chloro-2'-fluoro-2-[N-(methoxycarbonyl-methyl)-N-(4-nitrophenylsulfonyl)amino]benzophenone prepared in Example 2, step b, is dissolved in 100 ml of ethyl acetate and 5 ml of methanol and hydrogenated at ordinary pressure for 2 hours in the presence of 620 mg of 10% palladium-on-charcoal; the existence of 3 compounds (starting material, intermediate and expected product) is observed in TLC. The catalyst is filtered off, the solvent is evaporated off and the residue is chromatographed on silica gel. The expected compound is eluted with DCM containing 1% of methanol. After recrystallization from DCM/isopropyl ether, m.p.=168°-170° C.
Reaction SMILES: [N:1]([C@@H:4]1[C:9]([F:11])([F:10])[CH2:8][CH2:7][CH2:6][C@H:5]1[NH:12][C:13](=[O:19])[O:14][C:15]([CH3:18])([CH3:17])[CH3:16])=[N+]=[N-]>CO>[NH2:1][C@@H:4]1[C:9]([F:11])([F:10])[CH2:8][CH2:7][CH2:6][C@H:5]1[NH:12][C:13](=[O:19])[O:14][C:15]([CH3:17])([CH3:16])[CH3:18]
Reactant: CC(C)(C)OC(=O)N[C@@H]1CCCC(F)(F)[C@H]1N=[N+]=[N-]
Solvent: CO
Product: CC(C)(C)OC(=O)N[C@@H]1CCCC(F)(F)[C@H]1N
Reaction time: 48 h
Yield: 96.5 %

Procedure:
To a clean dry 1 L RBF charged with tert-butyl [(1R,2S)-2-azido-3,3-difluorocyclohexyl]carbamate 27 (18.84 g, 68.2 mmol) was added 400 mL methanol. The system was degassed and purged (3× with N2) before the addition of Pd/C (1.45 g). The reaction was stirred for 2 d under 1 atm of hydrogen. Upon reaction completion, the reaction was filtered through a plug of celite and concentrated to dryness to yield tert-butyl [(1R,2S)-2-amino-3,3-difluorocyclohexyl]carbamate 30 (16.47 g, 97% yield) as a pure white solid. 1H NMR (CDCl3, 500 MHz) 4.76-4.74 (1H, d, J=10 Hz), 3.61-3.56 (1H, m), 2.63-2.59 (1H, dd 0.1-9.5 Hz), 2.2-2.0 (2H, m), 1.8-1.68, (2H, m), 1.53-1.42 (11H, m), 1.29-1.21 (m, 2H); 19F NMR (CDCl3, 564 MHz) −101.7-−102.1 (1F, J=241 Hz), −114.3-−114.9 (1F, m)
Reaction SMILES: [C:1](N1C=CC=CC1=O)(N1C=CC=CC1=O)=[S:2].[Br:17][C:18]1[CH:19]=[C:20]2[C:25](=[CH:26][CH:27]=1)[CH:24]=[N:23][C:22]([NH2:28])=[CH:21]2>ClCCl>[Br:17][C:18]1[CH:19]=[C:20]2[C:25](=[CH:26][CH:27]=1)[CH:24]=[N:23][C:22]([N:28]=[C:1]=[S:2])=[CH:21]2
Reactant: O=c1ccccn1C(=S)n1ccccc1=O
Reactant: Nc1cc2cc(Br)ccc2cn1
Solvent: ClCCl
Product: S=C=Nc1cc2cc(Br)ccc2cn1
Temperature: 25 °C
Reaction time: 3 h

