Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [H-].[Al+3].[Li+].[H-].[H-].[H-].[I:7][C:8]1[CH:9]=[C:10]2[C:14](=[CH:15][CH:16]=1)[N:13]([CH:17]1[CH2:22][CH2:21][CH2:20][CH2:19][O:18]1)[N:12]=[C:11]2[C:23](N(OC)C)=[O:24]>C1COCC1>[I:7][C:8]1[CH:9]=[C:10]2[C:14](=[CH:15][CH:16]=1)[N:13]([CH:17]1[CH2:22][CH2:21][CH2:20][CH2:19][O:18]1)[N:12]=[C:11]2[CH:23]=[O:24]
Reactant: CON(C)C(=O)c1nn(C2CCCCO2)c2ccc(I)cc12
Agent: [Al+3]
Agent: [H-]
Agent: [Li+]
Solvent: C1CCOC1
Product: O=Cc1nn(C2CCCCO2)c2ccc(I)cc12
Reaction time: 0.5 h
Yield: 90 %

Procedure:
Lithium aluminum hydride (160 mg, 4.21 mmol) was added in portions to a cooled (0° C.) solution of 5-iodo-N-methoxy-N-methyl-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carboxamide (CXIII) (1.46 g, 3.5 mmol) in THF. Stirring was continued at 0° C. until the reaction was completed, approximately 30 min The reaction was quenched by the slow addition of EtOAc at 0° C., and the whole mixture was poured into 0.4 N aqueous NaHSO4. The organic layer was washed with brine, dried over MgSO4, concentrated, and purified on a silica gel column (100% EtOAc→3:97 MeOH:DCM) to give 5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carb aldehyde (CXIV) as a white solid (0.90 g, 3.15 mmol, 72% yield). 1H NMR (DMSO-d6) δ ppm 1.50-1.71 (m, 2H), 1.71-1.87 (m, 1H), 1.97-2.15 (m, 2H), 2.31-2.42 (m, 1H), 3.66-3.99 (m, 2H), 5.96-6.17 (m, 1H), 7.78 (d, J=6 Hz, 1H), 7.84 (d, J=6 Hz, 1H), 8.50 (s, 1H), 10.13 (s, 1H); ESIMS found for C13H13IN2O2 m/z 357 (M+H).
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[N:4][N:5]([CH3:26])[C:6]=1[C:7]1[CH:8]=[C:9]([NH:14][C:15](=[O:25])[C:16]2[CH:21]=[CH:20][C:19]([O:22][CH3:23])=[CH:18][C:17]=2[F:24])[CH:10]=[CH:11][C:12]=1[OH:13].C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.ClC1C=NN(C)C=1C1C=C(NC(=O)C2C=CC(OC)=CC=2F)C=CC=1O.C1COCC1.CC(OC(/N=N/C(OC(C)C)=O)=O)C.[F:91][C:92]([F:106])([F:105])[CH2:93][CH:94]([NH:97]C(=O)OC(C)(C)C)[CH2:95]O.[C:107]([OH:113])([C:109]([F:112])([F:111])[F:110])=[O:108]>C1COCC1>[F:110][C:109]([F:112])([F:111])[C:107]([OH:113])=[O:108].[NH2:97][CH:94]([CH2:93][C:92]([F:106])([F:105])[F:91])[CH2:95][O:13][C:12]1[CH:11]=[CH:10][C:9]([NH:14][C:15](=[O:25])[C:16]2[CH:21]=[CH:20][C:19]([O:22][CH3:23])=[CH:18][C:17]=2[F:24])=[CH:8][C:7]=1[C:6]1[N:5]([CH3:26])[N:4]=[CH:3][C:2]=1[Cl:1]
Reactant: CC(C)(C)OC(=O)NC(CO)CC(F)(F)F
Reactant: COc1ccc(C(=O)Nc2ccc(O)c(-c3c(Cl)cnn3C)c2)c(F)c1
Agent: CC(C)OC(=O)/N=N/C(=O)OC(C)C
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: C1CCOC1
Solvent: O=C(O)C(F)(F)F
Product: COc1ccc(C(=O)Nc2ccc(OCC(N)CC(F)(F)F)c(-c3c(Cl)cnn3C)c2)c(F)c1
Reaction time: 0.08 h
Yield: 24.4 %

Procedure:
N-(3-(4-chloro-1-methyl-1H-pyrazol-5-yl)-4-hydroxyphenyl)-2-fluoro-4-methoxybenzamide (20.0 mg, 53.2 μmol) was dissolved in anhydrous THF (0.3 mL). Triphenylphosphine (15.4 mg, 58.5 μmol), pre-dissolved in anhydrous THF (0.1 mL) was added to the N-(3-(4-chloro-1-methyl-1H-pyrazol-5-yl)-4-hydroxyphenyl)-2-fluoro-4-methoxybenzamide/THF solution. The reaction was stirred for 5 minutes and then DIAD (16.6 μl, 85.2 μmol), pre-dissolved in anhydrous THF (0.1 mL) was added to the reaction. The mixture was stirred at r.t. for 5 more minutes and then tert-butyl 4,4,4-trifluoro-1-hydroxybutan-2-ylcarbamate (16.2 mg, 66.5 μmol), pre-dissolved in anhydrous THF (0.1 mL) was added. The reaction was then stirred for 4 hours and checked by LC/MS. While the reaction had not gone to completion, pushing the reaction by heating or extending the reaction time did not seem to improve the yield. Thus, the solvent was evaporated, the resulting oil re-suspended in CH2Cl2 (0.5 mL) and TFA (20.5 μl, 266 μmol) was added (to remove the Boc-protecting group from the amine). The reaction was stirred overnight at room temperature. The next day, the solvent was removed and the resulting oil was re-dissolved in DMSO (1 mL). The product was purified by Prep LC/MS (0-50% B, 30 min) to yield N-[4-(2-amino-4,4,4-trifluoro-butoxy)-3-(4-chloro-2-methyl-2H-pyrazol-3-yl)-phenyl]-2-fluoro-4-methoxy-benzamide trifluoroacetate (8.1 mg, 13.0 μmol, 24.5%) as a colorless oil. LCMS m/z 501.3 (M+H); 1H NMR (400 MHz, MeOH-d4) δ ppm 2.48-2.86 (m, 2 H), 3.75 (d, J=2.78 Hz, 3 H), 3.87-3.97 (m, 1 H), 3.89 (s, 3 H), 4.10-4.43 (m, 2 H), 6.85 (dd, J=12.88, 2.27 Hz, t H), 6.91 (dd, J=8.72, 2.40 Hz, 1 H), 7.30 (dd, J=9.09, 2.27 Hz, 1 H), 7.61 (d, J=2.53 Hz, 1 H), 7.65-7.69 (m, 1 H), 7.76 (t, J=8.59 Hz, 1 H), 7.90 (dd, J=8.97, 2.65 Hz, 1 H).
Reaction SMILES: Cl[CH2:2][CH2:3][O:4][C:5]1[CH:10]=[CH:9][CH:8]=[CH:7][C:6]=1[C:11]([NH:14][C:15]1[C:16](=[O:34])[N:17]([C:21]2[CH:22]=[C:23]([CH:30]=[CH:31][C:32]=2[CH3:33])[C:24]([NH:26][CH:27]2[CH2:29][CH2:28]2)=[O:25])[CH:18]=[CH:19][N:20]=1)([CH3:13])[CH3:12].[CH3:35][NH2:36]>O1CCOCC1>[CH:27]1([NH:26][C:24](=[O:25])[C:23]2[CH:30]=[CH:31][C:32]([CH3:33])=[C:21]([N:17]3[CH:18]=[CH:19][N:20]=[C:15]([NH:14][C:11]([CH3:13])([C:6]4[CH:7]=[CH:8][CH:9]=[CH:10][C:5]=4[O:4][CH2:3][CH2:2][NH:36][CH3:35])[CH3:12])[C:16]3=[O:34])[CH:22]=2)[CH2:29][CH2:28]1
Reactant: Cc1ccc(C(=O)NC2CC2)cc1-n1ccnc(NC(C)(C)c2ccccc2OCCCl)c1=O
Reactant: CN
Solvent: C1COCCO1
Product: CNCCOc1ccccc1C(C)(C)Nc1nccn(-c2cc(C(=O)NC3CC3)ccc2C)c1=O
Temperature: 100 °C

Procedure:
3-[3-[[1-[2-(2-Chloroethoxy)phenyl]-1-methylethyl]amino]-2-oxo-1(2H)-pyrazinyl]-N-cyclopropyl-4-methyl-benzamide (Example 198e, 17.5 g) in dioxane (50 mL) was treated with 40% Methylamine solution (50 mL) under nitrogen. The resulting suspension was heated in a sealed system at 100° C. for 4 h. After cooling to room temperature, the solution was evaporated to dryness. The crude product was purified by flash chromatography (SiO2, eluent 10% methanol in dichloromethane and 1% triethylamine). Evaporation of the relevant fractions to dryness and trituration of the residue in diethyl ether gave a solid which was filtered off and dried to give the title compound (12.5 g) as an off white solid.
