Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [CH2:1]([O:3][C:4](=[O:17])[CH:5]([C:11]1[CH:16]=[CH:15][CH:14]=[CH:13][CH:12]=1)[C:6]([O:8][CH2:9][CH3:10])=[O:7])[CH3:2].[H-].[Na+].[C:20]1([CH3:31])[CH:25]=[CH:24][C:23]([CH2:26][CH2:27][CH2:28][CH2:29]Br)=[CH:22][CH:21]=1>O1CCCC1>[CH2:9]([O:8][C:6](=[O:7])[C:5]([C:11]1[CH:16]=[CH:15][CH:14]=[CH:13][CH:12]=1)([CH2:29][CH2:28][CH2:27][CH2:26][C:23]1[CH:22]=[CH:21][C:20]([CH3:31])=[CH:25][CH:24]=1)[C:4]([O:3][CH2:1][CH3:2])=[O:17])[CH3:10]
Reactant: Cc1ccc(CCCCBr)cc1
Reactant: CCOC(=O)C(C(=O)OCC)c1ccccc1
Agent: [H-]
Agent: [Na+]
Solvent: C1CCOC1
Product: CCOC(=O)C(CCCCc1ccc(C)cc1)(C(=O)OCC)c1ccccc1
Yield: 55 %

Procedure:
Phenylmalonic acid diethyl ester (8.8 mmol) dissolved in 5 ml absolute tetrahydrofuran is added dropwise to 20 ml absolute tetrahydrofuran and sodium hydride (9.7 mmol). Then 4-p-tolylbutyl bromide (8.8 mmol) dissolved in 10 ml absolute tetrahydrofuran is added after 15 minutes. It is heated for 3 days under reflux. The solvent is concentrated in a vacuum. The residue is taken up in 50 ml acette and extracted with 2×50 ml water. The organic phase is dried over magnesium sulfate, filtered and concentrated by evaporation. It is purified by chromatography on silica gel (heptane/ethyl acetate 9:1). Yield 55% colouriess oil.
Reaction SMILES: [CH3:1][S:2][C:3](SC)=[C:4]([C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1)[C:5]([C:7]1[CH:12]=[CH:11][CH:10]=[CH:9][CH:8]=1)=O.O.[NH2:22][NH2:23].O>C(O)C>[CH3:1][S:2][C:3]1[NH:23][N:22]=[C:5]([C:7]2[CH:12]=[CH:11][CH:10]=[CH:9][CH:8]=2)[C:4]=1[C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1
Reactant: CSC(SC)=C(C(=O)c1ccccc1)c1ccccc1
Reactant: NN
Solvent: O
Solvent: CCO
Product: CSc1[nH]nc(-c2ccccc2)c1-c1ccccc1
Yield: 89.3 %

Procedure:
To a suspension of 3,3-bis(methylthio)-1,2-diphenylprop-2-en-1-one (2.5 g, 8.32 mmol) in ethanol (20 mL), was added hydrazine hydrate (1.67 g, 33.3 mmol) at room temperature. The reaction was refluxed for 6 h. After cooling, the reaction was poured into water and extracted with ethyl acetate. The organic extract was dried over MgSO4 and concentrated under reduced pressure. The residue was purified by column chromatography to give the title compound (1.98 g). LCMS m/z=267.0 [M+H]+.
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[CH2:20][C@@H:19]([CH3:21])[N:18]2[C@H:10]([CH2:11][C:12]3[C:17]2=[N:16][C:15]([CH2:22][O:23][CH2:24][CH:25]2[CH2:27][CH2:26]2)=[C:14](Br)[CH:13]=3)[CH2:9]1)=[O:7])([CH3:4])([CH3:3])[CH3:2].C1(P(C2C=CC=CC=2)CCCP(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.C(N(CC)CC)C>CO.C([O-])(=O)C.[Pd+2].C([O-])(=O)C>[CH3:1][O:5][C:6]([C:14]1[CH:13]=[C:12]2[C:17]([N:18]3[C@H:10]([CH2:11]2)[CH2:9][N:8]([C:6]([O:5][C:1]([CH3:4])([CH3:3])[CH3:2])=[O:7])[CH2:20][C@H:19]3[CH3:21])=[N:16][C:15]=1[CH2:22][O:23][CH2:24][CH:25]1[CH2:27][CH2:26]1)=[O:7]
Reactant: C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H]2Cc3cc(Br)c(COCC4CC4)nc3N21
Agent: [Pd+2]
Agent: CC(=O)[O-]
Agent: c1ccc(P(CCCP(c2ccccc2)c2ccccc2)c2ccccc2)cc1
Solvent: CO
Solvent: CCN(CC)CC
Product: COC(=O)c1cc2c(nc1COCC1CC1)N1[C@H](C2)CN(C(=O)OC(C)(C)C)C[C@H]1C
Temperature: 100 °C
Reaction time: 48 h
Yield: 87 %

