Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [CH2:1]([S:3]([C:6]1[CH:7]=[C:8]([C:12]2[CH:20]=[CH:19][C:18]([OH:21])=[C:17]3[C:13]=2[C:14]2[CH:25]=[C:24]([CH3:26])[CH:23]=[N:22][C:15]=2[NH:16]3)[CH:9]=[CH:10][CH:11]=1)(=[O:5])=[O:4])[CH3:2].[CH3:27][N:28]([CH3:43])[CH2:29][CH2:30][CH2:31]OS(C1C=CC(C)=CC=1)(=O)=O.C(=O)([O-])[O-].[K+].[K+]>CN(C=O)C>[CH2:1]([S:3]([C:6]1[CH:7]=[C:8]([C:12]2[CH:20]=[CH:19][C:18]([O:21][CH2:31][CH2:30][CH2:29][N:28]([CH3:43])[CH3:27])=[C:17]3[C:13]=2[C:14]2[CH:25]=[C:24]([CH3:26])[CH:23]=[N:22][C:15]=2[NH:16]3)[CH:9]=[CH:10][CH:11]=1)(=[O:5])=[O:4])[CH3:2]
Reactant: Cc1ccc(S(=O)(=O)OCCCN(C)C)cc1
Reactant: CCS(=O)(=O)c1cccc(-c2ccc(O)c3[nH]c4ncc(C)cc4c23)c1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Product: CCS(=O)(=O)c1cccc(-c2ccc(OCCCN(C)C)c3[nH]c4ncc(C)cc4c23)c1
Temperature: 200 °C
Yield: 403.1 %

Procedure:
A 5 mL microwave vial was charged with Compound 157 (290 mg, 0.79 mmol), 3-(dimethylamino)propyl-4-methylbenzenesulfonate (224 mg, 0.87 mmol), potassium carbonate (218 mg, 1.58 mmol) and 2 mL of anhydrous DMF, under nitrogen atmosphere. The reaction mixture was heated at 200° C. for 30 min. in microwave with high absorption. The reaction was quenched with addition of water, and the solid precipitate out was collected by filtration and purified through preparative HPLC to provide title compound (1438 mg, 40%). 1H NMR (400 MHz, DMSO-d6) δ ppm 1.17 (t, J=7.33 Hz, 3H) 1.99 (qd, J=6.61, 6.44 Hz, 2H) 2.20 (s, 6H) 2.26 (s, 3H) 2.53-2.56 (m, 2H) 3.41 (q, J=7.33 Hz, 2H) 4.25 (t, J=6.19 Hz, 2H) 7.05-7.09 (m, 1H) 7.11-7.14 (m, 1H) 7.54 (d, J=1.52 Hz, 1H) 7.85 (t, J=7.83 Hz, 1H) 7.98 (t, J=6.95 Hz, 2H) 8.06-8.08 (m, 1H) 8.27 (d, J=1.77 Hz, 1H) 12.13 (s, 1H); [M+H] calc'd for C25H30N3O3S, 452.2; found, 452.4.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:8]=[CH:7][C:6]([N:9]([CH2:34][C:35]2[CH:36]=[N:37][CH:38]=[CH:39][C:40]=2[CH3:41])[CH:10]2[CH2:15][CH2:14][N:13]([C@H:16]([CH3:33])[CH2:17][CH2:18][NH:19][C:20](=[O:32])[C:21]3[C:29]([CH3:30])=[CH:28][C:24]([C:25]([OH:27])=O)=[CH:23][C:22]=3[CH3:31])[CH2:12][CH2:11]2)=[CH:5][CH:4]=1.C[CH2:43][N:44]=[C:45]=NCCCN(C)C.C1C=CC2N(O)N=NC=2C=1.CNC.CCN(C(C)C)C(C)C>CN(C=O)C>[CH3:1][O:2][C:3]1[CH:4]=[CH:5][C:6]([N:9]([CH2:34][C:35]2[CH:36]=[N:37][CH:38]=[CH:39][C:40]=2[CH3:41])[CH:10]2[CH2:15][CH2:14][N:13]([C@H:16]([CH3:33])[CH2:17][CH2:18][NH:19][C:20](=[O:32])[C:21]3[C:22]([CH3:31])=[CH:23][C:24]([C:25]([N:44]([CH3:45])[CH3:43])=[O:27])=[CH:28][C:29]=3[CH3:30])[CH2:12][CH2:11]2)=[CH:7][CH:8]=1
Reactant: CCN=C=NCCCN(C)C
Reactant: COc1ccc(N(Cc2cnccc2C)C2CCN([C@H](C)CCNC(=O)c3c(C)cc(C(=O)O)cc3C)CC2)cc1
Agent: CNC
Agent: On1nnc2ccccc21
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: COc1ccc(N(Cc2cnccc2C)C2CCN([C@H](C)CCNC(=O)c3c(C)cc(C(=O)N(C)C)cc3C)CC2)cc1
Temperature: 25 °C
Reaction time: 16 h
Yield: 39.8 %

