Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [CH2:1]([O:3][C:4]([C:6]1[NH:7][C:8]2[C:13]([C:14]=1[CH2:15][CH2:16][CH2:17][NH:18][C:19]([O:21][C:22]([CH3:25])([CH3:24])[CH3:23])=[O:20])=[CH:12][C:11]([NH2:26])=[CH:10][CH:9]=2)=[O:5])[CH3:2].C[Si]([N:31]=[C:32]=[O:33])(C)C>C(Cl)Cl.C(N(CC)CC)C>[CH2:1]([O:3][C:4]([C:6]1[NH:7][C:8]2[C:13]([C:14]=1[CH2:15][CH2:16][CH2:17][NH:18][C:19]([O:21][C:22]([CH3:25])([CH3:24])[CH3:23])=[O:20])=[CH:12][C:11]([NH:26][C:32]([NH2:31])=[O:33])=[CH:10][CH:9]=2)=[O:5])[CH3:2]
Reactant: C[Si](C)(C)N=C=O
Reactant: CCOC(=O)c1[nH]c2ccc(N)cc2c1CCCNC(=O)OC(C)(C)C
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CCOC(=O)c1[nH]c2ccc(NC(N)=O)cc2c1CCCNC(=O)OC(C)(C)C
Reaction time: 8 h

Procedure:
5-Amino-3-[3-(t-butoxycarbonylamino)-propyl]-1H-indole-2-carboxylic acid ethyl ester (40 mg, 0.11 mmol, 1.0 equiv) was dissolved in 10 mL of methylene chloride and 1 mL of triethylamine. Trimethylsilyl isocyanate was added and the solution was stirred overnight. In the morning the reaction was washed with 10 mL of water and the organic layer was concentrated. The crude residue was purified by flash chromatography on silica (10 g of SiO2) using 0% ethyl acetate in methylene chloride to 100% ethyl acetate graded over 25 min at a flow rate of 15 mL/min-then 100% ethylacetate for another 15 min. The fractions with pure product (TLC) were combined and concentrated to provide 5-ureido-3-[3-(t-butoxycarbonylamino)-propyl]-1H-indole-2-carboxylic acid ethyl ester as a white solid (41 mg). This material was used without further purification.
Reaction SMILES: [NH2:1][C:2]1[C:11]2[N:12]=[C:13]([CH2:20][O:21][CH2:22][CH3:23])[N:14]([CH2:15][C:16]([CH3:19])([OH:18])[CH3:17])[C:10]=2[C:9]2[N:8]=[CH:7][C:6](Br)=[CH:5][C:4]=2[N:3]=1.[Si:25]([O:32][CH2:33][C:34]1[CH:35]=[C:36](B(O)O)[CH:37]=[N:38][CH:39]=1)([C:28]([CH3:31])([CH3:30])[CH3:29])([CH3:27])[CH3:26].C(=O)([O-])[O-].[K+].[K+].COCCOC>Cl[Pd](Cl)([P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1)[P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1.O>[NH2:1][C:2]1[C:11]2[N:12]=[C:13]([CH2:20][O:21][CH2:22][CH3:23])[N:14]([CH2:15][C:16]([CH3:19])([OH:18])[CH3:17])[C:10]=2[C:9]2[N:8]=[CH:7][C:6]([C:36]3[CH:37]=[N:38][CH:39]=[C:34]([CH2:33][O:32][Si:25]([C:28]([CH3:31])([CH3:30])[CH3:29])([CH3:26])[CH3:27])[CH:35]=3)=[CH:5][C:4]=2[N:3]=1
Reactant: CCOCc1nc2c(N)nc3cc(Br)cnc3c2n1CC(C)(C)O
Reactant: CC(C)(C)[Si](C)(C)OCc1cncc(B(O)O)c1
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: O
Solvent: COCCOC
Product: CCOCc1nc2c(N)nc3cc(-c4cncc(CO[Si](C)(C)C(C)(C)C)c4)cnc3c2n1CC(C)(C)O
Temperature: 110 °C
Yield: 67.2 %