Procedure:
A mixture of 1.5 g (3.31 mmol) (4R,9aR)-7-bromo-6-cyclopropylmethoxymethyl-4-methyl-3,4,9,9a-tetrahydro-1H-2,4a,5-triaza-fluorene-2-carboxylic acid tert-butyl ester, 0.11 g (0.50 mmol) palladium(II) acetate, 0.68 g (1.66 mmol) 1,3-bis(diphenylphosphino)propane and 1.4 mL (1.0 g, 10.0 mmol) triethylamine in 15 mL MeOH was stirred for 48 h at 100° C. under a carbon monoxide atmosphere (50 bar). The reaction mixture was cooled to room temperature, filtered and partitioned between ethyl acetate and water. The organic phase was washed with brine, dried over magnesium sulphate, filtered and evaporated. The residue was purified by column chromatography over silica gel (0.030–0.063 mm) with ethyl acetate:n-hexane (1:3) as eluant to give the compound as a yellow oil (87%).
Reaction SMILES: CC1(C)C(C)(C)OB([C:9]2[CH:10]=[C:11]3[C:15](=[CH:16][CH:17]=2)[CH2:14][C@H:13]([NH:18][S:19]([CH:22]([CH3:24])[CH3:23])(=[O:21])=[O:20])[CH2:12]3)O1.[OH:26]OS([O-])=O.[K+]>CC(C)=O.O>[OH:26][C:9]1[CH:10]=[C:11]2[C:15](=[CH:16][CH:17]=1)[CH2:14][C@H:13]([NH:18][S:19]([CH:22]([CH3:24])[CH3:23])(=[O:21])=[O:20])[CH2:12]2
Reactant: CC(C)S(=O)(=O)N[C@H]1Cc2ccc(B3OC(C)(C)C(C)(C)O3)cc2C1
Reactant: O=S([O-])OO
Agent: [K+]
Solvent: CC(C)=O
Solvent: O
Product: CC(C)S(=O)(=O)N[C@H]1Cc2ccc(O)cc2C1

Procedure:
To a stirred solution of (S)-N-(5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2,3-dihydro-1H-inden-2-yl)propane-2-sulfonamide (6.95 mmol, 2.54 g) in Acetone (20.00 mL), a solution of Oxone(R), monopersulfate compound (7.65 mmol, 4.70 g) in Water (20 mL) was added dropwise over 2 min. The resultant solution was stirred for a further 10 min before being quenched with NaHSO3 (aq). The solution was extracted with DCM (×3), dried (MgSO4), filtered and concentrated in vacuo to give the crude product as a pale yellow oil (2.42 g). On standing the reaction mixture solidified to a pale yellow solid in an oily residue. The solid was triturated with heptane then ether to give the title compound as an off white solid (1.66 g, 94%). MS (ESI): m/z [M−H]− 254.0
Reaction SMILES: [NH2:1][C@H:2]([C:4]1[N:13]([C:14]2[CH:19]=[CH:18][CH:17]=[C:16]([O:20][CH2:21][C:22]([F:25])([F:24])[F:23])[CH:15]=2)[C:12](=[O:26])[C:11]2[C:6](=[CH:7][CH:8]=[CH:9][C:10]=2[Cl:27])[N:5]=1)[CH3:3].Cl[C:29]1[C:30]2[CH:37]=[CH:36][NH:35][C:31]=2[N:32]=[CH:33][N:34]=1.C(N(C(C)C)CC)(C)C>CC(O)(C)C>[N:32]1[C:31]2[NH:35][CH:36]=[CH:37][C:30]=2[C:29]([NH:1][C@H:2]([C:4]2[N:13]([C:14]3[CH:19]=[CH:18][CH:17]=[C:16]([O:20][CH2:21][C:22]([F:23])([F:25])[F:24])[CH:15]=3)[C:12](=[O:26])[C:11]3[C:6](=[CH:7][CH:8]=[CH:9][C:10]=3[Cl:27])[N:5]=2)[CH3:3])=[N:34][CH:33]=1
Reactant: C[C@H](N)c1nc2cccc(Cl)c2c(=O)n1-c1cccc(OCC(F)(F)F)c1
Reactant: Clc1ncnc2[nH]ccc12
Solvent: CC(C)(C)O
Solvent: CCN(C(C)C)C(C)C
Product: C[C@H](Nc1ncnc2[nH]ccc12)c1nc2cccc(Cl)c2c(=O)n1-c1cccc(OCC(F)(F)F)c1
Temperature: 120 °C
Reaction time: 28 h
Yield: 14.6 %