Procedure:
N-((R)-3-{4-[(4-Methoxy-phenyl)-(4-methyl-pyridin-3-ylmethyl)-amino]-piperidin-1-yl}-butyl)-3,5-dimethyl-terephthalamic acid (0.070 g, 0.12 mmol), EDCI (0.026 g, 0.13 mmol) and HOBT (0.019 g, 0.13 mmol) were combined in DMF (5 mL) to give a pale yellow solution. To this solution was added dimethylamine (2M in THF) (94 μL, 0.18 mmol) followed by DIPEA (33 μL, 0.18 mmol) and the resulting mixture was stirred at 25° C. for 16 h. Standard workup according to General Procedure C gave the crude product as a tan oil. Purification by column chromatography on silica gel (CH2Cl2:MeOH:NH4OH, 93:5:2, v/v/v) afforded N-((R)-3-{4-[(4-methoxy-phenyl)-(4-methyl-pyridin-3-ylmethyl)-amino]-piperidin-1-yl}-butyl)-2,6, N′,N′-tetramethyl-terephthalamide (0.028 g, 38%) as a white foam. 1H NMR (CDCl3) δ 0.99 (d, 3H, J=6.0 Hz), 1.26 (m, 1H), 1.37 (m, 1H), 1.62 (m, 2H), 1.78-1.85 (m, 3H), 2.14 (br t, 1H), 2.33 (s+m, 8H), 2.47 (br t, 1H), 2.74 (m, 3H), 2.94 (s, 3H), 3.06 (s, 3H), 3.32-3.46 (m, 2H), 3.66 (m, 1H), 3.72 (s, 3H), 4.10 (s, 2H), 6.66 (d, 2H, J=9.0 Hz), 6.73 (d, 2H, J=9.0 Hz), 6.93 (br t, 1H), 7.02 (d, 1H, J=3.0 Hz), 7.05 (s, 2H), 8.29 (s, 1H), 8.31 (d, 1H, J=6.0 Hz). 13C NMR (CDCl3) δ 13.8, 19.2, 19.6, 29.9, 30.7, 32.8, 39.0, 39.9, 44.8, 47.6, 51.8, 56.0, 58.8, 58.9, 114.8, 119.4, 125.3, 126.4, 133.8, 134.8, 143.0, 145.4, 148.3, 149.6. ES-MS m/z 586 (M+H), 608 (M+Na). Anal. Calcd. for C35H47N5O3.0.2 CH2Cl2: C, 70.14; H, 7.93; N, 11.62. Found: C, 70.06; H, 8.03; N, 11.54.
Reaction SMILES: [C:1]([O:5][C:6]([NH:8][C:9]1([C:15]([OH:17])=O)[CH2:14][CH2:13][O:12][CH2:11][CH2:10]1)=[O:7])([CH3:4])([CH3:3])[CH3:2].[NH2:18][C@@H:19]([CH2:23][C:24]1[CH:29]=[CH:28][C:27]([I:30])=[CH:26][CH:25]=1)[C:20]([NH2:22])=[O:21].C(N(C(C)C)C(C)C)C.CN(C(ON1N=NC2C=CC=CC1=2)=[N+](C)C)C.[B-](F)(F)(F)F>CN(C=O)C>[NH2:22][C:20](=[O:21])[C@@H:19]([NH:18][C:15]([C:9]1([NH:8][C:6](=[O:7])[O:5][C:1]([CH3:2])([CH3:3])[CH3:4])[CH2:10][CH2:11][O:12][CH2:13][CH2:14]1)=[O:17])[CH2:23][C:24]1[CH:29]=[CH:28][C:27]([I:30])=[CH:26][CH:25]=1
Reactant: CC(C)(C)OC(=O)NC1(C(=O)O)CCOCC1
Reactant: NC(=O)[C@@H](N)Cc1ccc(I)cc1
Agent: CN(C)C(On1nnc2ccccc21)=[N+](C)C
Agent: F[B-](F)(F)F
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: CC(C)(C)OC(=O)NC1(C(=O)N[C@@H](Cc2ccc(I)cc2)C(N)=O)CCOCC1
Temperature: 25 °C
Reaction time: 48 h
Yield: 118.4 %

