Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [N:1]([CH2:4][CH2:5][CH2:6][C:7]1[C:15]2[C:10](=[CH:11][CH:12]=[C:13]([Cl:16])[CH:14]=2)[NH:9][CH:8]=1)=[N+]=[N-].C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.O>C1COCC1>[Cl:16][C:13]1[CH:14]=[C:15]2[C:10](=[CH:11][CH:12]=1)[NH:9][CH:8]=[C:7]2[CH2:6][CH2:5][CH2:4][NH2:1]
Reactant: [N-]=[N+]=NCCCc1c[nH]c2ccc(Cl)cc12
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: C1CCOC1
Solvent: O
Product: NCCCc1c[nH]c2ccc(Cl)cc12
Temperature: 25 °C
Reaction time: 22 h
Yield: 33.6 %

Procedure:
To a solution of 3-(3-Azidopropyl)-5-chloro-1H-indole (0.299 g; 1.27 mmol) in THF (9 mL) were added triphenylphosphine (0.354 g; 1.34 mmol) and water (0.6 mL). The reaction mixture was stirred at room temperature for 22 hours and was then concentrated under reduced pressure. The residue was dissolved in dichloromethane (10 mL) and 10 mL of 6N hydrochloric acid were added. After separation, the aqueous layer was further extracted with dichloromethane (2×10 mL) and the pH was adjusted to 14 with an aqueous solution of sodium hydroxide 6N. This basic solution was extracted dichloromethane (3×20 mL) and the combined organic layer was dried over magnesium sulphate, and evaporated to afford 0.089 g (34%) of 3-(5-Chloro-1H-indol-3-yl)propan-1-amine as a white solid.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:8]=[CH:7][C:6]([S:9][CH2:10][CH2:11][NH:12][C:13](=[O:16])[CH:14]=[CH2:15])=[CH:5][CH:4]=1.C=O.[C:19]1(C)C=CC(S(O)(=O)=O)=CC=1>C1C=CC=CC=1>[CH3:1][O:2][C:3]1[CH:8]=[CH:7][C:6]2[S:9][CH2:10][CH2:11][N:12]([C:13](=[O:16])[CH:14]=[CH2:15])[CH2:19][C:5]=2[CH:4]=1
Reactant: Cc1ccc(S(=O)(=O)O)cc1
Reactant: C=CC(=O)NCCSc1ccc(OC)cc1
Agent: C=O
Solvent: c1ccccc1
Product: C=CC(=O)N1CCSc2ccc(OC)cc2C1
Temperature: 80 °C
Reaction time: 16 h

Procedure:
A mixture of compound 32 (280 mg), paraformaldehyde (600 mg), p-toluenesulfonic acid (140 mg) in benzene (7.0 mL) was stirred at 80° C. for 16 h. The reaction mixture was filtered and washed with sat. NaHCO3 solution (2×3 mL). The solvents were removed by evaporation under reduced pressure to give product 33 as an oil. Yield: 253 mg, 86%.
Reaction SMILES: [C:1]([N:4]1[CH2:9][CH2:8][CH:7](/[C:10](=[N:18]/[NH:19][S:20]([C:23]2[CH:28]=[CH:27][C:26]([CH3:29])=[CH:25][CH:24]=2)(=[O:22])=[O:21])/[CH2:11][C:12]2[CH:17]=[CH:16][N:15]=[CH:14][N:13]=2)[CH2:6][CH2:5]1)(=[O:3])[CH3:2].O1CCCC1.[Cl:35][C:36]1[CH:44]=[CH:43][C:39]([C:40](Cl)=O)=[CH:38][CH:37]=1>CN(C)C1C=CN=CC=1.C(N(CC)CC)C>[Cl:35][C:36]1[CH:44]=[CH:43][C:39]([C:40]2[N:19]([S:20]([C:23]3[CH:28]=[CH:27][C:26]([CH3:29])=[CH:25][CH:24]=3)(=[O:22])=[O:21])[N:18]=[C:10]([CH:7]3[CH2:8][CH2:9][N:4]([C:1](=[O:3])[CH3:2])[CH2:5][CH2:6]3)[C:11]=2[C:12]2[CH:17]=[CH:16][N:15]=[CH:14][N:13]=2)=[CH:38][CH:37]=1
Reactant: CC(=O)N1CCC(/C(Cc2ccncn2)=N/NS(=O)(=O)c2ccc(C)cc2)CC1
Reactant: O=C(Cl)c1ccc(Cl)cc1
Agent: CN(C)c1ccncc1
Solvent: CCN(CC)CC
Solvent: C1CCOC1
Product: CC(=O)N1CCC(c2nn(S(=O)(=O)c3ccc(C)cc3)c(-c3ccc(Cl)cc3)c2-c2ccncn2)CC1