Procedure:
Under nitrogen, to (S)-2-(1-aminoethyl)-5-chloro-3-(3-(2,2,2-trifluoroethoxy)phenyl)quinazolin-4(3H)-one (80 mg, 0.20 mmol, 1.0 equiv) in t-BuOH (0.2 mL) at 23° C. was added 4-chloro-7H-pyrrolo[2,3-d]pyrimidine (34 mg, 0.22 mmol, 1.1 equiv) and diisopropylethylamine (70 μL, 0.40 mmol, 2.0 equiv). After stirring for 28 hr at 120° C. in a sealed tube, the reaction mixture was concentrated in vacuo and the residue was purified by preparative TLC eluting with CH2Cl2/MeOH to afford 15 mg of the title compound (15% yield).
Reaction SMILES: [F:1][C:2]1[CH:3]=[C:4]([CH:28]=[C:29]([F:31])[CH:30]=1)[CH2:5][C@H:6]([NH:20]C(=O)OC(C)(C)C)[C@H:7]([OH:19])[CH2:8][NH:9][CH2:10][C:11]1[CH:16]=[CH:15][CH:14]=[C:13]([O:17][CH3:18])[CH:12]=1.[F:32][C:33]([F:38])([F:37])[C:34]([OH:36])=[O:35]>C(Cl)Cl>[F:32][C:33]([F:38])([F:37])[C:34]([OH:36])=[O:35].[NH2:20][C@@H:6]([CH2:5][C:4]1[CH:28]=[C:29]([F:31])[CH:30]=[C:2]([F:1])[CH:3]=1)[C@H:7]([OH:19])[CH2:8][NH:9][CH2:10][C:11]1[CH:16]=[CH:15][CH:14]=[C:13]([O:17][CH3:18])[CH:12]=1
Reactant: COc1cccc(CNC[C@@H](O)[C@H](Cc2cc(F)cc(F)c2)NC(=O)OC(C)(C)C)c1
Solvent: ClCCl
Solvent: O=C(O)C(F)(F)F
Product: COc1cccc(CNC[C@@H](O)[C@@H](N)Cc2cc(F)cc(F)c2)c1
Reaction time: 1 h

Procedure:
tert-Butyl (1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-3-[(3-methoxybenzyl)amino]propylcarbamate (VII, EXAMPLE 4, 258 mg, 0.59 mmol) is dissolved in methylene chloride (1 mL) at 20–25 degrees C., and trifluoroacetic acid (1 mL) is added with stirring under nitrogen. The reaction mixture is stirred at 20–25 degrees C. for 1 hour, whereupon the reaction mixture is concentrated under reduced pressure to give the title compound. The title compound is used in the next reaction without further purification.
Reaction SMILES: [NH2:1][C:2]1[CH:6]=[C:5]([C:7]2[CH:12]=[CH:11][C:10]([Cl:13])=[CH:9][CH:8]=2)[S:4][C:3]=1[C:14]([O:16]C)=O.[CH3:18][O:19][C:20]1[CH:21]=[C:22]([CH:24]=[CH:25][C:26]=1[O:27][CH2:28][C:29]([CH3:36])([N:31]1[CH2:35][CH2:34][CH2:33][CH2:32]1)[CH3:30])[NH2:23].[CH3:37]N(C(OC)OC)C>C(O)C>[Cl:13][C:10]1[CH:9]=[CH:8][C:7]([C:5]2[S:4][C:3]3[C:14](=[O:16])[N:23]([C:22]4[CH:24]=[CH:25][C:26]([O:27][CH2:28][C:29]([CH3:36])([N:31]5[CH2:35][CH2:34][CH2:33][CH2:32]5)[CH3:30])=[C:20]([O:19][CH3:18])[CH:21]=4)[CH:37]=[N:1][C:2]=3[CH:6]=2)=[CH:12][CH:11]=1
Reactant: COc1cc(N)ccc1OCC(C)(C)N1CCCC1
Reactant: COC(=O)c1sc(-c2ccc(Cl)cc2)cc1N
Reactant: COC(OC)N(C)C
Solvent: CCO
Product: COc1cc(-n2cnc3cc(-c4ccc(Cl)cc4)sc3c2=O)ccc1OCC(C)(C)N1CCCC1
Temperature: 110 °C
Reaction time: 3 h
Yield: 8 %