Procedure:
4-(tert-Butoxycarbonylamino)tetrahydro-2H-pyran-4-carboxylic acid (0.801 g), (S)-2-amino-3-(4-iodophenyl)propanamide (Example 1, step (ii), 0.947 g) and N-ethyl-N-isopropylpropan-2-amine (1.422 mL) were dissolved in DMF (10 mL) and to the solution was added TBTU (1.573 g). The reaction mixture was stirred, at room temperature, for 2 days. The reaction mixture was evaporated to dryness dissolved in dichloromethane (20 mL) and evaporated onto silica. The silica was put on the top of a silica column and eluted with 20% ethyl acetate in isohexane then 50% ethyl acetate in isohexane then 100% ethyl acetate followed by 10% then 20% methanol in ethyl acetate to afford the sub-titled compound (2.00 g).
Reaction SMILES: [CH2:1]([NH:6][C:7]1[N:8]=[CH:9][NH:10][C:11]=1[C:12]1[NH:16][N:15]=[C:14]([C:17]2[CH:22]=[CH:21][CH:20]=[CH:19][CH:18]=2)[N:13]=1)[CH2:2][CH2:3][CH2:4][CH3:5].C1N=CN([C:28](N2C=NC=C2)=[O:29])C=1>C1COCC1>[CH2:1]([N:6]1[C:7]2[N:8]=[CH:9][NH:10][C:11]=2[C:12]2=[N:13][C:14]([C:17]3[CH:22]=[CH:21][CH:20]=[CH:19][CH:18]=3)=[N:15][N:16]2[C:28]1=[O:29])[CH2:2][CH2:3][CH2:4][CH3:5]
Reactant: CCCCCNc1nc[nH]c1-c1nc(-c2ccccc2)n[nH]1
Reactant: O=C(n1ccnc1)n1ccnc1
Solvent: C1CCOC1
Product: CCCCCn1c(=O)n2nc(-c3ccccc3)nc2c2[nH]cnc21
Temperature: 70 °C
Reaction time: 2 h
Yield: 45.6 %

Procedure:
N-pentyl-5-(3-phenyl-1H-1,2,4-triazol-5-yl)-1H-imidazol-4-amine (50 mg, 0.17 mmol) and N,N-carbonyldiimidazole (50 mg, 0.3 mmol) were dissolved in THF (10 mL) and stirred at 70° C. for 2 hours. The reaction mixture was concentrated under reduced pressure, and the residue was purified by preparative LCMS (method B) to yield the desired product (25 mg, 45% yield). LCMS calculated for C17H19N6O(M+H): 323.2. found 323.1.
Reaction SMILES: Cl.[Br:2][C:3]1[CH:4]=[C:5]([C@H:9]([NH2:11])[CH3:10])[CH:6]=[N:7][CH:8]=1.C(N(CC)C(C)C)(C)C.[C:21](Cl)(=[O:23])[CH3:22]>C(Cl)Cl>[Br:2][C:3]1[CH:4]=[C:5]([C@H:9]([NH:11][C:21](=[O:23])[CH3:22])[CH3:10])[CH:6]=[N:7][CH:8]=1
Reactant: C[C@@H](N)c1cncc(Br)c1
Reactant: CC(=O)Cl
Agent: Cl
Solvent: CCN(C(C)C)C(C)C
Solvent: ClCCl
Product: CC(=O)N[C@H](C)c1cncc(Br)c1
Temperature: 25 °C
Reaction time: 2 h

Procedure:
To a vial is added (1R)-1-(5-bromo(3-pyridyl))ethylamine HCl (500 mg, 2.1 mmol) in 2.5 ml of DCM, followed by the addition of N,N-diisopropylethylamine (816 mg, 2.52 mmol). Then acetyl chloride 1M in DCM solution (2.5 ml, 2.5 mmol) is added at 0° C. The reaction mixture is stirred at room temperature for 2 hours. The reaction mixture is diluted with DCM, washed with water, brine, dried over anhydrous Na2SO4, filtered and concentrated to give the crude product. Purification by the flash column chromatography affords 273 mg of N-[(R)-1-(5-bromo-pyridin-3-yl)-ethyl]-acetamide.
Reaction SMILES: [NH2:1][CH2:2][CH2:3][N:4]1[C:16]2[C:15]3[CH:14]=[CH:13][C:12]([C:17]4[CH:18]=[N:19][CH:20]=[CH:21][CH:22]=4)=[CH:11][C:10]=3[N:9]=[C:8]([NH2:23])[C:7]=2[N:6]=[C:5]1[CH2:24][O:25][CH2:26][CH3:27].[CH:28]([N:31]=[C:32]=[O:33])([CH3:30])[CH3:29]>C(Cl)(Cl)Cl>[NH2:23][C:8]1[C:7]2[N:6]=[C:5]([CH2:24][O:25][CH2:26][CH3:27])[N:4]([CH2:3][CH2:2][NH:1][C:32]([NH:31][CH:28]([CH3:30])[CH3:29])=[O:33])[C:16]=2[C:15]2[CH:14]=[CH:13][C:12]([C:17]3[CH:18]=[N:19][CH:20]=[CH:21][CH:22]=3)=[CH:11][C:10]=2[N:9]=1
Reactant: CCOCc1nc2c(N)nc3cc(-c4cccnc4)ccc3c2n1CCN
Reactant: CC(C)N=C=O
Solvent: ClC(Cl)Cl
Product: CCOCc1nc2c(N)nc3cc(-c4cccnc4)ccc3c2n1CCNC(=O)NC(C)C
Yield: 28.5 %