Procedure:
A suspension of 1-[4-amino-7-bromo-2-(ethoxymethyl)-1H-imidazo[4,5-c][1,5]naphthyridin-1-yl]-2-methylpropan-2-ol (1.5 g, 3.80 mmol), 5-(tert-butyldimethylsilanyloxymethyl)pyridine-3-boronic acid (1.22 g, 4.57 mmol), potassium carbonate (1.74 g, 12.6 mmol), dichlorobis(triphenylphosphine)palladium(II)(0.027 g, 0.038 mmol), DME (13 mL), and water (7 mL) was stirred under a nitrogen atmosphere and then heated at 110° C. in a pressure vessel for 6 hours and allowed to cool to room temperature. An analysis by LC/MS indicated the reaction was incomplete, and additional dichlorobis(triphenylphosphine)palladium(II)(0.035 g) was added. The reaction was heated at 110 C for 16 hours and allowed to cool to room temperature. The DME was removed under reduced pressure, and the resulting mixture was extracted with dichloromethane (3×25 mL). The combined organic extracts were dried over magnesium sulfate, filtered, and concentrated under reduced pressure. The resulting brown solid was dissolved in dichloromethane (15 mL) purified by chromatography according to the method described in Example 62 to provide 1.37 g of 1-{4-amino-7-[5-(tert-butyldimethylsilanyloxymethyl)pyridin-3-yl]-2-(ethoxymethyl)-1H-imidazo[4,5-c][1,5]naphthyridin-1-yl]-2-methylpropan-2-ol as a yellow solid.
Reaction SMILES: [NH2:1][CH:2]1[CH:11]([CH2:12][C:13]2[CH:18]=[CH:17][C:16]([Cl:19])=[C:15]([Cl:20])[CH:14]=2)[C:10]2[CH:9]=[C:8]([OH:21])[CH:7]=[CH:6][C:5]=2[CH2:4][CH2:3]1.C(N(CC)CC)C.[C:29](=O)([O:35]C(C)(C)C)[O:30][C:31]([CH3:34])([CH3:33])[CH3:32]>O1CCCC1>[Cl:20][C:15]1[CH:14]=[C:13]([CH:18]=[CH:17][C:16]=1[Cl:19])[CH2:12][CH:11]1[C:10]2[C:5](=[CH:6][CH:7]=[C:8]([OH:21])[CH:9]=2)[CH2:4][CH2:3][CH:2]1[NH:1][C:29](=[O:35])[O:30][C:31]([CH3:34])([CH3:33])[CH3:32]
Reactant: CC(C)(C)OC(=O)OC(C)(C)C
Reactant: NC1CCc2ccc(O)cc2C1Cc1ccc(Cl)c(Cl)c1
Solvent: CCN(CC)CC
Solvent: C1CCOC1
Product: CC(C)(C)OC(=O)NC1CCc2ccc(O)cc2C1Cc1ccc(Cl)c(Cl)c1

Procedure:
7-Amino-8-(3,4-dichlorobenzyl)-5,6,7,8-tetrahydronaphthalen-2-ol (10.8 g) and triethylamine (14.01 mL, 101 mmol) were dissolved in dry tetrahydrofuran (200 mL). Di-tert-butyl carbonate (7.31 g, 33.5 mmol) was added in small portions at room temperature. The reaction mixture was stirred over night. The solvent was evaporated in vacuo. The residue was dissolved in ethyl acetate (300 mL) and washed with water (2×200 mL). The ethyl acetate solution of the crude product was dried (Na2SO4). The solvent was evaporated in vacuo and the crude product was used for the next step without further purification. Yield: 12.2 g.
Reaction SMILES: CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.[Cl:25][C:26]1[CH:31]=[C:30]([Cl:32])[C:29]([O:33][CH3:34])=[CH:28][C:27]=1[N:35]1[CH2:40][CH2:39][NH:38][CH2:37][CH2:36]1.[Cl:41][C:42]1[C:43]([C:52]([F:55])([F:54])[F:53])=[N:44][N:45]([CH2:48][C:49](O)=[O:50])[C:46]=1[CH3:47]>>[Cl:41][C:42]1[C:43]([C:52]([F:54])([F:53])[F:55])=[N:44][N:45]([CH2:48][C:49]([N:38]2[CH2:39][CH2:40][N:35]([C:27]3[CH:28]=[C:29]([O:33][CH3:34])[C:30]([Cl:32])=[CH:31][C:26]=3[Cl:25])[CH2:36][CH2:37]2)=[O:50])[C:46]=1[CH3:47]
Reactant: Cc1c(Cl)c(C(F)(F)F)nn1CC(=O)O
Reactant: COc1cc(N2CCNCC2)c(Cl)cc1Cl
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Product: COc1cc(N2CCN(C(=O)Cn3nc(C(F)(F)F)c(Cl)c3C)CC2)c(Cl)cc1Cl