Procedure:
This reaction was carried out in a 100 ml round bottom flask. N′-[(1E)-1-(1-acetylpiperidin-4-yl)-2-pyrimidin-4-ylethylidene]-4-methylbenzenesulfonohydrazide (7) (5g, 11 mmol) was charged to the reactor, followed by tetrahydrofuran (“THF”, 31 ml), which, in turn, was followed by 2.15 ml of triethylamine (“TEA”, 2.15 ml) and 4-dimethylaminopyridine (“DMAP”, 0.134 g). 4-Chlorobenzoyl chloride (8) (“4-CBC”, 2.09 ml) was then charged all at once while stirring the mixture. The reaction was brought to reflux. Liquid chromatography indicated that the reaction was complete in just over 1 hr. The solution was washed with saturated ammonium chloride (2×25 ml), and the THF was removed in vacuo to yield a yellow oil (11.18 g), which solidified upon sitting. Recrystallization from ethanol/water yielded 4.88 g of a white powder (76% yield). The product had the following characteristics: 1H NMR (CDCl3, 300 MHz) δ 9.20 (1H, s), 7.63 (2H, d, J=8.4 Hz), 7.45 (2H, d, J=8.4 Hz), 7.30 (2H, d, J=8.1 Hz), 7.29 (1H, s), 7.21 (2H, d, J=8.4 Hz), 6.64 (1H, d, J=5.1 Hz), 4.71–4.52 (1H, m), 4.01–3.82 (1H, m), 3.59–3.44 (1H, m), 3.28–3.08 (1H, m), 2.84–2.58 (1H, m), 2.46 (3H, s), 2.16 (3H, s), 2.02–1.62 (4H, m). 13C NMR (CDCl3, 75 MHz) δ 169.11, 158.91, 146.39, 136.80, 134.55, 132.01, 130.13, 129.19, 126.72, 34.91, 31.15, 22.01, 21.69.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:47]=[C:46]([O:48][CH3:49])[CH:45]=[CH:44][C:4]=1[CH2:5][NH:6][C:7]1[C:8]2[CH:15]=[CH:14][N:13]([C@H:16]3[C@@H:20]4[O:21][C:22]([CH3:25])([CH3:24])[O:23][C@@H:19]4[C@@H:18]([CH2:26][NH:27][CH:28]4[CH2:31][CH:30]([CH2:32][CH2:33][C:34]([O:36][CH2:37][C:38]5[CH:43]=[CH:42][CH:41]=[CH:40][CH:39]=5)=[O:35])[CH2:29]4)[O:17]3)[C:9]=2[N:10]=[CH:11][N:12]=1.I[CH:51]([CH3:53])[CH3:52].C([O-])([O-])=O.[K+].[K+]>CC#N>[CH3:1][O:2][C:3]1[CH:47]=[C:46]([O:48][CH3:49])[CH:45]=[CH:44][C:4]=1[CH2:5][NH:6][C:7]1[C:8]2[CH:15]=[CH:14][N:13]([C@H:16]3[C@@H:20]4[O:21][C:22]([CH3:25])([CH3:24])[O:23][C@@H:19]4[C@@H:18]([CH2:26][N:27]([CH:51]([CH3:53])[CH3:52])[CH:28]4[CH2:31][CH:30]([CH2:32][CH2:33][C:34]([O:36][CH2:37][C:38]5[CH:39]=[CH:40][CH:41]=[CH:42][CH:43]=5)=[O:35])[CH2:29]4)[O:17]3)[C:9]=2[N:10]=[CH:11][N:12]=1
Reactant: COc1ccc(CNc2ncnc3c2ccn3[C@@H]2O[C@H](CNC3CC(CCC(=O)OCc4ccccc4)C3)[C@H]3OC(C)(C)O[C@H]32)c(OC)c1
Reactant: CC(C)I
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC#N
Product: COc1ccc(CNc2ncnc3c2ccn3[C@@H]2O[C@H](CN(C(C)C)C3CC(CCC(=O)OCc4ccccc4)C3)[C@H]3OC(C)(C)O[C@H]32)c(OC)c1
Temperature: 25 °C
Yield: 70.6 %