Procedure:
A solution of 1-(2-aminoethyl)-2-ethoxymethyl-7-(pyridin-3-yl)-1H-imidazo[4,5-c]quinolin-4-amine (2.50 g, 6.90 mmol) in chloroform (50 mL) was treated with isopropyl isocyanate (0.65 mL, 6.9 mmol) according to the method described in Examples 377-379. The crude product was purified by column chromatography on silica gel (eluting with 94:6 chloroform:methanol) followed by trituration with acetonitrile (15 mL/g) at 95° C. The mixture was cooled in an ice bath, isolated by filtration, and dried for one hour in a vacuum oven at 100° C. to provide 0.88 g of N-{2-[4-amino-2-ethoxymethyl-7-(pyridin-3-yl)-1H-imidazo[4,5-c]quinolin-1-yl]ethyl}-N′-(1-methylethyl)urea as a white solid, mp 194-196° C.
Reaction SMILES: [CH3:1][C:2]([C:8]1[CH:9]=[C:10]2[C:15](=[C:16]([C:18]3[CH:19]=[C:20]([CH:24]=[CH:25][CH:26]=3)[C:21]([OH:23])=O)[CH:17]=1)[N:14]=[CH:13][CH:12]=[CH:11]2)([S:4]([CH3:7])(=[O:6])=[O:5])[CH3:3].C1N=CN(C(N2C=NC=C2)=O)C=1.[F:39][C:40]1[CH:45]=[CH:44][C:43]([C:46](=[N:48]O)[NH2:47])=[CH:42][CH:41]=1>CN(C=O)C.O>[F:39][C:40]1[CH:45]=[CH:44][C:43]([C:46]2[N:48]=[C:21]([C:20]3[CH:19]=[C:18]([C:16]4[CH:17]=[C:8]([C:2]([CH3:1])([S:4]([CH3:7])(=[O:5])=[O:6])[CH3:3])[CH:9]=[C:10]5[C:15]=4[N:14]=[CH:13][CH:12]=[CH:11]5)[CH:26]=[CH:25][CH:24]=3)[O:23][N:47]=2)=[CH:42][CH:41]=1
Reactant: NC(=NO)c1ccc(F)cc1
Reactant: CC(C)(c1cc(-c2cccc(C(=O)O)c2)c2ncccc2c1)S(C)(=O)=O
Agent: O=C(n1ccnc1)n1ccnc1
Solvent: O
Solvent: CN(C)C=O
Product: CC(C)(c1cc(-c2cccc(-c3nc(-c4ccc(F)cc4)no3)c2)c2ncccc2c1)S(C)(=O)=O
Temperature: 120 °C
Reaction time: 18 h

Procedure:
To a solution of acid from step 2 in DMF (0.05M) was added CDI (2 eq) and 4-fluoro-N′-hydroxybenzenecarboximidamide (2 eq). The reaction mixture was stirred at rt for 15 min and 18 h at 120° C. The reaction mixture cooled to rt, diluted with water and extracted with EtOAc. The organic extracts were washed with brine, dried over MgSO4, filtered and concentrated. The residue was purified by flash chromatography (hexane:EtOAc, 20:80) to afforded the title compound.
Reaction SMILES: [NH:1]1[C:5]2[CH:6]=[CH:7][CH:8]=[N:9][C:4]=2[N:3]=[CH:2]1.Cl[CH2:11][C:12]1[CH:30]=[CH:29][C:15]([C:16]([N:18]([CH:24]2[CH2:28][CH2:27][CH2:26][CH2:25]2)[CH:19]2[CH2:23][CH2:22][CH2:21][CH2:20]2)=[O:17])=[CH:14][N:13]=1>CC(N(C)C)=O>[CH:24]1([N:18]([CH:19]2[CH2:20][CH2:21][CH2:22][CH2:23]2)[C:16]([C:15]2[CH:14]=[N:13][C:12]([CH2:11][N:9]3[CH:8]=[CH:7][C:6]4=[N:3][CH:2]=[N:1][C:5]4=[CH:4]3)=[CH:30][CH:29]=2)=[O:17])[CH2:28][CH2:27][CH2:26][CH2:25]1
Reactant: c1cnc2nc[nH]c2c1
Reactant: O=C(c1ccc(CCl)nc1)N(C1CCCC1)C1CCCC1
Solvent: CC(=O)N(C)C
Product: O=C(c1ccc(Cn2ccc3ncnc-3c2)nc1)N(C1CCCC1)C1CCCC1
Temperature: 25 °C
Reaction time: 60 h