Procedure:
Title compound was prepared following the HATU mediated coupling protocol P, wherein 1-(2,4-Dichloro-5-methoxyphenyl)-piperazine and (4-Chloro-5-methyl-3-trifluoromethyl-pyrazol-1-yl)-acetic acid were used as the coupling components, to give the product as a solid: 1H NMR (DMSO-d6, 400 MHz) 7.50 (s, 1H), 6.84 (s, 1H), 5.37 (s, 2H), 3.85 (s, 3H), 3.62 (m, 4H), 3.07 (m, 2H), 3.00 (m, 2H), 2.19 (s, 3H) ppm; MS (ES) M+H expected=485.1, found=485.0.
Reaction SMILES: [Br:1][C:2]1[CH:7]=[C:6]([OH:8])[C:5]([O:9][CH3:10])=[CH:4][C:3]=1[CH2:11][C:12]([OH:14])=[O:13].S(=O)(=O)(O)O.[CH3:20]O>>[Br:1][C:2]1[CH:7]=[C:6]([OH:8])[C:5]([O:9][CH3:10])=[CH:4][C:3]=1[CH2:11][C:12]([O:14][CH3:20])=[O:13]
Reactant: COc1cc(CC(=O)O)c(Br)cc1O
Reactant: CO
Agent: O=S(=O)(O)O
Product: COC(=O)Cc1cc(OC)c(O)cc1Br

Procedure:
2-Bromo-4-hydroxy-5-methoxyphenylacetic acid is refluxed in methanol in the presence of sulfuric acid, to give methyl 2-(2-bromo-4-hydroxy-5-methoxyphenyl)acetate.
Reaction SMILES: [CH2:1]([O:8][C:9]([N:11]1[CH2:19][CH2:18][CH:14]([C:15]([OH:17])=O)[CH2:13][CH2:12]1)=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.C(N1C=CN=C1)(N1C=CN=C1)=O.[C:32]([O:36][C:37]([N:39]1[CH2:44][CH2:43][NH:42][CH2:41][CH2:40]1)=[O:38])([CH3:35])([CH3:34])[CH3:33]>O1CCCC1.ClCCl>[C:32]([O:36][C:37]([N:39]1[CH2:44][CH2:43][N:42]([C:15]([CH:14]2[CH2:13][CH2:12][N:11]([C:9]([O:8][CH2:1][C:2]3[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=3)=[O:10])[CH2:19][CH2:18]2)=[O:17])[CH2:41][CH2:40]1)=[O:38])([CH3:35])([CH3:33])[CH3:34]
Reactant: CC(C)(C)OC(=O)N1CCNCC1
Reactant: O=C(O)C1CCN(C(=O)OCc2ccccc2)CC1
Agent: O=C(n1ccnc1)n1ccnc1
Solvent: ClCCl
Solvent: C1CCOC1
Product: CC(C)(C)OC(=O)N1CCN(C(=O)C2CCN(C(=O)OCc3ccccc3)CC2)CC1
Temperature: 25 °C
Reaction time: 2 h
Yield: 89.3 %

Procedure:
To a solution of N-benzyloxycarbonyl isonipecotic acid (123.64 g) in tetrahydrofuran (300 ml) at 0° C. was added a solution of carbonyldiimidazole (68.80 g) in tetrahydrofuran (500 ml) and dichloromethane (300 ml). The resulting solution was stirred at ambient temperature for 2 hours. This solution was cooled to 0° C. and a solution of 1-(tert-butoxycarbonyl)piperazine (87.02 g) in tetrahydrofuran (200 ml) added dropwise over 20 minutes. The suspension obtained was stirred at ambient temperature for 48 hours. Solvent was evaporated. The residue was dissolved in diethyl ether/dichloromethane (1500 ml) and washed with water, 2M aqueous citric acid solution, saturated aqueous sodium bicarbonate solution, dried (Na2SO4) and evaporated to give 1-(tert-butoxycarbonyl)-4-[1-benzyloxycarbonylpiperidin-4-ylcarbonyl]piperazine (180.00 g) as a solid.
Reaction SMILES: [OH:1][C:2]1[CH:11]=[C:10]([CH3:12])[C:9]2[C:4](=[CH:5][CH:6]=[CH:7][CH:8]=2)[N:3]=1.[I-].C[N+]1C=CN([C:20](=[O:29])[N:21]([CH3:28])[C:22]2[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=2)C=1.C(N(CC)CC)C>C(#N)C>[CH3:12][C:10]1[C:9]2[C:4](=[CH:5][CH:6]=[CH:7][CH:8]=2)[N:3]=[C:2]([O:1][C:20](=[O:29])[N:21]([CH3:28])[C:22]2[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=2)[CH:11]=1
Reactant: CN(C(=O)n1cc[n+](C)c1)c1ccccc1
Reactant: Cc1cc(O)nc2ccccc12
Agent: [I-]
Solvent: CCN(CC)CC
Solvent: CC#N
Product: Cc1cc(OC(=O)N(C)c2ccccc2)nc2ccccc12
Temperature: 25 °C
Reaction time: 18 h
Yield: 27.4 %