Procedure:
Methyl 3-amino-5-(4-chlorophenyl)thiophene-2-carboxylate (0.639 g, 0.2390 mmol) was taken up in DMF-DMA (3 mL) and heated to 110° C. The reaction was stirred for 3 h and then concentrated. 3-Methoxy-4-(2-methyl-2-pyrrolidin-1-ylpropoxy)aniline (0.0631 g, 0.2390 mmol) in absolute ethanol (3 mL) was added to the residue and the mixture was then concentrated. Fresh absolute ethanol (1 mL) was added and the reaction heated to reflux. The reaction was stirred for 18 h and then cooled to RT and the precipitate was collected to give 0.010 g (0.020 mmol, 8%) of the product as a white solid. 1H NMR (CDCl3) δ 8.15 (s, 1H), 7.65 (d, 2H, J=8.3 Hz), 7.53 (s, 1H), 7.44 (d, 2H, J=8.5 Hz), 7.18 (d, 1H, J=8.3 Hz), 6.96 (s, 1H), 6.88 (d, 1H, J=8.3 Hz), 3.83 (s, 3H, 2.77 (s, 2H), 2.72 (bs, 4H), 1.78 (bs, 4H), 1.36 (s, 6H).
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:4]=[C:5]([CH:9]=[CH:10][CH:11]=1)[C:6]([Cl:8])=[O:7].[NH2:12][CH:13]1[CH:18]2[CH2:19][CH2:20][N:15]([CH2:16][CH2:17]2)[CH2:14]1>CCOCC>[ClH:8].[N:15]12[CH2:20][CH2:19][CH:18]([CH2:17][CH2:16]1)[CH:13]([NH:12][C:6](=[O:7])[C:5]1[CH:9]=[CH:10][CH:11]=[C:3]([O:2][CH3:1])[CH:4]=1)[CH2:14]2
Reactant: NC1CN2CCC1CC2
Reactant: COc1cccc(C(=O)Cl)c1
Solvent: CCOCC
Product: COc1cccc(C(=O)NC2CN3CCC2CC3)c1
Product: Cl
Temperature: 25 °C
Reaction time: 16 h
Yield: 89.1 %

Procedure:
In a closed system, a solution of 3-methoxybenzoyl chloride (7.18 g, 0.04206 mole) in 30 ml ether was added dropwise to a stirred solution of 3-aminoquinuclidine (5.30 g, 0.04206 mole) in 100 ml of ether. The reaction mixture was stirred at ambient temperature for 16 hr. The solid hydrochloride salt was collected under nitrogen and dried in vacuo at ambient temperature to give 11.12 g (87.1%) of the product. The material was recrystallized from absolute ethanol-isopropyl ether to give 7.69 g. The product was vacuum dried for 20 hr over refluxing ethanol, and then for 24 hr over refluxing isooctane; m.p. 214°-215° C.
Reaction SMILES: [F:1][C:2]1[CH:10]=[C:9]([OH:11])[CH:8]=[CH:7][C:3]=1[C:4]([OH:6])=O.[CH2:12]([N:16]1[C:24]2[N:23]=[C:22]([Cl:25])[NH:21][C:20]=2[C:19](=[O:26])[N:18]([CH2:27][CH2:28][CH2:29][CH2:30][C:31](=[NH:34])[NH:32]O)[C:17]1=[O:35])[CH2:13][CH2:14][CH3:15]>CS(C)=O>[CH2:12]([N:16]1[C:24]2[N:23]=[C:22]([Cl:25])[NH:21][C:20]=2[C:19](=[O:26])[N:18]([CH2:27][CH2:28][CH2:29][CH2:30][C:31]2[N:32]=[C:4]([C:3]3[CH:7]=[CH:8][C:9]([OH:11])=[CH:10][C:2]=3[F:1])[O:6][N:34]=2)[C:17]1=[O:35])[CH2:13][CH2:14][CH3:15]
Reactant: CCCCn1c(=O)n(CCCCC(=N)NO)c(=O)c2[nH]c(Cl)nc21
Reactant: O=C(O)c1ccc(O)cc1F
Solvent: CS(C)=O
Product: CCCCn1c(=O)n(CCCCc2noc(-c3ccc(O)cc3F)n2)c(=O)c2[nH]c(Cl)nc21
Temperature: 25 °C
Reaction time: 2 h
Yield: 31.9 %