Procedure:
To a stirred solution of imidazopyridine (540 mg, 4.5 mmol) in dimethylacetamide (100 mL) under argon, the product of Example D (1.6 g,) was added in one portion. The reaction temperature was slowly raised to 80°-85° C. and was stirred for 60 h. The reaction flask was cooled to room temperature and the solvent was removed under reduced pressure at <45° C. The residue obtained was triturated with excess of dry ether and filtered.
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[CH2:13][CH2:12][CH:11]([NH2:14])[CH2:10][CH2:9]1)=[O:7])([CH3:4])([CH3:3])[CH3:2].[Cl:15][C:16]1[CH:21]=[CH:20][C:19]([CH2:22][C:23](O)=[O:24])=[CH:18][CH:17]=1.CCN=C=NCCCN(C)C.C1C=CC2N(O)N=NC=2C=1.CN1CCOCC1>ClCCl>[C:1]([O:5][C:6]([N:8]1[CH2:13][CH2:12][CH:11]([NH:14][C:23](=[O:24])[CH2:22][C:19]2[CH:20]=[CH:21][C:16]([Cl:15])=[CH:17][CH:18]=2)[CH2:10][CH2:9]1)=[O:7])([CH3:4])([CH3:2])[CH3:3]
Reactant: CC(C)(C)OC(=O)N1CCC(N)CC1
Reactant: O=C(O)Cc1ccc(Cl)cc1
Agent: CCN=C=NCCCN(C)C
Agent: On1nnc2ccccc21
Solvent: CN1CCOCC1
Solvent: ClCCl
Product: CC(C)(C)OC(=O)N1CCC(NC(=O)Cc2ccc(Cl)cc2)CC1
Temperature: 25 °C
Reaction time: 8 h

Procedure:
To a solution of 4-amino-piperidine 1-carboxylic acid tert-butyl ester (0.44 g, 2.2 mmol) and 4-chlorophenyl acetic acid (0.34 g, 2 mmol) in dichloromethane (10 mL) were added EDCI (0.55 g, 2.8 mmol), HOBT (0.42 g, 2.8 mmol) and N-methylmorpholine (0.6 g, 6 mmol) and the resulting mixture was stirred at room temperature overnight. The reaction mixture was concentrated in vacuo, diluted with dichloromethane and extracted with saturated aqueous sodium bicarbonate solution. The aqueous layer was back extracted twice with dichloromethane. The combined organics were dried over sodium sulfate and concentrated in vacuo. Crude product was purified using a short plug of silica gel using ethyl acetate to give the desired product 1H-NMR (CDCL3) δ: 1.15-1.25 (2H, m), 1.40 (9H, s), 1.80-1.90 (2H, m), 2.85 (2H, dd), 3.5 (2H, s), 4.00 (1H, br s), 5.20 (1H, d), 7.15-7.35 (4H, m). ESI-MS m/z: 353 (M+1), UV retention time: 2.47 min.
Reaction SMILES: [CH3:1][O:2][C:3]([C:5]1[S:6][C:7]([Br:25])=[CH:8][C:9]=1[N:10]([CH:20]([CH2:23][OH:24])[CH2:21][OH:22])[C:11]([C@H:13]1[CH2:18][CH2:17][C@H:16]([CH3:19])[CH2:15][CH2:14]1)=[O:12])=[O:4].C=O.[C:28]([O-])(O)=O.[Na+]>O1CCOCC1>[CH3:1][O:2][C:3]([C:5]1[S:6][C:7]([Br:25])=[CH:8][C:9]=1[N:10]([CH:20]1[CH2:23][O:24][CH2:28][O:22][CH2:21]1)[C:11]([C@H:13]1[CH2:18][CH2:17][C@H:16]([CH3:19])[CH2:15][CH2:14]1)=[O:12])=[O:4]
Reactant: COC(=O)c1sc(Br)cc1N(C(=O)[C@H]1CC[C@H](C)CC1)C(CO)CO
Reactant: O=C([O-])O
Agent: C=O
Agent: [Na+]
Solvent: C1COCCO1
Product: COC(=O)c1sc(Br)cc1N(C(=O)[C@H]1CC[C@H](C)CC1)C1COCOC1
Temperature: 80 °C
Reaction time: 0.23 h