Procedure:
A mixture of benzyl 3-(3-((((3aR,4R,6R,6aR)-6-(4-((2,4-dimethoxybenzyl)amino)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,2-dimethyltetrahydrofuro[3,4-d][1,3]dioxol-4-yl)methyl)amino)cyclobutyl)propanoate (4 g, 5.95 mmol), 2-iodopropane (6 g, 35.72 mmol) and K2CO3 (2.5 g, 17.86 mmol) in CH3CN (50 mL) was stirred at reflux for 2 days. The mixture was cooled to rt, filtered and the filtered cake was washed with CH3CN (20 mL). The filtrate was concentrated and the residue was purified by Combi-Flash (80 g silica gel, start EA:DCM:MeOH=10:10:0 to 10:10:1 by gradient, 60 mL/min, 40 min, 2.4 L total solvent volume) to afford the desired compound (3 g, yield: 71%) as a yellow solid. 1H NMR (500 MHz, MeOD): δH 8.15 (s, 1H), 7.38-7.29 (m, 5H), 7.19 (d, J=4.0 Hz, 1H), 7.14 (d, J=8.0 Hz, 1H), 6.65 (d, J=3.0 Hz, 1H), 6.53 (d, J=2.0 Hz, 1H), 6.41 (dd, J=8.5 and 2.0 Hz, 1H), 6.20 (d, J=2.5 Hz, 1H), 5.36-5.32 (m, 1H), 5.09 (s, 1H), 5.07 (s, 1H), 4.94-4.89 (m, 3H), 4.65 (s, 2H), 4.17-4.14 (m, 1H), 3.82 (s, 3H), 3.75 (s, 3H), 3.41-3.35 (m, 0.5H), 3.04-2.95 (m, 0.5H), 2.94-2.86 (m, 1H), 2.72-2.52 (m, 2H), 2.25 (t, J=7.5 Hz, 1H), 2.21 (t, J=8.0 Hz, 1H), 2.05-1.90 (m, 2H), 1.90-1.82 (m, 0.5H), 1.76-1.70 (m, 0.5H), 1.65-1.55 (m, 5H), 1.42-1.34 (m, 4H), 0.95 (d, J=6.5 Hz, 3H), 0.83-0.80 (m, 3H) ppm; ESI-MS (m/z): 714.4 [M+1]+.
Reaction SMILES: [O:1]1[C:5]2([CH2:10][CH2:9][NH:8][CH2:7][CH2:6]2)[O:4][CH2:3][CH2:2]1.C([O-])([O-])=O.[K+].[K+].C(#N)C.Br[CH2:21][CH2:22][CH2:23][CH:24]=[CH2:25]>O>[CH2:25]([N:8]1[CH2:9][CH2:10][C:5]2([O:4][CH2:3][CH2:2][O:1]2)[CH2:6][CH2:7]1)[CH2:24][CH2:23][CH:22]=[CH2:21]
Reactant: C1CC2(CCN1)OCCO2
Reactant: C=CCCCBr
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: O
Solvent: CC#N
Product: C=CCCCN1CCC2(CC1)OCCO2
Temperature: 25 °C
Reaction time: 8 h
Yield: 83.9 %

Procedure:
To a mixture of 15 g (0.105 mol) of 1,4-dioxa-8-azaspiro[4.5]decane, 15.93 g (0.115 mol) of K2CO3, and 100 ml of acetonitrile is added dropwise 14.41 ml (0.105 mol) of 5-bromopentene. The mixture is stirred overnight at room temperature and then at 65° C. for 2 hours. After cooling, the mixture is diluted with water and extracted with methylene chloride. The combined extracts are washed with brine, dried over Na2SO4, and concentrated in vacuo to furnish 18.62 g (84%) of title compound as an oil: IR (neat) 2940 and 1090 cm-1 ; NMR (CDCl3) δ5.84 (m, 1H), 5.02 (m, 2H), 3.96 (s, 4H), 2.70-1.40 (m, 14H).
Reaction SMILES: [NH2:1][CH2:2][CH2:3][CH2:4][CH2:5][CH2:6][OH:7].C(N(CC)CC)C.[C:15](OC(=O)C)(=[O:17])[CH3:16]>CO>[C:15]([NH:1][CH2:2][CH2:3][CH2:4][CH2:5][CH2:6][OH:7])(=[O:17])[CH3:16]
Reactant: NCCCCCO
Reactant: CC(=O)OC(C)=O
Solvent: CO
Solvent: CCN(CC)CC
Product: CC(=O)NCCCCCO
Temperature: 25 °C
Reaction time: 8 h