Procedure:
CDl (45 mg, 0.28 mmol) in anhydrous DMSO (0.5 ml) was added to 2-fluoro-4-hydroxybenzoic acid (40 mg, 0.25 mmol) and stirred at rt for 2 h. 5-(3-Butyl-8-chloro-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-1-yl)-N-hydroxypentanimidamide (100 mg, 0.28 mmol) in DMSO (0.4 ml) was added and the resulting mixture heated at 90° C. for 18 h. Purification by MDAP afforded the title compound as a solid (38 mg, 28%).
Reaction SMILES: [Cl:1][C:2]1[CH:13]=[C:12]([F:14])[C:11]([N:15]2[C:20](=[O:21])[C:19]([CH3:22])=[CH:18][N:17]([CH3:23])[C:16]2=[O:24])=[CH:10][C:3]=1[C:4]([O:6][CH:7]([CH3:9])[CH3:8])=[O:5].[Br:25]N1C(=O)CCC1=O.C(OOC(=O)C1C=CC=CC=1)(=O)C1C=CC=CC=1>C(Cl)(Cl)(Cl)Cl>[Cl:1][C:2]1[CH:13]=[C:12]([F:14])[C:11]([N:15]2[C:20](=[O:21])[C:19]([CH2:22][Br:25])=[CH:18][N:17]([CH3:23])[C:16]2=[O:24])=[CH:10][C:3]=1[C:4]([O:6][CH:7]([CH3:9])[CH3:8])=[O:5]
Reactant: O=C1CCC(=O)N1Br
Reactant: Cc1cn(C)c(=O)n(-c2cc(C(=O)OC(C)C)c(Cl)cc2F)c1=O
Agent: O=C(OOC(=O)c1ccccc1)c1ccccc1
Solvent: ClC(Cl)(Cl)Cl
Product: CC(C)OC(=O)c1cc(-n2c(=O)c(CBr)cn(C)c2=O)c(F)cc1Cl

Procedure:
A solution of 3.5 g of isopropyl 2-chloro-4-fluoro-5-[3,6-dihydro-3,5-dimethyl-2,6-dioxo-1(2H)-pyrimidinyl]-benzoate in 100 ml of carbon tetrachloride is heated to reflux temperature while stirring for 1 hour with 1.8 g of N-bromosuccinimide and some dibenzoyl peroxide. The reaction mixture is irradiated with a 150 W bulb. The succinimide is filtered off under suction and the filtrate is evaporated to dryness under reduced pressure. The residue is purified by chromatography on a silica gel column using methylene chloride/ethyl acetate (7:1) as the eluent. There is obtained isopropyl 2-chloro-4-fluoro-5-[5-bromomethyl-3,6-dihydro-3-methyl-2,6-dioxo-1(2H)-pyrimidinyl]-benzoate, 1H--NMR (CDCl3, 400 MHz) 7.84 ppm. (d, 1H), 7.58 ppm (s, 1H), 7.36 ppm (d, 1H), 5.24 ppm (m, 1H), 4.35 ppm (d, 1H), 4.29 ppm (d, 1H), 3.48 ppm (s, 3H), 1.37 ppm (2d, 6H).
Reaction SMILES: [F:1][C:2]1[CH:22]=[CH:21][C:5]([CH2:6][CH:7]2[CH2:16][C:15]3[C:10](=[CH:11][CH:12]=[CH:13][CH:14]=3)[CH2:9][N:8]2[CH2:17][CH2:18][CH2:19][NH2:20])=[CH:4][CH:3]=1.[Cl:23][C:24]1[CH:29]=[CH:28][C:27]([N:30]=[C:31]=[O:32])=[CH:26][CH:25]=1>>[Cl:23][C:24]1[CH:29]=[CH:28][C:27]([NH:30][C:31]([NH:20][CH2:19][CH2:18][CH2:17][N:8]2[CH:7]([CH2:6][C:5]3[CH:21]=[CH:22][C:2]([F:1])=[CH:3][CH:4]=3)[CH2:16][C:15]3[C:10](=[CH:11][CH:12]=[CH:13][CH:14]=3)[CH2:9]2)=[O:32])=[CH:26][CH:25]=1
Reactant: O=C=Nc1ccc(Cl)cc1
Reactant: NCCCN1Cc2ccccc2CC1Cc1ccc(F)cc1
Product: O=C(NCCCN1Cc2ccccc2CC1Cc1ccc(F)cc1)Nc1ccc(Cl)cc1