Procedure:
A mixture of 5-bromo-3-[(2-hydroxy-1-hydroxymethyl-ethyl)-(trans-4-methyl-cyclohexanecarbonyl)-amino]-thiophene-2-carboxylic acid methyl ester (18 mg, 0.041 mmol), paraformaldehyde (6 mg) and boron trifluoride-diethyl etherate (15 μl, 0.12 mmol) in dry dioxane (0.6 mL) was stirred at 80° C. for 14 min. It was cooled and added to ice and NaHCO3 solution mixture, extracted with ethyl acetate, washed with brine, dried and evaporated. Pure 5-bromo-3-[[1,3]dioxan-5-yl-(trans-4-methyl-cyclohexanecarbonyl)-amino]-thiophene-2-carboxylic acid methyl ester was obtained after chromatography over silica gel (hexane:ethyl acetate—9:1 as eluent) (15 mg; 81%).
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:4]=[C:5]([CH:9]=[CH:10]C=1N)[C:6]([OH:8])=[O:7].[H-].[Na+].CI.[CH3:17][N:18]([CH:20]=O)[CH3:19]>>[CH3:1][O:2][C:3]1[CH:4]=[C:5]([CH:9]=[CH:10][C:20]=1[N:18]([CH3:17])[CH3:19])[C:6]([OH:8])=[O:7]
Reactant: CN(C)C=O
Reactant: COc1cc(C(=O)O)ccc1N
Agent: [H-]
Agent: [Na+]
Solvent: CI
Product: COc1cc(C(=O)O)ccc1N(C)C
Reaction time: 0.5 h

Procedure:
To a solution of 3-methoxy-4-aminobenzoic acid (1.5 g, 9 mmol) in DMF (10 mL) was added sodium hydride (60% in mineral oil, 1.5 g, 37.5 mmol) at 0° C. in portions. After stirring for 30 minutes, methyl iodide (6 g, 45 mmol) was added. The mixture was stirred overnight and quenched by addition of water. The aqueous mixture was extracted with dichloromethane (2×20 mL), dried over sodium sulfate and concentrated in vacuo. Purification by flash chromatography eluting with hexane/EtOAc (4:1) afforded 3-methoxy-4-dimethylaminobenzoic acid as an oil (1.8 g).
Reaction SMILES: [Cu][C:2]#[N:3].[NH2:4][C:5]1[CH:14]=[CH:13][C:12](Br)=[CH:11][C:6]=1[C:7]([O:9][CH3:10])=[O:8]>CN1CCCC1=O.C(N)CN>[CH3:10][O:9][C:7](=[O:8])[C:6]1[CH:11]=[C:12]([C:2]#[N:3])[CH:13]=[CH:14][C:5]=1[NH2:4]
Reactant: COC(=O)c1cc(Br)ccc1N
Reactant: N#C[Cu]
Solvent: NCCN
Solvent: CN1CCCC1=O
Product: COC(=O)c1cc(C#N)ccc1N
Temperature: 180 °C
Reaction time: 4 h
Yield: 72.2 %

Procedure:
Copper(I) cyanide (available from Alfa Aesar; 10.71 g, 0.12 mol) was added to a stirred solution of methyl 2-amino-5-bromobenzoate (available from Aldrich Chemical Company, Inc.; 25.0 g, 0.11 mol) in N-methyl-2-pyrrolidone (50 mL) and the mixture was stirred at 180° C. for 4 h. The reaction mixture was cooled to room temperature, diluted with aqueous ethylenediamine (water:ethylenediamine=1:1; 250 mL), and filtered through pad of Celite. The filtrate was extracted with EtOAc (3×100 mL), and the combined organic layers were washed with water (100 mL) and brine (100 mL), dried over sodium sulfate, filtered, evaporated under reduced pressure, and purified by silica gel chromatography (100-200 mesh), using 5-10% ethyl acetate/hexanes as eluent, to give 2-amino-5-cyanobenzoic acid methyl ester (14.0 g, 73%) as a yellow powder. 1H NMR (400 MHz, DMSO-d6) δ 8.05 (d, J=1.9 Hz, 1H), 7.57 (dd, J=1.9, 8.8 Hz, 1H), 7.44 (br s, 2H), 6.88 (d, J=8.8 Hz, 1H), 3.81 (s, 3H).
Reaction SMILES: C(=O)([O-])[O-].[K+].[K+].Br[CH2:8][CH2:9][N:10]=[C:11]=[S:12].[Cl:13][C:14]1[C:15]([O:24][C:25]2[CH:29]=[C:28]([CH3:30])[NH:27][N:26]=2)=[N:16][CH:17]=[C:18]([C:20]([F:23])([F:22])[F:21])[CH:19]=1.Cl>CN(C=O)C>[CH:9]([NH:10][C:11]([N:27]1[C:28]([CH3:30])=[CH:29][C:25]([O:24][C:15]2[C:14]([Cl:13])=[CH:19][C:18]([C:20]([F:23])([F:22])[F:21])=[CH:17][N:16]=2)=[N:26]1)=[S:12])=[CH2:8]
Reactant: Cc1cc(Oc2ncc(C(F)(F)F)cc2Cl)n[nH]1
Reactant: S=C=NCCBr
Agent: Cl
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Product: C=CNC(=S)n1nc(Oc2ncc(C(F)(F)F)cc2Cl)cc1C
Temperature: 25 °C
Reaction time: 3 h
Yield: 6.1 %