Procedure:
To a solution of 1,1′-thiocarbonyldipyridin-2(1H)-one (0.251 g, 1.080 mmol) in dichloromethane at room temperature was added 6-bromoisoquinolin-3-amine (0.241 g, 1.080 mmol). The solution was stirred at room temperature for 3 hours. LC/MS indicated formation of the desired product. The deep orange solution was purified by silica gel chromatography (0-10% ethyl acetate-hexanes) to afford: 6-bromo-3-isothiocyanatoisoquinoline (0.1 g, 0.377 mmol, 35% yield) as a yellow oil. R.T.=2.54; [M+H]+=267.04.
Reaction SMILES: [CH2:1]([O:8][C:9]1[CH:10]=[C:11]([CH:18]=[CH:19][C:20]2[N:21]=[C:22]3[CH:27]=[C:26]([CH3:28])[CH:25]=[CH:24][N:23]3[CH:29]=2)[CH:12]=[CH:13][C:14]=1[N+:15]([O-:17])=[O:16])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.P(Cl)(Cl)(Cl)=O.CN(C)[CH:37]=[O:38]>>[CH2:1]([O:8][C:9]1[CH:10]=[C:11]([CH:18]=[CH:19][C:20]2[N:21]=[C:22]3[CH:27]=[C:26]([CH3:28])[CH:25]=[CH:24][N:23]3[C:29]=2[CH:37]=[O:38])[CH:12]=[CH:13][C:14]=1[N+:15]([O-:17])=[O:16])[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: CN(C)C=O
Reactant: Cc1ccn2cc(C=Cc3ccc([N+](=O)[O-])c(OCc4ccccc4)c3)nc2c1
Solvent: O=P(Cl)(Cl)Cl
Product: Cc1ccn2c(C=O)c(C=Cc3ccc([N+](=O)[O-])c(OCc4ccccc4)c3)nc2c1

Procedure:
A solution of 2-[2-(3-benzyloxy-4-nitrophenyl)vinyl]-7-methylimidazo[1,2-a]pyridine (9.00 g) in N,N-dimethylformamide (50 ml), was added dropwise to a solution of phosphorus oxychloride (6.36 ml) in N,N-dimethylformamide (90 ml) at ambient temperature with stirring. After the mixture was stirred for 6 hours, the solvent was evaporated in vacuo. The residue was mixed with water (200 ml) and dichloromethane (300 ml) and made basic with aqueous potassium carbonate. The resulting precipitate was collected, washed with water and recrystallized from a mixture of methanol, chloroform and dioxane to give 2-[2-(3-benzyloxy-4-nitrophenyl)vinyl]-3-formyl-7-methylimidazo[1,2-a]pyridine (5.15 g).
Reaction SMILES: [N:1]1[CH:6]=[CH:5][C:4]([C:7](=[N:10][OH:11])[CH2:8][CH3:9])=[CH:3][CH:2]=1.[Li+].CC([N-]C(C)C)C.[C:20]([O:27][CH2:28][CH3:29])(=[O:26])[C:21]([O:23]CC)=O>C1COCC1>[OH:11][N:10]=[C:7]([C:4]1[CH:3]=[CH:2][N:1]=[CH:6][CH:5]=1)[CH:8]([CH3:9])[C:21](=[O:23])[C:20]([O:27][CH2:28][CH3:29])=[O:26]
Reactant: CCC(=NO)c1ccncc1
Reactant: CCOC(=O)C(=O)OCC
Agent: CC(C)[N-]C(C)C
Agent: [Li+]
Solvent: C1CCOC1
Product: CCOC(=O)C(=O)C(C)C(=NO)c1ccncc1
Temperature: 0 °C
Reaction time: 1.5 h
Yield: 60 %

Procedure:
1-(Pyridin-4-yl)propan-1-one oxime (5.3 g, 35.3 mmol) was dissolved in 120 mL of THF and cooled to 0° C. LDA solution (41 mL, 81.3 mmol, 2M in heptane/THF/ethyl benzene) was added dropwise, and the reaction mixture was stirred at 0° C. for 1.5 hour and then warmed to room temperature. The mixture was then transferred to a syringe and added dropwise to a flask containing a pre-cooled mixture of diethyl oxalate (24 mL, 177 mmol) and THF (100 mL) at 0° C. After the addition was complete, the reaction mixture was stirred at room temperature for 18 hours. The mixture was cooled in an ice bath and quenched with 150 mL of 10% hydrochloric acid. EtOAc (150 mL) was added and solid NaHCO3 was added with vigorous stirring the aqueous layer was basic (pH>8). The aqueous layer was extracted with additional EtOAc and the combined organic layer was dried over MgSO4 and concentrated. The crude product was purified by chromatography (10-60% EtOAc/hexanes) to give 5.3 g of the title compound. MS: (+) m/z 251.43 (M+1).
Reaction SMILES: COC1C=CC(C[N:8]2[C:16]3[CH:15]=[CH:14][N:13]=[C:12]([NH:17][CH:18]4[CH2:23][CH2:22][O:21][CH2:20][CH2:19]4)[C:11]=3[C:10]([O:24][C:25]3[CH:30]=[CH:29][CH:28]=[CH:27][CH:26]=3)=[N:9]2)=CC=1.FC(F)(F)S(O)(=O)=O>C(Cl)Cl>[O:24]([C:10]1[C:11]2[C:12]([NH:17][CH:18]3[CH2:23][CH2:22][O:21][CH2:20][CH2:19]3)=[N:13][CH:14]=[CH:15][C:16]=2[NH:8][N:9]=1)[C:25]1[CH:26]=[CH:27][CH:28]=[CH:29][CH:30]=1
Reactant: COc1ccc(Cn2nc(Oc3ccccc3)c3c(NC4CCOCC4)nccc32)cc1
Agent: O=S(=O)(O)C(F)(F)F
Solvent: ClCCl
Product: c1ccc(Oc2n[nH]c3ccnc(NC4CCOCC4)c23)cc1
Temperature: 25 °C
Reaction time: 2 h