Procedure:
The reaction and treatment were carried out in the same manner as in Example 208 using 3-[3-(4-fluorobenzyl)-3,4-dihydroisoquinolin-2(1H)-yl]propanamine obtained in Example 214-b) as a starting material, and using 4-chlorophenyl isocyanate instead of phenyl isocyanate to obtain a title compound as a pale yellow amorphous substance.
Reaction SMILES: Br[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[S:8][CH3:9].[C:10]([C:13]1[CH:18]=[CH:17][C:16](B(O)O)=[CH:15][CH:14]=1)([OH:12])=[O:11].C(=O)([O-])[O-].[K+].[K+]>O.O1CCOCC1.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>[CH3:9][S:8][C:3]1[CH:4]=[CH:5][CH:6]=[CH:7][C:2]=1[C:16]1[CH:17]=[CH:18][C:13]([C:10]([OH:12])=[O:11])=[CH:14][CH:15]=1
Reactant: CSc1ccccc1Br
Reactant: O=C(O)c1ccc(B(O)O)cc1
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: O
Solvent: C1COCCO1
Product: CSc1ccccc1-c1ccc(C(=O)O)cc1
Temperature: 25 °C

Procedure:
A stirred mixture containing 4.15 g (0.025 mole) of 2-bromothioanisole, 5.08 g. (0.0025 mole) of 4-carboxybenzeneboronic acid, 10.36 g (0.075 mol) of potassium carbonate and 0.45 g (0.00063 mol) of dichlorobis(triphenylphosphine)palladium(II) in 40 mL of water and 20 mL of 1,4-dioxane was heated under reflux for two hours under nitrogen. The reacton mixture was allowed to cool to room temperature and filtered. The dioxane was removed in vacuo, the residue was diluted with 100 mL of water and then acidified with 20% hydrochloric acid. The crude product (6.1 g) was recrystallized from ethanol to yield the title compound, m.p. 220-222° C.
Reaction SMILES: Br[C:2]1[S:3][CH:4]=[C:5]([CH2:7][O:8][C:9]2[CH:14]=[CH:13][N:12]([C:15]3[CH:16]=[CH:17][C:18]4[N:22]=[C:21]([CH:23]5[CH2:25][CH2:24]5)[N:20]([CH3:26])[C:19]=4[CH:27]=3)[C:11](=[O:28])[CH:10]=2)[N:6]=1.[CH:29]1(B(O)O)[CH2:31][CH2:30]1.C(=O)([O-])[O-].[K+].[K+].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>[CH:23]1([C:21]2[N:20]([CH3:26])[C:19]3[CH:27]=[C:15]([N:12]4[CH:13]=[CH:14][C:9]([O:8][CH2:7][C:5]5[N:6]=[C:2]([CH:29]6[CH2:31][CH2:30]6)[S:3][CH:4]=5)=[CH:10][C:11]4=[O:28])[CH:16]=[CH:17][C:18]=3[N:22]=2)[CH2:25][CH2:24]1
Reactant: Cn1c(C2CC2)nc2ccc(-n3ccc(OCc4csc(Br)n4)cc3=O)cc21
Reactant: OB(O)C1CC1
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: [K+]
Solvent: O
Solvent: COCCOC
Product: Cn1c(C2CC2)nc2ccc(-n3ccc(OCc4csc(C5CC5)n4)cc3=O)cc21
Temperature: 150 °C
Yield: 24.7 %

Procedure:
A mixture of 4-((2-bromo-1,3-thiazol-4-yl)methoxy)-1-(2-cyclopropyl-1-methyl-1H-benzimidazol-6-yl)pyridin-2(1H)-one (54 mg), cyclopropylboronic acid (30.4 mg), tetrakis(triphenylphosphine)palladium (6.8 mg), potassium carbonate (65.3 mg), DME (1.5 ml) and water (0.5 ml) was heated at 150° C. for 20 min under microwave irradiation. The reaction mixture was then cooled to room temperature, poured into water and extracted with EtOAc. The extract was washed with brine, dried over MgSO4, concentrated and purified by silica gel column chromatography (hexane/EtOAc then EtOAc/MeOH). The resulting solid was recrystallized from EtOH-water to give the title compound (12.2 mg) as a white solid.
Reaction SMILES: [Cl:1][C:2]1[N:7]=[C:6]([NH2:8])[CH:5]=[N:4][CH:3]=1.[C:9](Cl)(=[O:11])[CH3:10]>C(Cl)Cl.O>[Cl:1][C:2]1[N:7]=[C:6]([NH:8][C:9](=[O:11])[CH3:10])[CH:5]=[N:4][CH:3]=1
Reactant: CC(=O)Cl
Reactant: Nc1cncc(Cl)n1
Solvent: O
Solvent: ClCCl
Product: CC(=O)Nc1cncc(Cl)n1
Reaction time: 1 h
Yield: 52.8 %