Procedure:
Potassium carbonate (0.76 g, 5.5 mmol) and 2-bromoethyl isothiocyanate (0.83 g, 5 mmol) were added to a solution of 3-(3-chloro-5-trifluoromethylpyridin-2-yloxy)-5-methylpyrazole (1.39 g, 5.0 mmol) in DMF (15 ml), and the mixture was stirred at room temperature for 3 hours. After completion of the reaction, the reaction mixture was poured into 2N hydrochloric acid (30 ml) and extracted with ethyl acetate (30 ml×3). An organic layer was washed with water, dried over anhydrous magnesium sulfate and filtered to remove a desiccant, and the solvent was distilled off from the filtrate under reduced pressure. The resultant crude product was purified with a silica gel column (ethyl acetate/hexane=1/20→1/10), to give a white solid of N-vinyl-3-(3-chloro-5-trifluoromethylpyridin-2-yloxy)-5-methylpyrazole-1-carbothioamide (0.11 g, yield: 5.0%). mp: 90-92° C.; 1H-NMR (CDCl3, TMS, ppm): δ 2.87 (d, J=0.8 Hz, 3H), 4.79 (d, J=8.6 Hz, 1H), 5.00 (dd, J=0.9 and 15.7 Hz, 1H), 6.19 (q, J=0.8 Hz, 1H), 7.45 (ddd, J=0.9, 8.6 and 15.7 Hz, 1H), 8.04 (d, J=2.1 Hz, 1H), 8.36 (m, 1H), 10.15-10.55 (m, 1H).
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:19]=[C:18]([O:20][CH3:21])[CH:17]=[CH:16][C:4]=1[CH2:5][N:6]1[C:10](=O)[C@H:9]([CH:12]([CH3:14])[CH3:13])[NH:8][C:7]1=[O:15].O.O.O.O.O.O.O.O.O.O.S([O-])([O-])(=O)=O.[Na+].[Na+]>C1COCC1>[CH3:1][O:2][C:3]1[CH:19]=[C:18]([O:20][CH3:21])[CH:17]=[CH:16][C:4]=1[CH2:5][N:6]1[CH2:10][C@H:9]([CH:12]([CH3:14])[CH3:13])[NH:8][C:7]1=[O:15]
Reactant: COc1ccc(CN2C(=O)N[C@@H](C(C)C)C2=O)c(OC)c1
Agent: O=S(=O)([O-])[O-]
Agent: [Na+]
Solvent: C1CCOC1
Solvent: O
Product: COc1ccc(CN2C[C@H](C(C)C)NC2=O)c(OC)c1
Temperature: 0 °C
Yield: 62.9 %

Procedure:
To a solution of (S)-3-(2,4-dimethoxybenzyl)-5-isopropyl-imidazolidine-2,4-dione (0.550 g, 1.88 mmol) in THF (50 mL) at ambient temperature was added bis(2-methoxyethoxy)aluminumhydride (Red-Al) (2.69 ml, 9.41 mmol) and the resultant mixture heated at reflux for 1 hour. The reaction mixture was cooled to 0° C. and sodium sulfate decahydrate was added portion-wise. The resultant thick emulsion was diluted with THF and filtered through a pad of Celite. The filtrate was concentrated to a clear oil. Purification of the crude material by column chromatography, eluting with 1-5% MeOH/dichloromethane, afforded (S)-1-(2,4-dimethoxybenzyl)-4-isopropylimidazolidin-2-one as a colorless solid (0.329 g, 63%). LCMS (APCI+) m/z 279 [M+H]+.
Reaction SMILES: Br[C:2]1[CH:12]=[CH:11][C:5]([C:6]([O:8][CH2:9][CH3:10])=[O:7])=[CH:4][CH:3]=1.B([O-])([O-])O[C:15]1[CH:20]=[CH:19][N:18]=[CH:17][CH:16]=1.C(=O)([O-])O.[Na+].COCCOC>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.O>[N:18]1[CH:19]=[CH:20][C:15]([C:2]2[CH:12]=[CH:11][C:5]([C:6]([O:8][CH2:9][CH3:10])=[O:7])=[CH:4][CH:3]=2)=[CH:16][CH:17]=1
Reactant: CCOC(=O)c1ccc(Br)cc1
Reactant: [O-]B([O-])Oc1ccncc1
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: COCCOC
Solvent: O
Product: CCOC(=O)c1ccc(-c2ccncc2)cc1
Reaction time: 3 h
Yield: 56.3 %