Procedure:
The crude 1-(4-methoxybenzyl)-3-phenoxy-N-(tetrahydro-2H-pyran-4-yl)-1H-pyrazolo[4,3-c]pyridin-4-amine from step 1 was added to methylene chloride (5 mL) and trifluoromethanesulfonic acid (0.5 mL), and the resulting mixture was stirred at room temperature for two hours. The mixture was concentrated under reduced pressure and the residue was purified by reverse phase HPLC to give 3-phenoxy-N-(tetrahydro-2H-pyran-4-yl)-1H-pyrazolo[4,3-c]pyridin-4-amine: LC-MS (Method G): m/z=311.1; 1H NMR (400 MHz, DMSO): δ 12.43 (s, 1H), 7.73 (d, J=6.1, 1H), 7.42 (t, J=7.9, 2H), 7.26 (d, J=8.0, 2H), 7.19 (t, J=7.3, 1H), 6.60 (d, J=6.1, 1H), 5.43 (d, J=7.7, 1H), 4.19 (m, 1H), 3.79 (d, J=11.6, 2H, 1.83 (d, J=12.4, 2H), 1.43 (m, 2H).
Reaction SMILES: [CH2:1]([C:5]1([CH2:19][CH2:20][CH2:21][CH:22]=[CH2:23])[CH2:13][C:12]2[C:7](=[CH:8][CH:9]=[C:10]([O:14][CH2:15][O:16][CH3:17])[CH:11]=2)[C:6]1=[O:18])[CH2:2][CH2:3][CH3:4].[CH2:24]([Mg]Br)[CH:25]=[CH2:26]>O1CCCC1>[CH2:1]([C:5]1([CH2:19][CH2:20][CH2:21][CH:22]=[CH2:23])[CH2:13][C:12]2[C:7](=[CH:8][CH:9]=[C:10]([O:14][CH2:15][O:16][CH3:17])[CH:11]=2)[C:6]1([C:25]([CH3:26])=[CH2:24])[OH:18])[CH2:2][CH2:3][CH3:4]
Reactant: C=CC[Mg]Br
Reactant: C=CCCCC1(CCCC)Cc2cc(OCOC)ccc2C1=O
Solvent: C1CCOC1
Product: C=CCCCC1(CCCC)Cc2cc(OCOC)ccc2C1(O)C(=C)C
Temperature: 25 °C

Procedure:
A solution of 2-butyl-5-(methoxymethoxy)-2-(4-pentenyl)-1-indanone (400 mg, 1.27 mmol) in anhydrous tetrahydrofuran (THF, 5 mL) was placed under a N2 atmosphere, cooled in a dry ice-acetone bath, stirred, and treated with 2-propenyl magnesium bromide, (1M in THF, 1.9 mL, 1.9 mmol). After warming to room temperature, the mixture was treated with additional 2-propenyl magnesium bromide (1M in THF, 6 mL, 6 mmol) and stirred at room temperature overnight. The mixture was quenched with saturated aqueous NH4Cl, dried over MgSO4, filtered through a pad of silica, and concentrated under vacuum to afford an oil. The crude product was purified by Biotage™ (Charlottesville, Va.) flash chromatography on a 40S (4.0×7.0 cm) silica gel column, eluting with 19:1 hexanes-EtOAc. The product-containing fractions were evaporated under vacuum to afford 2-butyl-1-isopropenyl-5-(methoxymethoxy)-2-(4-pentenyl)-1-indanol as an oil.
Reaction SMILES: [NH2:1][C:2]1[C:3]2[C:10]([C:11]3[CH:16]=[CH:15][C:14]([O:17][C:18]4[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=4)=[CH:13][CH:12]=3)=[C:9](F)[N:8]([C@@H:25]3[CH2:29][CH2:28][N:27]([C:30]([O:32][C:33]([CH3:36])([CH3:35])[CH3:34])=[O:31])[CH2:26]3)[C:4]=2[N:5]=[CH:6][N:7]=1.[CH3:37][O:38][Na]>CO>[NH2:1][C:2]1[C:3]2[C:10]([C:11]3[CH:16]=[CH:15][C:14]([O:17][C:18]4[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=4)=[CH:13][CH:12]=3)=[C:9]([O:38][CH3:37])[N:8]([C@@H:25]3[CH2:29][CH2:28][N:27]([C:30]([O:32][C:33]([CH3:36])([CH3:35])[CH3:34])=[O:31])[CH2:26]3)[C:4]=2[N:5]=[CH:6][N:7]=1
Reactant: CO[Na]
Reactant: CC(C)(C)OC(=O)N1CC[C@@H](n2c(F)c(-c3ccc(Oc4ccccc4)cc3)c3c(N)ncnc32)C1
Solvent: CO
Product: COc1c(-c2ccc(Oc3ccccc3)cc2)c2c(N)ncnc2n1[C@@H]1CCN(C(=O)OC(C)(C)C)C1
Yield: 90 %