Procedure:
A mixture of 2-hydroxy-4-methylquinoline (0.48 g, 3.00 mmol) ), 1-methyl-3-(methyl-phenyl-carbamoyl)-3H-imidazol-1-ium iodide (1.03 g, 3.00 mmol) and triethylamine (0.42 ml, 3.00 mmol) in acetonitrile (15 ml) was stirred at room temperature for 18 hours followed by heating at 50° C. for 4 days. The solvent was evaporated in vacuo and the residue was purified by flash column chromatography (SiO2, ethyl acetate:heptane (30:70)) yielding the title compound (0.24 g, 27% yield) as a white solid.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2([C:13]([OH:15])=O)[CH2:12][CH2:11][CH2:10][CH2:9]2)=[CH:4][CH:3]=1.[NH2:16][CH2:17][CH2:18][CH2:19][N:20]1[CH2:25][CH2:24][CH:23]([C:26]2[N:31]=[C:30]([NH:32][C:33](=[O:37])[CH:34]([CH3:36])[CH3:35])[CH:29]=[CH:28][CH:27]=2)[CH2:22][CH2:21]1>>[Cl:1][C:2]1[CH:3]=[CH:4][C:5]([C:8]2([C:13]([NH:16][CH2:17][CH2:18][CH2:19][N:20]3[CH2:25][CH2:24][CH:23]([C:26]4[CH:27]=[CH:28][CH:29]=[C:30]([NH:32][C:33](=[O:37])[CH:34]([CH3:35])[CH3:36])[N:31]=4)[CH2:22][CH2:21]3)=[O:15])[CH2:9][CH2:10][CH2:11][CH2:12]2)=[CH:6][CH:7]=1
Reactant: CC(C)C(=O)Nc1cccc(C2CCN(CCCN)CC2)n1
Reactant: O=C(O)C1(c2ccc(Cl)cc2)CCCC1
Product: CC(C)C(=O)Nc1cccc(C2CCN(CCCNC(=O)C3(c4ccc(Cl)cc4)CCCC3)CC2)n1

Procedure:
Example 84 was prepared from 1-(4-chlorophenyl)cyclopentanecarboxylic acid and N-{6-[1-(3-aminopropyl)-4-piperidinyl]-2-pyridinyl}-2-methylpropanamide according to the procedures described in Scheme 10: 1H NMR (400 MHz, CDCl3) δ 8.07 (d, 1H, J=8.4 Hz), 7.81 (s, 1H), 7.66 (t,1H, J=7.6 Hz), 7.36–7.33 (m, 2H), 7.30–7.27 (m, 2H), 6.90 (d, 1H, J=6.8 Hz), 6.60 (br s, 1H), 3.28 (dd, 2H, J=5.6, 12.0 Hz), 2.95 (d, 2H, J=11.6 Hz), 2.55–2.49 (m, 4H), 2.33 (t, 2H, J=6.4 Hz), 2.00–1.61 (m, 14H), 1.26 (d, 6H, J=6.8 Hz); ESMS m/e: 511.3 (M+H)+.
Reaction SMILES: Br[C:2]1[CH:7]=[CH:6][C:5]([N+:8]([O-:10])=[O:9])=[CH:4][C:3]=1[CH3:11].CCN(C(C)C)C(C)C.[C:21]([O:25][CH3:26])(=[O:24])[CH:22]=[CH2:23].C1(C)C=CC=CC=1P(C1C=CC=CC=1C)C1C=CC=CC=1C>C(#N)CC.CC([O-])=O.CC([O-])=O.[Pd+2]>[CH3:26][O:25][C:21](=[O:24])[CH:22]=[CH:23][C:2]1[CH:7]=[CH:6][C:5]([N+:8]([O-:10])=[O:9])=[CH:4][C:3]=1[CH3:11]
Reactant: Cc1cc([N+](=O)[O-])ccc1Br
Reactant: C=CC(=O)OC
Agent: [Pd+2]
Agent: CC(=O)[O-]
Agent: Cc1ccccc1P(c1ccccc1C)c1ccccc1C
Solvent: CCN(C(C)C)C(C)C
Solvent: CCC#N
Product: COC(=O)C=Cc1ccc([N+](=O)[O-])cc1C
Temperature: 110 °C
Yield: 91.1 %