Procedure:
To a mixture of ethyl 4-bromobenzoate (2.29 g), 4-pyridyl borate (1.23 g), 1 M sodium hydrogen carbonate solution (30 ml) and 1,2-dimethoxyethane (40 ml) was added tetrakis(triphenylphosphine)palladium (0.3 g) and the mixture was stirred for 3 hours with reflux under nitrogen atmosphere. To the mixture was added water and the solution was extracted with ethyl acetate. The extract was washed with water, dried (MgSO4) and concentrated. The residue was subjected to silica gel chromatography, and eluted with hexane-ethyl acetate (2:1) to give the title compound as crystals (1.15 g, 50.7%).
Reaction SMILES: [NH2:1][C:2]1[N:6]=[CH:5][NH:4][N:3]=1.[Cl:7][C:8]1[CH:19]=[C:18]([Cl:20])[CH:17]=[CH:16][C:9]=1[CH:10]=[C:11]([C:14]#[N:15])[C:12]#[N:13]>N1C=CC=CC=1>[NH2:15][C:14]1[N:3]2[N:4]=[CH:5][N:6]=[C:2]2[N:1]=[C:10]([C:9]2[CH:16]=[CH:17][C:18]([Cl:20])=[CH:19][C:8]=2[Cl:7])[C:11]=1[C:12]#[N:13]
Reactant: Nc1nc[nH]n1
Reactant: N#CC(C#N)=Cc1ccc(Cl)cc1Cl
Solvent: c1ccncc1
Product: N#Cc1c(-c2ccc(Cl)cc2Cl)nc2ncnn2c1N

Procedure:
A solution of 157 mg (1.87 mmol) of 3-amino-1,2,4-triazole and 417 mg (1.87 mmol) of (2,4-dichlorobenzylidene)malononitrile (Intermediate 1) in 4.7 mL of anhydrous pyridine was stirred at reflux under air for 22 h and then cooled and concentrated in vacuo. The residue was partitioned between 5% aqueous citric acid solution and a 1:1 mixture of ethyl acetate and tetrahydrofuran. The organic phase was washed once more with the citric acid solution and then (after addition of some more tetrahydrofuran) with saturated aqueous sodium chloride solution. The combined aqueous fractions were re-extracted with a 2:3 mixture of ethyl acetate and tetrahydrofuran. The combined organics were dried over magnesium sulfate, filtered, and concentrated in vacuo. Purification of the residue by flash chromatography on silica gel (gradient elution with 2-3% methanol in dichloromethane) afforded the title compound as an amber-colored glass, which was used without further purification. LC-MS 305 (M+1).
Reaction SMILES: [CH2:1]([O:5][C:6]1[C:11]([F:12])=[C:10](F)[N:9]=[CH:8][N:7]=1)[C:2]#[C:3][CH3:4].[CH3:14][CH:15]1[CH2:20][CH:19]([CH3:21])[CH2:18][NH:17][CH2:16]1>C1(C)C=CC=CC=1>[CH2:1]([O:5][C:6]1[C:11]([F:12])=[C:10]([N:17]2[CH2:18][CH:19]([CH3:21])[CH2:20][CH:15]([CH3:14])[CH2:16]2)[N:9]=[CH:8][N:7]=1)[C:2]#[C:3][CH3:4]
Reactant: CC#CCOc1ncnc(F)c1F
Reactant: CC1CNCC(C)C1
Solvent: Cc1ccccc1
Product: CC#CCOc1ncnc(N2CC(C)CC(C)C2)c1F
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 75.2 %

Procedure:
0.53 g of 4-(2-butynyloxy)-5,6-difluoropyrimidine and 0.39 g of 3,5-dimethylpiperidine (mixture of about cis:trans=7:3) were added to 1 ml of toluene, then the mixture was stirred at room temperature for 30 minutes. Then the reaction mixture was subjected to silica gel column chromatography to obtain 0.6 g of 4-(2-butynyloxy)-5-fluoro-6-(3,5-dimethylpiperidino)pyrimidine (referred as the present compound (4) hereinafter).