Procedure:
To a solution of 6-chloropyrazin-2-amine (1.00 g, 7.72 mmol) in DCM (20 mL) was added acetyl chloride (0.659 mL, 9.26 mmol) at RT and the reaction mixture was stirred for 1 h. The reaction mixture was diluted with water (100 mL) and extracted with DCM (2×100 mL). The combined organic layer was dried over sodium sulfate, filtered and evaporated under reduced pressure to give a residue which was purified by CombiFlash (REDISEP®, silica gel, 12 g, 25% EtOAc/petroleum ether) to give N-(6-chloropyrazin-2-yl)acetamide (0.700 g, 52.9%). LCMS Condition B-39: retention time 1.67 min, [M+1]=170.0. 1H NMR (400 MHz, DMSO-d6) δ ppm 2.14 (s, 3H), 8.47 (s, 1H), 9.29 (s, 1H), 11.09 (br s, 1H).
Reaction SMILES: [F:1][C:2]1[CH:3]=[C:4]2[C:8](=[CH:9][CH:10]=1)[NH:7][CH:6]=[C:5]2[CH:11]1[CH2:16][CH2:15][NH:14][CH2:13][CH2:12]1.Br[CH2:18][CH2:19][C:20]1[CH:25]=[C:24]([N+:26]([O-:28])=[O:27])[CH:23]=[CH:22][C:21]=1[CH3:29].C(N(CC)CC)C>CN(C)C=O.CC(=O)CC>[F:1][C:2]1[CH:3]=[C:4]2[C:8](=[CH:9][CH:10]=1)[NH:7][CH:6]=[C:5]2[CH:11]1[CH2:16][CH2:15][N:14]([CH2:18][CH2:19][C:20]2[CH:25]=[C:24]([N+:26]([O-:28])=[O:27])[CH:23]=[CH:22][C:21]=2[CH3:29])[CH2:13][CH2:12]1
Reactant: Fc1ccc2[nH]cc(C3CCNCC3)c2c1
Reactant: Cc1ccc([N+](=O)[O-])cc1CCBr
Solvent: CN(C)C=O
Solvent: CCC(C)=O
Solvent: CCN(CC)CC
Product: Cc1ccc([N+](=O)[O-])cc1CCN1CCC(c2c[nH]c3ccc(F)cc23)CC1
Yield: 76.3 %