Procedure:
To a solution of 2-bromo-5-nitrotoluene (3.11 g, 14.39 mmol) in propionitrile (105 mL) is added DIPEA (5.1 mL, 29.28 mmol). The mixture is degassed three times. Methyl acrylate (5.2 mL, 57.74 mmol) is added and the mixture is degassed. Tri-o-tolylphosphine (1.77 g, 5.82 mmol) and Pd(OAc)2 (0.64 g, 2.85 mmol) are added and the mixture is degassed a final two times followed by heating at 110° C. for 4 h. Upon cooling, the mixture is passed through Celite and the filtrate is concentrated. The residue is partitioned between Et2O and 1N HCl. The organics are washed with saturated NaHCO3 and brine, and dried with Na2SO4. The crude material is purified by flash chromatography to yield the title compound (2.90 g, 91%).
Reaction SMILES: [N:1]#[N:2].[C:3]([NH:6][C:7]1[NH:8][C:9](=[O:37])[C:10]2[N:11]=[CH:12][N:13]([CH2:16][O:17][CH:18]([CH2:28][O:29]CC3C=CC=CC=3)[CH2:19][O:20]CC3C=CC=CC=3)[C:14]=2[N:15]=1)(=[O:5])[CH3:4].[H][H]>CO.O.[OH-].[OH-].[Pd+2]>[N:1]#[N:2].[C:3]([NH:6][C:7]1[NH:8][C:9](=[O:37])[C:10]2[N:11]=[CH:12][N:13]([CH2:16][O:17][CH:18]([CH2:19][OH:20])[CH2:28][OH:29])[C:14]=2[N:15]=1)(=[O:5])[CH3:4]
Reactant: CC(=O)Nc1nc2c(ncn2COC(COCc2ccccc2)COCc2ccccc2)c(=O)[nH]1
Reactant: [H][H]
Agent: [Pd+2]
Agent: N#N
Agent: [OH-]
Solvent: O
Solvent: CO
Product: CC(=O)Nc1nc2c(ncn2COC(CO)CO)c(=O)[nH]1
Yield: 44.5 %

Procedure:
To a solution of N2 -acetyl-9-(1,3-dibenzyloxy-2-propoxymethyl)guanine (4.62 g, 9.67 mmol) in 150 ml of methanol plus 40 ml of water was added 20% palladium hydroxide on carbon as a slurry in 10 ml of water. The mixture was hydrogenated on a Parr hydrogenator at 60 psi of hydrogen for 38 hours then filtered through celite and concentrated to a white solid. Recrystallization from methanol/ethyl acetate gave 1.4 g of N2 -acetyl-9-(1,3-dihydroxy-2-propoxymethyl)guanine, mp 205-208° C.
Reaction SMILES: C([Li])CCC.Br[C:7]1[CH:8]=[CH:9][CH:10]=[C:11]2[C:16]=1[CH2:15][CH:14]([N:17]([CH2:21][CH2:22][CH3:23])[CH2:18][CH2:19][CH3:20])[CH2:13][CH2:12]2.[CH3:24][Sn:25](Cl)([CH3:27])[CH3:26].O>C1COCC1>[CH2:18]([N:17]([CH2:21][CH2:22][CH3:23])[CH:14]1[CH2:13][CH2:12][C:11]2[C:16](=[C:7]([Sn:25]([CH3:27])([CH3:26])[CH3:24])[CH:8]=[CH:9][CH:10]=2)[CH2:15]1)[CH2:19][CH3:20]
Reactant: C[Sn](C)(C)Cl
Reactant: CCCN(CCC)C1CCc2cccc(Br)c2C1
Agent: [Li]CCCC
Solvent: C1CCOC1
Solvent: O
Product: CCCN(CCC)C1CCc2cccc([Sn](C)(C)C)c2C1
Temperature: 25 °C
Reaction time: 1.5 h
Yield: 152.2 %