Procedure:
A solution of 5-amino-1-pentanol (0.650 g, 6.31 mmol) in methanol (15 mL) is cooled to 0° C. and treated with triethylamine (1.62 mL, 11.6 mmol) followed by acetic anhydride (0.891 mL, 9.45 mmol). The reaction mixture is stirred at room temperature overnight. Additional triethylamine (1.6 mL, 11.6 mmol) and acetic anhydride (0.9 mL, 9.5 mmol) is added at room temperature and the solution is stirred 16 h further. Concentration in vacuo and flash chromatography affords 5-acetamido-1-pentanol. To a solution of 5-acetamido-1-pentanol (22.2 mmol) in dry dichloromethane (50 mL) is added 2,6-di-tert-butyl-4-methylpyridine (4.6 g, 22.2 mmol) and triflic anhydride (3.7 mL, 22.2 mmol) at 0° C. The reaction is stirred at room temperature for 20 min, poured into water, and extracted with dichloromethane. The combined extracts are dried over anhydrous sodium sulfate and concentrated in vacuo and to afford 5-acetamido-1-pentyl triflate (30) which is used without further purification.
Reaction SMILES: [NH2:1][C:2]1[CH:3]=[CH:4][CH:5]=[C:6]2[C:11]=1[NH:10][C:9](=[O:12])[CH:8]([NH:13][C:14](=[O:20])[O:15][C:16]([CH3:19])([CH3:18])[CH3:17])[CH2:7]2.[H-].[Na+].[CH2:23](Br)[C:24]1[CH:29]=[CH:28][CH:27]=[CH:26][CH:25]=1>CN(C)C=O>[NH2:1][C:2]1[CH:3]=[CH:4][CH:5]=[C:6]2[C:11]=1[N:10]([CH2:23][C:24]1[CH:29]=[CH:28][CH:27]=[CH:26][CH:25]=1)[C:9](=[O:12])[CH:8]([NH:13][C:14](=[O:20])[O:15][C:16]([CH3:17])([CH3:19])[CH3:18])[CH2:7]2
Reactant: CC(C)(C)OC(=O)NC1Cc2cccc(N)c2NC1=O
Reactant: BrCc1ccccc1
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: CC(C)(C)OC(=O)NC1Cc2cccc(N)c2N(Cc2ccccc2)C1=O
Temperature: 25 °C
Reaction time: 1 h

Procedure:
tert-Butyl 8-amino-2-oxo-1,2,3,4-tetrahydroquinolin-3-ylcarbamate produced in Example 6 (10 g) was added to N,N-dimethylformamide (100 mL), and sodium hydride (1.65 g) was added thereto under cooling on ice. The mixture was stirred at room temperature for one hour. Subsequently, under cooling on ice, benzyl bromide (6.48 g) was added to the mixture, and stirring was performed at room temperature for one hour. The reaction mixture was filtered, and the filtrate was concentrated under reduced pressure, to thereby recover a residue. The residue was purified through silica gel column chromatography (ethyl acetate:n-hexane=1:2), whereby the title compound (10.8 g) was yielded.
Reaction SMILES: Br[C:2]1[CH:3]=[C:4]2[C:9](=[CH:10][CH:11]=1)[C:8](=[O:12])[NH:7][C:6](=[O:13])[C:5]2=[CH:14][NH:15][C:16]1[CH:21]=[CH:20][C:19]([N:22]2[CH2:27][CH2:26][N:25]([CH3:28])[CH2:24][CH2:23]2)=[CH:18][CH:17]=1.C([Si](C(C)C)(C(C)C)[N:33]1[CH:37]=[CH:36][C:35](B(O)O)=[CH:34]1)(C)C.C(=O)([O-])[O-].[Cs+].[Cs+]>CN(C)C=O>[CH3:28][N:25]1[CH2:26][CH2:27][N:22]([C:19]2[CH:18]=[CH:17][C:16]([NH:15][CH:14]=[C:5]3[C:4]4[C:9](=[CH:10][CH:11]=[C:2]([C:35]5[CH:36]=[CH:37][NH:33][CH:34]=5)[CH:3]=4)[C:8](=[O:12])[NH:7][C:6]3=[O:13])=[CH:21][CH:20]=2)[CH2:23][CH2:24]1
Reactant: CC(C)[Si](C(C)C)(C(C)C)n1ccc(B(O)O)c1
Reactant: CN1CCN(c2ccc(NC=C3C(=O)NC(=O)c4ccc(Br)cc43)cc2)CC1
Agent: O=C([O-])[O-]
Agent: [Cs+]
Solvent: CN(C)C=O
Product: CN1CCN(c2ccc(NC=C3C(=O)NC(=O)c4ccc(-c5cc[nH]c5)cc43)cc2)CC1
Temperature: 180 °C
Yield: 31.2 %