Procedure:
To a solution of (R)-tert-butyl 3-(4-amino-6-fluoro-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)pyrrolidine-1-carboxylate (3) (250 mg, 0.51 mmol) in MeOH was added MeONa. The resulting mixture was heated to reflux under N2 overnight. After cooling down to r. t., the reaction mixture was concentrated and the residue was partitioned between DCM and water. The layers were separated. The organic phase was washed with brine, dried over Na2SO4 and concentrated under reduced pressure to give (R)-tert-butyl 3-(4-amino-6-methoxy-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)pyrrolidine-1-carboxylate (87) (230 mg, 90% yield) as a yellow solid. LC-MS (ESI): m/z (M+1) 502.1.
Reaction SMILES: [Cl:1][C:2]1[N:7]=[C:6]([S:8][C:9]2[CH:10]=[C:11]([NH2:15])[CH:12]=[CH:13][CH:14]=2)[CH:5]=[CH:4][N:3]=1.[C:16](O)(=[O:19])[CH:17]=[CH2:18]>>[Cl:1][C:2]1[N:7]=[C:6]([S:8][C:9]2[CH:10]=[C:11]([NH:15][C:16](=[O:19])[CH:17]=[CH2:18])[CH:12]=[CH:13][CH:14]=2)[CH:5]=[CH:4][N:3]=1
Reactant: C=CC(=O)O
Reactant: Nc1cccc(Sc2ccnc(Cl)n2)c1
Product: C=CC(=O)Nc1cccc(Sc2ccnc(Cl)n2)c1
Yield: 68 %

Procedure:
In a procedure analogous to Example 15, reaction of 3-(2-chloropyrimidin-4-ylthio)benzenamine (300 mg, 1.26 mmol) and acrylic acid (173 μL, 2.52 mmol) furnished the product (250 mg, 68%).
Reaction SMILES: [CH3:1][O:2][CH2:3][CH2:4][O:5][C:6]1[CH:7]=[C:8]2[CH:14]=[C:13]([C:15]([OH:17])=O)[NH:12][C:9]2=[CH:10][N:11]=1.Cl.Cl.[CH:20]([N:23]1[CH2:28][CH2:27][CH:26]([NH2:29])[CH2:25][CH2:24]1)([CH3:22])[CH3:21].CN(C=O)C.CCN(C(C)C)C(C)C>>[CH:20]([N:23]1[CH2:28][CH2:27][CH:26]([NH:29][C:15]([C:13]2[NH:12][C:9]3=[CH:10][N:11]=[C:6]([O:5][CH2:4][CH2:3][O:2][CH3:1])[CH:7]=[C:8]3[CH:14]=2)=[O:17])[CH2:25][CH2:24]1)([CH3:22])[CH3:21]
Reactant: CC(C)N1CCC(N)CC1
Reactant: COCCOc1cc2cc(C(=O)O)[nH]c2cn1
Agent: Cl
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: COCCOc1cc2cc(C(=O)NC3CCN(C(C)C)CC3)[nH]c2cn1
Temperature: 25 °C
Reaction time: 4 h