Procedure:
Butyllithium (1.2M in hexane; 2.8 ml; 3.4 mmol) was added to a solution of 8-bromo-2-di-n-propylamino-1,2,3,4-tetrahydronaphthalene (1 g; 3.22 mmol) in THF (50 ml) at -78° C. After 1.5 hr., a solution of trimethyltin chloride (1.3 g, 2.0 mmol) in THF (20 ml) was added. The reaction mixture was allowed to warm to room temperature, stirred overnight at room temperature, poured into water, and extracted with methylene chloride. The extract was dried (Na2SO4) and concentrated to give the crude product. Purification by chromatography using 1:10 methanol:methylene chloride gave 1.2 g of the desired product which was used directly in the next step.
Reaction SMILES: [F:1][C:2]([F:14])([F:13])[C:3]1[CH:12]=[CH:11][C:6]2[NH:7][C:8](=O)[NH:9][C:5]=2[CH:4]=1.O=P(Cl)(Cl)[Cl:17]>>[Cl:17][C:8]1[NH:7][C:6]2[CH:11]=[CH:12][C:3]([C:2]([F:14])([F:13])[F:1])=[CH:4][C:5]=2[N:9]=1
Reactant: O=c1[nH]c2ccc(C(F)(F)F)cc2[nH]1
Reactant: O=P(Cl)(Cl)Cl
Product: FC(F)(F)c1ccc2[nH]c(Cl)nc2c1

Procedure:
Reflux 5-trifluoromethyl-1,3-dihydro-benzimidazol-2-one (17 g; Meanwell et al. (1995) J. Org. Chem. 60(6):1565-1582) for 14 hours in POCl3 (200 mL). Evaporate the solvent in vacuo, then carefully neutralize with saturated NaHCO3, and extract with EtOAc. Dry over Na2SO4, concentrate under vacuum, and purify by flash chromatography (1:1 hexanes/EtOAc) to obtain 2-chloro-5-trifluoromethyl-1H-benzimidazole. B. 1′-(5-Trifluoromethyl-1H-benzimidazol-2-yl)-spiro[isobenzofuran-1,4′-piperidin]-3-one hydrochloride
Reaction SMILES: N1C=CC=CC=1.[C:7]1([S:13][CH:14]=[CH:15][C:16](Cl)=[O:17])[CH:12]=[CH:11][CH:10]=[CH:9][CH:8]=1.Cl.[CH2:20]([O:27][NH2:28])[C:21]1[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=1>C1COCC1>[CH2:20]([O:27][NH:28][C:16](=[O:17])[CH:15]=[CH:14][S:13][C:7]1[CH:12]=[CH:11][CH:10]=[CH:9][CH:8]=1)[C:21]1[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=1
Reactant: O=C(Cl)C=CSc1ccccc1
Reactant: NOCc1ccccc1
Agent: Cl
Solvent: c1ccncc1
Solvent: C1CCOC1
Product: O=C(C=CSc1ccccc1)NOCc1ccccc1
Temperature: 25 °C
Reaction time: 3 h
Yield: 81.2 %

Procedure:
Pyridine (2.7 ml) was added to THF (80 ml) solution of 3-(phenylthio)acryloyl chloride (3.0 g) and hydrochloric acid salt of O-benzylhydroxylamine (2.6 g) under ice-cooling and stirred at the same temperature for one hour and at room temperature for three hours. The reaction mixture was concentrated under reduced pressure. Chloroform (150 ml) was added to the residue, washed successively with 1N hydrochloric acid, pure water and aqueous saturated sodium chloride solution, dried over anhydrous magnesium sulfate and concentrated under reduced pressure. The residue was subjected to silica gel column chromatography (hexane:ethyl acetate 2:1) to obtain N-benzyloxy-3-(phenylthio)acrylamide (3.5 g) as colorless oil. N-benzyloxy-3-(phenylthio)acrylamide (1.0 g) was dissolved to acetonitrile (70 ml), carbon tetrabromide (2.3 g) and triphenylphosphine (1.8 g) were added thereto under ice-cooling, then heat refluxing for four hours. The reaction mixture was concentrated under reduced pressure. The residue was subjected to silica gel column chromatography (hexane:ethyl acetate 20:1) to obtain N-benzyloxy-3-(phenylthio)acrylimidoyl bromide (1.1 g) as light yellow oil.
Reaction SMILES: [C:1]([O:5][C:6]([NH:8][C:9]([CH3:14])([CH3:13])[C:10]([OH:12])=O)=[O:7])([CH3:4])([CH3:3])[CH3:2].CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.Cl.[CH3:40][C@H:41]1[CH2:46][O:45][CH2:44][CH2:43][N:42]1[C:47]1[N:48]=[C:49]([C:62]2[CH:63]=[N:64][C:65]([NH2:68])=[N:66][CH:67]=2)[C:50]2[CH2:55][CH2:54][N:53]([C@@:56]3([CH3:61])[CH2:60][CH2:59][NH:58][CH2:57]3)[C:51]=2[N:52]=1.O>CN(C=O)C>[NH2:68][C:65]1[N:66]=[CH:67][C:62]([C:49]2[C:50]3[CH2:55][CH2:54][N:53]([C@@:56]4([CH3:61])[CH2:60][CH2:59][N:58]([C:10](=[O:12])[C:9]([NH:8][C:6](=[O:7])[O:5][C:1]([CH3:2])([CH3:3])[CH3:4])([CH3:14])[CH3:13])[CH2:57]4)[C:51]=3[N:52]=[C:47]([N:42]3[CH2:43][CH2:44][O:45][CH2:46][C@@H:41]3[CH3:40])[N:48]=2)=[CH:63][N:64]=1
Reactant: C[C@H]1COCCN1c1nc(-c2cnc(N)nc2)c2c(n1)N([C@@]1(C)CCNC1)CC2
Reactant: CC(C)(C)OC(=O)NC(C)(C)C(=O)O
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: Cl
Agent: F[P-](F)(F)(F)(F)F
Solvent: CN(C)C=O
Solvent: O
Product: C[C@H]1COCCN1c1nc(-c2cnc(N)nc2)c2c(n1)N([C@@]1(C)CCN(C(=O)C(C)(C)NC(=O)OC(C)(C)C)C1)CC2
Temperature: 0 °C
Reaction time: 0.67 h
Yield: 77.8 %