Procedure:
A mixture of 5-fluoro-3-(piperidin-4-yl)-1H-indole (2.7 g) in dimethyl formamide (75 mL), 2-(2-bromoethyl)-1-methyl-4-nitrobenzene (3.7 g) in butanone (200 mL) and triethylamine (9.3 mL) was boiled under reflux for 20 h, and the resulting mixture was concentrated in vacuo. The residue was purified by flash chromatography on silicagel (eluent:ethyl acetate/triethylamine 100:4) to give 5-fluoro-3-{1-[2-(2-methyl-5-nitrophenyl)ethyl]piperidin-4-yl}-1H-indole (3.6 g), which subsequently was dissolved in acetic acid (25 ml) followed by the addition of ethanol (75 mL) and platinum oxide (50 mg). The resulting mixture was shaken under 3 atmosphere hydrogen pressure for 3 h at room temperature. The mixture was reduced in vacuo (50 mL), poured onto an ice/water mixture followed by the addition of aqueous ammonia to basic pH. The aqueous phase was extracted with an ethyl acetate/tetrahydrofuran mixture, and the combined organic phase was washed with brine, dried (MgSO4), filtered and concentrated in vacuo. The residue was purified by flash chromatography on silicagel (eluent:ethyl acetate/ethanol/triethylamine 100:4:4) to give 3-{1-[2-(5-amino-2-methylphenyl)ethyl]piperidin-4-yl}-5-fluoro-1H-indole (1.0 g), which subsequently was dissolved in tetrahydrofuran (45 mL) and triethylamine (1.3 mL) at 5° C. followed by the addition of cyclobutancarbonyl chloride (0.3 g) in tetrahydrofuran (15 mL). The resulting mixture was stirred at 5° C. for 1 h, filtered and concentrated in vacuo. The residue was purified by flash chromatography on silicagel (eluent:ethyl acetate/ethanol/triethylamine 100:4:4) to give the crude product that was isolated as the oxalate salt from ethyl acetate as a white crystalline compound (0.7 g). Mp 116-125° C. 1H NMR (DMSO-d6): 1.75-1.85 (m, 1H); 1.85-2.05 (m, 3H); 2.05-2.25 (m, 6H); 2.30 (s, 3H); 2.90-3.25 (m, 8H); 3.65 (d, 2H); 6.85-6.95 (m, 1H); 7.10 (d, 1H); 7.25 (s, 1H); 7.30-7.40 (m, 2H); 7.40 (d, 1H); 7.55 (s, 1H); 9.65 (s, 1H); 11.00 (s, 1H). MS m/z: 434 (MH+).
Reaction SMILES: [F:1][C:2]([F:29])([F:28])[C:3]([NH:5][CH2:6][CH2:7][O:8][CH2:9][C:10]#[C:11][CH2:12][C:13]1[C:14](=[O:27])[NH:15][C:16](=[O:26])[N:17]([CH:25]=1)[C@@H:18]1[O:24][C@H:21]([CH2:22][OH:23])[CH2:20][CH2:19]1)=[O:4].O=P(Cl)(Cl)Cl.[P:35](OC)([O:39]C)([O:37]C)=[O:36]>>[P:35]([O:23][CH2:22][C@H:21]1[O:24][C@@H:18]([N:17]2[CH:25]=[C:13]([CH2:12][C:11]#[C:10][CH2:9][O:8][CH2:7][CH2:6][NH:5][C:3](=[O:4])[C:2]([F:28])([F:1])[F:29])[C:14](=[O:27])[NH:15][C:16]2=[O:26])[CH2:19][CH2:20]1)([OH:39])([OH:37])=[O:36]
Reactant: O=C(NCCOCC#CCc1cn([C@H]2CC[C@@H](CO)O2)c(=O)[nH]c1=O)C(F)(F)F
Reactant: COP(=O)(OC)OC
Solvent: O=P(Cl)(Cl)Cl
Product: O=C(NCCOCC#CCc1cn([C@H]2CC[C@@H](COP(=O)(O)O)O2)c(=O)[nH]c1=O)C(F)(F)F
Reaction time: 2.5 h

Procedure:
To a solution of 5 (30 mg, 0.0738 mmol) in P(O)(OCH3)3 (0.5 mL) was treated with POCl3 (70 μL, 0.73 mmol) at 0° C., followed by stirring at r.t for 2-3 h and then evaporating solvent under reduced pressure and purification by preparative reverse phase HPLC to afford the corresponding mono phosphate 6. 31P NMR (CD3OD, 121.4 MHz) δ 0.79 (s); 19F NMR (CDCl3), 282.2 MHz) δ −77.37 (s, CF3). To a dried solution of 6 in DMF (1 mL) were added 1,1′-carbonyldiimidazole (CDI, 33 mg, 0.21 mmol), followed by stirring at r.t. for 5 h and then quenching with MeOH (8 μL, 0.21 mmol). A solution of tetrabutylammonium pyrophosphate (TBAPP, 143.0 mg, 0.33 mmol) and tributyl amine (0.15 mL, 0.66 mmol) in DMF (1.5 mL) was added to the above solution at r.t. under Ar, followed by stirring overnight and then quenched with 2.0 M TEAB. After evaporating solvent, the organic residue was purified by preparative reverse phase HPLC with 100 mM TEAA/AcCN (0 to 50% gradient) to give the corresponding triphosphate 7. 1H NMR (D2O, 300 MHz) δ 7.74 (s, 1H, H6), 5.95 (dd, 1H, H1′, J=3.3 and 6.3 Hz), 4.29-4.20 (m, 1H, H4′), 4.18-4.07 (m, 3H, CH2 and H5′), 4.02-3.92 (m, 1H, H5′), 3.58 (t, 2H, CH2, J=5.1 Hz), 3.38 (t, 2H, CH2, J=5.1 Hz), 3.20 (s, 2H, CH2), 2.35-2.22 (m, 1H, H2), 2.10-1.92 (m, 3H, H2, and 2H3′). 31P NMR (D2O, 121.4 MHz) δ −10.52 (d, J=19.2 Hz), −10.95 (d, J=20.3 Hz), −22.96 (t, J=20.3 Hz); 19F NMR (D2O, 282.2 MHz) δ −76.37 (s, CF3). Removal of trifluoro acetate (TFA) protecting group was accomplished by treatment with NH4OH (33%, 500 μL) at 60° C. for 20 min and then at r.t for 1 h to give the corresponding triphosphate 8 (17 mM, 500 μL).