Procedure:
To a suspension of 6-bromo-4-{[4-(4-methyl-piperazin-1-yl)-phenylamino]-methylene}-4H-isoquinoline-1,3-dione (0.2 g, 0.45 mmol) in N,N-dimethylformamide (5 mL) is added N-triisopropylsilyl-3-pyrrole boronic acid (0.16 g, 0.54 mmol), followed by 300 μL of 2M aqueous cesium carbonate and tetrakis triphenylphosphine palladium (30 mg, 0.025 mmol). The reaction mixture is subjected to microwave heating at 180° C. for 300 seconds. The reaction mixture is then divided into 3 fractions and purified by C18 reverse phase HPLC. The pure fractions were combined and concentrated to yield 60 mg of 4-{[4-(4-methyl-piperazin-1-yl)-phenylamino]-methylene}-6-(1H-pyrrol-3-yl)-4H-isoquinoline-1,3-dione.
Reaction SMILES: [NH2:1][C:2]1[CH:3]=[C:4]([O:24][CH3:25])[CH:5]=[C:6]2[C:11]=1[N:10]=[CH:9][CH:8]=[C:7]2[CH:12]=[CH:13][C:14]1[CH:19]=[CH:18][CH:17]=[C:16]([C:20]([F:23])([F:22])[F:21])[CH:15]=1.Br[CH:27]([CH3:42])[CH2:28][CH2:29][CH2:30][N:31]1[C:35](=[O:36])[C:34]2=[CH:37][CH:38]=[CH:39][CH:40]=[C:33]2[C:32]1=[O:41].C(N(CC)CC)C>C(Cl)(Cl)Cl>[CH3:25][O:24][C:4]1[CH:5]=[C:6]2[C:11](=[C:2]([NH:1][CH:27]([CH3:42])[CH2:28][CH2:29][CH2:30][N:31]3[C:35](=[O:36])[C:34]4=[CH:37][CH:38]=[CH:39][CH:40]=[C:33]4[C:32]3=[O:41])[CH:3]=1)[N:10]=[CH:9][CH:8]=[C:7]2[CH:12]=[CH:13][C:14]1[CH:19]=[CH:18][CH:17]=[C:16]([C:20]([F:21])([F:22])[F:23])[CH:15]=1
Reactant: CC(Br)CCCN1C(=O)c2ccccc2C1=O
Reactant: COc1cc(N)c2nccc(C=Cc3cccc(C(F)(F)F)c3)c2c1
Solvent: ClC(Cl)Cl
Solvent: CCN(CC)CC
Product: COc1cc(NC(C)CCCN2C(=O)c3ccccc3C2=O)c2nccc(C=Cc3cccc(C(F)(F)F)c3)c2c1
Yield: 78.6 %

Procedure:
A mixture of 8.4 g (0.025 mole) of 8-amino-6-methoxy-4-(3-trifluoromethylstyryl)quinoline, 7.3 g (0.025 mole) of 4-bromo-1-phthalimidopentane and 2.5 g of triethylamine was heated in an oil bath at 130°-135° for 12 hr. The reaction mixture ws dissolved in chloroform and passed through a silica gel column to give 11 g of crude product which was used without further purification. Crystallization from ethanol provided an analytical sample as yellow needles, mp 154°-156°.
Reaction SMILES: [CH2:1]([O:8][C:9]1[C:14](=[O:15])[CH:13]=[CH:12][N:11]([CH3:16])[C:10]=1[CH:17]([OH:22])[C:18]([F:21])([F:20])[F:19])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.CCN(CC)CC.[CH3:30][S:31](Cl)(=[O:33])=[O:32]>C(Cl)Cl>[CH2:1]([O:8][C:9]1[C:14](=[O:15])[CH:13]=[CH:12][N:11]([CH3:16])[C:10]=1[CH:17]([O:22][S:31]([CH3:30])(=[O:33])=[O:32])[C:18]([F:20])([F:21])[F:19])[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: Cn1ccc(=O)c(OCc2ccccc2)c1C(O)C(F)(F)F
Reactant: CS(=O)(=O)Cl
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: Cn1ccc(=O)c(OCc2ccccc2)c1C(OS(C)(=O)=O)C(F)(F)F
Reaction time: 3 h
Yield: 19.4 %