Procedure:
To a solution of 2-tert-butoxycarbonylamino-2-methyl-propionic acid (728 mg, 3.58 mmol) in anhydrous DMF (13.8 mL) at 0° C. was added HATU (1570 mg, 4.13 mmol) portionwise, and the mixture was stirred at 0° C. for 40 min. 5-{2-[(3S)-3-methylmorpholin-4-yl]-7-[(3S)-3-methylpyrrolidin-3-yl]-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl}pyrimidin-2-amine hydrochloride (1294 mg, 2.757 mmol) and TEA (1.92 ml, 13.8 mmol) were added and the reaction mixture was stirred at room temperature for 2 h. Water was added, the mixture was extracted with EtOAc (3 times), the combined organic layers were washed with brine, and dried over Na2SO4. The residue was purified via ISCO silica gel chromatography (40 g column) using a gradient of 0-100% EtOAc containing 10% MeOH/EtOAc to give the title compound (1247 mg, 78%) as a yellow solid. 1H NMR (400 MHz, DMSO-d6) δ 8.73 (s, 2 H), 6.59 (br s, 3 H), 4.67-4.54 (m, 1 H), 4.23 (d, J=11.5 Hz, 1 H), 3.92 (d, J=14.2 Hz, 1 H), 3.83 (d, J=11.4 Hz, 1 H), 3.70-3.40 (m, 7 H), 3.22-3.05 (m, 6 H), 2.12-2.02 (m, 1 H), 1.37 (s, 9 H), 1.35 (s, 6 H), 1.31 (s, 3 H). m/z (APCI+) for C29H43N9O4 582.7 (M+H)+.
Reaction SMILES: [CH3:1][C:2]([OH:13])([CH3:12])[CH2:3][N:4]1[CH:8]=[C:7]([N+:9]([O-])=O)[CH:6]=[N:5]1.[H][H]>CO.[Pd]>[NH2:9][C:7]1[CH:6]=[N:5][N:4]([CH2:3][C:2]([CH3:12])([OH:13])[CH3:1])[CH:8]=1
Reactant: CC(C)(O)Cn1cc([N+](=O)[O-])cn1
Reactant: [H][H]
Agent: [Pd]
Solvent: CO
Product: CC(C)(O)Cn1cc(N)cn1
Temperature: 25 °C
Reaction time: 16 h
Yield: 83.5 %