Procedure:
To a solution of 820 mg (3.47 mmol) of 5-(2-Methoxy-ethoxy)-1H-pyrrolo[2,3-c]pyridine-2-carboxylic acid and 745 mg (3.47 mmol) 1-isopropyl-piperidin-4-ylamine dihydrochloride in 30 mL absolute DMF 1.13 g (3.47 mmol) TOTU and 1.81 mL (10.41 mmol) DIPEA were added and the mixture was stirred for 4 h at room temperature. The solvent was removed in vacuo, the residue dissolved in CH2Cl2 and the CH2Cl2 phase washed with a saturated NaHCO3 solution. The organic phase was concentrated and the residue purified by chromatography over silica gel using CH2Cl2/MeOH/HOAc/H2O=90/10/1/1 as eluent. The fractions containing the product were combined and concentrated. The residue was dissolved in CH2Cl2 and the CH2Cl2 phase was washed with a saturated NaHCO3 solution. The phases were separated and the organic phase dried over Na2SO4. After filtration the solvent was removed in vacuo. Yield: 461 mg.
Reaction SMILES: [CH2:1]([O:3][C:4](=[O:42])[CH2:5][C:6]1[CH:11]=[CH:10][CH:9]=[C:8]([O:12][C:13]2[CH:18]=[CH:17][C:16](B3OC(C)(C)C(C)(C)O3)=[CH:15][C:14]=2[CH2:28][N:29]2[C@@H:33]([CH3:34])[C@@H:32]([C:35]3[CH:40]=[CH:39][CH:38]=[CH:37][CH:36]=3)[O:31][C:30]2=[O:41])[CH:7]=1)[CH3:2].Br[C:44]1[NH:45][CH:46]=[C:47]([CH3:49])[N:48]=1>>[CH2:1]([O:3][C:4](=[O:42])[CH2:5][C:6]1[CH:11]=[CH:10][CH:9]=[C:8]([O:12][C:13]2[CH:18]=[CH:17][C:16]([C:44]3[NH:45][CH:46]=[C:47]([CH3:49])[N:48]=3)=[CH:15][C:14]=2[CH2:28][N:29]2[C@@H:33]([CH3:34])[C@@H:32]([C:35]3[CH:36]=[CH:37][CH:38]=[CH:39][CH:40]=3)[O:31][C:30]2=[O:41])[CH:7]=1)[CH3:2]
Reactant: Cc1c[nH]c(Br)n1
Reactant: CCOC(=O)Cc1cccc(Oc2ccc(B3OC(C)(C)C(C)(C)O3)cc2CN2C(=O)O[C@H](c3ccccc3)[C@@H]2C)c1
Product: CCOC(=O)Cc1cccc(Oc2ccc(-c3nc(C)c[nH]3)cc2CN2C(=O)O[C@H](c3ccccc3)[C@@H]2C)c1

Procedure:
Prepared according to the procedure described in Example 19, Step 3, using the following starting materials: {3-[2-((4S,5R)-4-methyl-2-oxo-5-phenyl-oxazolidin-3-ylmethyl)-4-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-phenoxy]-phenyl}-acetic acid ethyl ester and 2-bromo-4-methyl-1H-imidazole.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4](/[CH:8]=[CH:9]/[CH2:10][CH2:11][N:12]2C(=O)C3=CC=CC=C3C2=O)[CH:5]=[CH:6][CH:7]=1.CN>C(O)C>[Cl:1][C:2]1[CH:3]=[C:4](/[CH:8]=[CH:9]/[CH2:10][CH2:11][NH2:12])[CH:5]=[CH:6][CH:7]=1
Reactant: O=C1c2ccccc2C(=O)N1CC/C=C/c1cccc(Cl)c1
Agent: CN
Solvent: CCO
Product: NCC/C=C/c1cccc(Cl)c1
Temperature: 25 °C
Yield: 68.6 %

Procedure:
A solution of trans-N-[4-(3-chlorophenyl)-but-3-enyl]-phthalimide (0.50 g) and methylamine (2 M in tetrahydrofuran, 8 mL) in 20 mL ethanol was heated to reflux for 4 h. The solution was cooled to rt and the solvent was removed in vacuo. The resulting residue was dissolved in ethyl acetate and extracted 3 times with 1 M hydrochloric acid. The combined acid layers were made basic with potassium hydroxide to pH 9 and extracted with ethyl acetate. The ethyl acetate layer was dried over sodium sulfate and the solvent was removed in vacuo to yield 0.20 g of trans-4-(3-chlorophenyl)-but-3-enylamine.