Procedure:
To a suspension of 3-benzyloxy-1-methyl-2-(2,2,2-trifluoro-1-hydroxy-ethyl)-1H-pyridin-4-one (4 g) in CH2Cl2 (80 mL) was added Et3N (2.40 mL, 17.5 mmol), followed by methanesulfonyl chloride (1.25 mL, 16.2 mmol) at ice-water bath temperature. The resulting mixture was then stirred for 3 h. The reaction mixture was quenched with water and extracted twice with CH2Cl2 (2×50 mL). The combined organic fractions were washed with brine and dried over anhydrous sodium sulfate, filtered and concentrated to dryness. The residue was purified by flash column chromatography on silica gel using a mixture of CH2Cl2 and MeOH (95/5, v/v) as eluant, thereby affording the product, methanesulfonic acid 1-(3-benzyloxy-1-methyl-4-oxo-1,4-dihydro-pyridin-2-yl)-2,2,2-trifluoro-ethyl ester (0.97 g, 19.4% yield). MS-ESI (m/z): 391.9 [M+1]+, 206, 91.
Reaction SMILES: [C:1]([O:5][C:6]([NH:8][C@H:9]([CH2:29][C:30]1[CH:35]=[C:34]([F:36])[C:33]([F:37])=[CH:32][C:31]=1[F:38])[CH2:10][C:11]([N:13]1[CH2:18][CH2:17][N:16]2[C:19]([C:25]([F:28])([F:27])[F:26])=[N:20][C:21]([C:22](O)=[O:23])=[C:15]2[CH2:14]1)=[O:12])=[O:7])([CH3:4])([CH3:3])[CH3:2].[CH:39]1([NH2:42])[CH2:41][CH2:40]1.O=C1N(P(Cl)(N2CCOC2=O)=O)CCO1.C(N(CC)CC)C>ClCCl>[C:1]([O:5][C:6](=[O:7])[NH:8][C@H:9]([CH2:29][C:30]1[CH:35]=[C:34]([F:36])[C:33]([F:37])=[CH:32][C:31]=1[F:38])[CH2:10][C:11]([N:13]1[CH2:18][CH2:17][N:16]2[C:19]([C:25]([F:28])([F:27])[F:26])=[N:20][C:21]([C:22](=[O:23])[NH:42][CH:39]3[CH2:41][CH2:40]3)=[C:15]2[CH2:14]1)=[O:12])([CH3:2])([CH3:3])[CH3:4]
Reactant: CC(C)(C)OC(=O)N[C@@H](CC(=O)N1CCn2c(C(F)(F)F)nc(C(=O)O)c2C1)Cc1cc(F)c(F)cc1F
Reactant: NC1CC1
Agent: O=C1OCCN1P(=O)(Cl)N1CCOC1=O
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CC(C)(C)OC(=O)N[C@@H](CC(=O)N1CCn2c(C(F)(F)F)nc(C(=O)NC3CC3)c2C1)Cc1cc(F)c(F)cc1F
Yield: 47.1 %

Procedure:
(R)-7-[3-tert-Butoxycarbonylamino-4-(2,4,5-trifluoro-phenyl)-butyryl]-3-trifluoromethyl-5,6,7,8-tetrahydro-imidazo[1,5-a]pyrazine-1-carboxylic acid 2a (0.2 g, 0.36 mmol), cyclopropylamine (0.05 g, 0.54 mmol) and bis(2-oxo-3-oxazolidinyl)phosphinic chloride (0.18 g, 0.72 mmol) were dissolved in 20 mL of dichloromethane under stirring, and triethylamine (0.36 g, 3.6 mmol) was added to the solution at room temperature. The reaction mixture was reacted at room temperature for 2 hours, and then concentrated under reduced pressure. The resulting residue was purified by silica gel column chromatography to obtain the title compound (R)-[3-(1-cyclopropylcarbamoyl-3-trifluoromethyl-5,6-dihydro-8H-imidazo[1,5-a]pyrazin-7-yl)-3-oxo-1-(2,4,5-trifluoro-benzyl)-propyl]-carbamic acid tert-butyl ester 15a (0.1 g, yield 45%) as an oil.
Reaction SMILES: Cl.[NH2:2]O.C(=O)(O)[O-].[Na+].O.[N:10]1[C:18]2[CH:17]=[C:16]([C:19]#[N:20])[N:15]=[CH:14][C:13]=2[NH:12][CH:11]=1>C(O)C>[N:10]1[C:18]2[CH:17]=[C:16]([C:19](=[NH:2])[NH2:20])[N:15]=[CH:14][C:13]=2[NH:12][CH:11]=1
Reactant: N#Cc1cc2nc[nH]c2cn1
Reactant: NO
Agent: Cl
Agent: O=C([O-])O
Agent: [Na+]
Solvent: O
Solvent: CCO
Product: N=C(N)c1cc2nc[nH]c2cn1
Temperature: 100 °C
Reaction time: 0.25 h