Procedure:
2-methyl-1-(4-nitro-1H-pyrazol-1-yl)propan-2-ol (2.0 g, 10.8 mmol) was dissolved in MeOH (50 mL) and 10% Pd/C (240 mg) was added. A hydrogen balloon was fitted over the reaction and the reaction was allowed to stir at rt for 16 hrs. The reaction was checked using the polar APCI method and LCMS showed 70% complete with 30% starting material remaining. Another 200 mg of 10% Pd/C was added and the balloon was re-charged with fresh hydrogen. After 4 hrs, the reaction was complete. The reaction was filtered through Celite, washing with MeOH (three×50 mL) and the combined filtrate was concentrated to dryness. Purification was accomplished via flash chromatography eluting with gradient of 3%-20% MeOH in DCM. The pure fractions were pooled and concentrated to afford the title compound (1.4 g, 84% yield) as a purple solid. 1H NMR (400 MHz, chloroform-d) δ ppm 1.14 (s, 6H), 3.92 (s, 2H), 7.04 (s, 1H), 7.19 (s, 1H); m/z (APCI+) for C7H13N3O 156.0 (M+H)+.
Reaction SMILES: [Cl:1][C:2]1[N:3]=[CH:4][C:5]2[NH:11][C:10](=[O:12])[CH:9]([CH3:13])[CH2:8][N:7]([CH:14]3[CH2:18][CH2:17][CH2:16][CH2:15]3)[C:6]=2[N:19]=1.[C:20](=O)([O-])[O-].[Cs+].[Cs+].CI>CN(C)C=O>[Cl:1][C:2]1[N:3]=[CH:4][C:5]2[N:11]([CH3:20])[C:10](=[O:12])[CH:9]([CH3:13])[CH2:8][N:7]([CH:14]3[CH2:18][CH2:17][CH2:16][CH2:15]3)[C:6]=2[N:19]=1
Reactant: O=C([O-])[O-]
Reactant: CC1CN(C2CCCC2)c2nc(Cl)ncc2NC1=O
Agent: [Cs+]
Solvent: CN(C)C=O
Solvent: CI
Product: CC1CN(C2CCCC2)c2nc(Cl)ncc2N(C)C1=O
Reaction time: 4 h
Yield: 92 %

Procedure:
To a solution of 46.72 g (0.166 mole) of (rac)-2-chloro-9-cyclopentyl-7-methyl-5,7,8,9-tetrahydro-pyrimido[4,5-b][1,4]diazepin-6-one in 1000 mL of dimethylformamide was added 81.32 g (0.25 mole) of cesium carbonate, followed by 70.88 g (0.499 mole) of methyl iodide. After stirring four hours, the mixture filtered and then concentrated under reduced pressure. The residue was taken up in ethyl acetate and washed four times with water, once with brine and dried over anhydrous sodium sulfate. The mixture was filtered and then concentrated under reduced pressure to give 45 g of (rac)-2-chloro-9-cyclopentyl-5,7-dimethyl-5,7,8,9-tetrahydro-pyrimido[4,5-b][1,4]diazepin-6-one (VII-1). This material was used subsequent steps without further purification.
Reaction SMILES: [Br-].[C:2]1(C([PH3+])(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.C([Li])CCC.[F:27][C:28]([F:42])([F:41])[C:29]1[CH:40]=[CH:39][C:32]2[CH:33](O)[O:34][CH:35]([CH:36]=[CH2:37])[C:31]=2[CH:30]=1>CCOCC.CCCCCC>[F:27][C:28]([F:42])([F:41])[C:29]1[CH:40]=[CH:39][C:32]([CH:33]=[CH2:2])=[C:31]([CH:35]([OH:34])[CH:36]=[CH2:37])[CH:30]=1
Reactant: C=CC1OC(O)c2ccc(C(F)(F)F)cc21
Reactant: [PH3+]C(c1ccccc1)(c1ccccc1)c1ccccc1
Agent: [Br-]
Agent: [Li]CCCC
Solvent: CCCCCC
Solvent: CCOCC
Product: C=Cc1ccc(C(F)(F)F)cc1C(O)C=C
Temperature: 0 °C
Reaction time: 8 h
Yield: 81.8 %

Procedure:
Triphenylmethylphosphonium bromide (1.71 g, 4.78 mmol) was dissolved in ether (20.00 mL). After cooling to 0° C., a 1.60 M solution of n-butyllithium in hexane (2.72 mL) was added rapidly by syringe and the resulting orange mixture was warmed to room temperature and stirred overnight. The stirring was stopped to allow the solids to settle and then the yield was transferred via cannula to a solution of 5-(trifluoromethyl)-3-vinyl-1,3-dihydro-2-benzofuran-1-ol (1.00 g, 4.34 mmol) in ether (10.00 mL) while stirring at 0° C. Following the addition, the ice bath was removed and the mixture was heated to reflux overnight. The reaction was allowed to cool and then the solids filtered off and washed with a small amount of ether. Most of the solvents were evaporated and the crude product was loaded onto silica gel and eluted with hexane/EtOAc (10:1) to give the desired product (0.81 g, 82%), LC-MS [M+1]=229.2.