Procedure:
Hydroxylamine hydrochloride (27.2 mg, 0.39 mmol), sodium bicarbonate (49.4 mg, 0.59 mmol), and water (0.392 mL) were combined in a vial and stirred for 15 minutes. This solution was added to a vial containing 4-(5-chloropyridin-3-yl)-2-[(4aR,7aR)-hexahydrocyclopenta[b][1,4]oxazin-4(4aH)-yl]-3-[(1R or S)-1-(trans-4-methylcyclohexyl)ethyl]-3H-imidazo[4,5-c]pyridine-6-carbonitrile (99 mg, 0.196 mmol), dissolved in ethanol (0.915 mL). The mixture was sealed and heated at 100° C. for 1 hour. The reaction was cooled to room temperature, quenched with water, and extracted with ethyl acetate (2×). The combined organic layers were dried over sodium sulfate, filtered, and concentrated to afford 4-(5-chloropyridin-3-yl)-2-[(4aR,7aR)-hexahydrocyclopenta[b][1,4]oxazin-4(4aH)-yl]-N-hydroxy-3-[(1R or S)-1-(trans-4-methylcyclohexyl)ethyl]-3H-imidazo[4,5-c]pyridine-6-carboximidamide. MS ESI calc'd. for C28H36ClN7O2 [M+H]+ 538. found 538.
Reaction SMILES: [CH2:1]([O:3]/[CH:4]=[CH:5]/[CH3:6])[CH3:2].N1C=CC=CC=1.[Cl:13][C:14]([Cl:19])([Cl:18])[C:15](Cl)=[O:16]>C(Cl)Cl>[Cl:13][C:14]([Cl:19])([Cl:18])[C:15](=[O:16])/[C:5](/[CH3:6])=[CH:4]/[O:3][CH2:1][CH3:2]
Reactant: O=C(Cl)C(Cl)(Cl)Cl
Reactant: C/C=C/OCC
Solvent: c1ccncc1
Solvent: ClCCl
Product: CCO/C=C(\C)C(=O)C(Cl)(Cl)Cl
Temperature: 50 °C
Reaction time: 24 h
Yield: 18.6 %

Procedure:
A mixture of (E)-1-ethoxyprop-1-ene (6.41 mL, 57.9 mmol) and pyridine (4.68 mL, 57.9 mmol) was added to a soln. of 2,2,2-trichloroacetyl chloride (10.53 g, 57.9 mmol) in DCM (15 mL) at −10° C. at a rate of 6-10 drops/min. After the addition was completed, the mixture was stirred at r.t for 24 hrs. Filtered, and the filtrate was concentrated in reduced pressure (at first the temperature of the water bath was r.t, after most DCM was evaporated off, water bath was warmed to 50° C. to afford (E)-1,1,1-trichloro-4-ethoxy-3-methylbut-3-en-2-one (2.55 g, 10.79 mmol, 18.64% yield). 1H-NMR (500 MHz, CDCl3): δ: 7.96 (s, 1H), 4.21 (q, J=7.1 Hz, 2H), 1.94 (s, 3H), 1.41 (t, J=7.2 Hz, 3H). This material was taken into Step G2 without further purification.
Reaction SMILES: [Br:1][C:2]1[CH:3]=[C:4]2[C:9](=[CH:10][CH:11]=1)[N:8]=[C:7](Cl)[C:6]([I:13])=[CH:5]2.[CH3:14][O:15][C:16]1[CH:23]=[CH:22][C:19]([CH2:20][NH2:21])=[CH:18][CH:17]=1.O>CN1CCCC1=O>[Br:1][C:2]1[CH:3]=[C:4]2[C:9](=[CH:10][CH:11]=1)[N:8]=[C:7]([NH:21][CH2:20][C:19]1[CH:22]=[CH:23][C:16]([O:15][CH3:14])=[CH:17][CH:18]=1)[C:6]([I:13])=[CH:5]2
Reactant: Clc1nc2ccc(Br)cc2cc1I
Reactant: COc1ccc(CN)cc1
Solvent: CN1CCCC1=O
Solvent: O
Product: COc1ccc(CNc2nc3ccc(Br)cc3cc2I)cc1
Temperature: 130 °C

Procedure:
A glass microwave reaction vessel was charged with 6-bromo-2-chloro-3-iodoquinoline (0.918 g, 2.492 mmol) and 4-methoxybenzylamine (2.279 mL, 17.44 mmol) in N-methyl-2-pyrrolidinone (3.56 mL). The reaction mixture was stirred and heated in a microwave reactor at 130° C. for 20 min. The solution was poured into water and extracted with diethyl ether. The combined organic extracts were washed with saturated ammonium chloride, water, saturated sodium chloride, and dried over magnesium sulfate. The solution was filtered and concentrated in vacuo to give the crude material 6-bromo-3-iodo-N-(4-methoxybenzyl)quinolin-2-amine as a tan solid which was used without further purification.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([OH:8])=[CH:4][C:3]=1[F:9].C(=O)([O-])[O-].[K+].[K+].CCN(C(C)C)C(C)C.[CH2:25]([O:27][CH:28]([O:31][CH2:32][CH3:33])[CH2:29]Br)[CH3:26]>CN(C=O)C>[Cl:1][C:2]1[CH:7]=[CH:6][C:5]([O:8][CH2:29][CH:28]([O:31][CH2:32][CH3:33])[O:27][CH2:25][CH3:26])=[CH:4][C:3]=1[F:9]
Reactant: CCOC(CBr)OCC
Reactant: Oc1ccc(Cl)c(F)c1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: CCOC(COc1ccc(Cl)c(F)c1)OCC
Temperature: 100 °C
Reaction time: 16 h
Yield: 104.6 %

Procedure:
To 4-chloro-3-fluorophenol (3.66 g, 25 mmol) in DMF (30 ml) at room temperature was added potassium carbonate (6.91 g, 50.0 mmol), DIEA (8.73 ml, 50.0 mmol) and then bromoacetaldehyde diethylacetal (7.52 ml, 50.0 mmol). The mixture was stirred at 100° C. for 16 hr. The mixture was cooled to room temperature and then quenched with water and extracted with EtOAc two times, dried over magnesium sulfate, filtered, concentrated. The residue was purified via Biotage (0-20% AcOEt/heptane; SNAP25 column) giving 13a (6.87 g, quant) as a colorless oil.
Reaction SMILES: [NH2:1][C@@H:2]([CH3:17])[C@@H:3]([C:5]1[CH:6]=[CH:7][C:8]([OH:16])=[C:9]([NH:11][S:12]([CH3:15])(=[O:14])=[O:13])[CH:10]=1)[OH:4].[CH2:18]([O:20][C:21]1[CH:22]=[C:23]([CH:26]=[C:27]([O:29][CH2:30][CH3:31])[CH:28]=1)[CH:24]=O)[CH3:19].O>CO>[CH2:30]([O:29][C:27]1[CH:26]=[C:23]([CH:22]=[C:21]([O:20][CH2:18][CH3:19])[CH:28]=1)[CH2:24][NH:1][C@@H:2]([CH3:17])[C@@H:3]([C:5]1[CH:6]=[CH:7][C:8]([OH:16])=[C:9]([NH:11][S:12]([CH3:15])(=[O:14])=[O:13])[CH:10]=1)[OH:4])[CH3:31]
Reactant: CCOc1cc(C=O)cc(OCC)c1
Reactant: C[C@H](N)[C@H](O)c1ccc(O)c(NS(C)(=O)=O)c1
Solvent: O
Solvent: CO
Product: CCOc1cc(CN[C@@H](C)[C@H](O)c2ccc(O)c(NS(C)(=O)=O)c2)cc(OCC)c1
Temperature: 25 °C
Reaction time: 2.5 h
Yield: 53.5 %

Procedure:
To a solution of the amine (4) (127 mg, 0.486 mmol) and 3,5-diethoxybenzaldehyde (123 mg, 0.632 mmol) in methanol (3.3 mL) was added borane-pyridine complex (155 μL, 1.46 mmol) at 40° C. and the resulting mixture was stirred for 2.5 hours. The reaction mixture was cooled to room temperature and water was added thereto, followed by extraction with a mixed solvent (ethyl acetate:methanol=10:1) and subsequent washing of the organic layer with saturated brine. The organic layer was dried and concentrated and the obtained crude product was purified by amine silica gel column chromatography (eluent; chloroform:methanol=7:1) to obtain the desired amine (10) as a yellow solid (114 mg, Yield: 54%).
Reaction SMILES: [C@@H:1]12[N:8]([CH3:9])[C@@H:5]([CH2:6][CH2:7]1)[CH2:4][CH:3]=[C:2]2[C:10]([O:12]CC)=O.[Si](Cl)(C)(C)[CH3:16].[Li]C>C1COCC1>[CH3:9][N:8]1[CH:5]2[CH2:6][CH2:7][CH:1]1[C:2]([C:10](=[O:12])[CH3:16])=[CH:3][CH2:4]2
Reactant: CCOC(=O)C1=CC[C@@H]2CC[C@H]1N2C
Reactant: C[Si](C)(C)Cl
Agent: [Li]C
Solvent: C1CCOC1
Product: CC(=O)C1=CCC2CCC1N2C
Temperature: -100 °C
Reaction time: 16 h

Procedure:
To a mixture of ethyl trop-2-ene-2-carboxylate (3.43 g, 0.019 mol) and Me3SiCl (10.32 g, 0.095 mol) in THF (70 mL) cooled to -100° C., MeLi (1.4 M, 17.07 n%L, 0.0239 mol) was added dropwise. After warming up to room temperature, the reaction mixture was stirred for 16 hours. Excess Me3SiCl and THF was evaporated off and the resulting residue was stirred with EtOH (6 mL) followed by water (6 mL). The mixture was then made acidic (6N HCl )and extracted with ether. The aqueous layer was made basic (solid K2CO3)and extracted with chloroform, dried (K2CO3) and concentrated to give