Reaction SMILES: [H-].[Na+].[Br:3][C:4]1[CH:12]=[CH:11][CH:10]=[C:9]2[C:5]=1[CH:6]=[CH:7][NH:8]2.Br[CH2:14][CH2:15][CH2:16][CH2:17][CH3:18]>CN(C)C=O>[Br:3][C:4]1[CH:12]=[CH:11][CH:10]=[C:9]2[C:5]=1[CH:6]=[CH:7][N:8]2[CH2:14][CH2:15][CH2:16][CH2:17][CH3:18]
Reactant: Brc1cccc2[nH]ccc12
Reactant: CCCCCBr
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: CCCCCn1ccc2c(Br)cccc21
Reaction time: 0.5 h
Yield: 98 %

Procedure:
To a mixture of sodium hydride (2.54 g, 66.3 mmol, 60% dispersion in mineral oil) in anhydrous N,N-dimethylformamide (50.0 mL) was added 4-bromoindole (10.0 g, 51.0 mmol) at 0° C. The reaction mixture was stirred for 0.5 h followed by the addition of 1-bromopentane (9.25 g, 61.2 mmol) at 0° C. The reaction mixture was stirred at ambient temperature for 6 h and quenched with brine solution (20.0 mL). The reaction mixture was diluted with water (100 mL) and extracted with ether (3×200 mL). The combined organic layers was washed with brine (100 mL), dried over anhydrous sodium sulfate and filtered. The filtrate was concentrated in vacuo to dryness. The residue was subjected to column chromatography eluting with hexane (100%) to give the title compound (13.3 g, 98%) as a yellow oil: 1H NMR (300 MHz, CDCl3) δ 7.30-7.27 (m, 2H), 7.14 (t, 1H), 6.88 (t, 1H), 6.55 (d, 1H), 4.08 (t, 2H), 1.87-1.77 (m, 2H), 1.39-1.22 (m, 4H), 0.89 (t, 3H); 13C NMR (75 MHz, CDCl3) δ 136.3, 129.2, 128.4, 122.2, 122.1, 114.9, 108.7, 101.3, 46.8, 29.9, 29.1, 22.3, 13.9.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[C:12]3[CH2:13][N:14]([C:17](=[O:19])[CH3:18])[CH2:15][CH2:16][C:11]=3[N:10]([CH2:20][C@@H:21]3[CH2:23][O:22]3)[N:9]=2)=[CH:4][C:3]=1[CH3:24].[Cl:25][C:26]1[CH:27]=[CH:28][C:29]2[NH:33][C:32](=[O:34])[N:31]([CH:35]3[CH2:40][CH2:39][NH:38][CH2:37][CH2:36]3)[C:30]=2[CH:41]=1>CCO.C(Cl)Cl>[C:17]([N:14]1[CH2:15][CH2:16][C:11]2[N:10]([CH2:20][C@@H:21]([OH:22])[CH2:23][N:38]3[CH2:37][CH2:36][CH:35]([N:31]4[C:30]5[CH:41]=[C:26]([Cl:25])[CH:27]=[CH:28][C:29]=5[NH:33][C:32]4=[O:34])[CH2:40][CH2:39]3)[N:9]=[C:8]([C:5]3[CH:6]=[CH:7][C:2]([Cl:1])=[C:3]([CH3:24])[CH:4]=3)[C:12]=2[CH2:13]1)(=[O:19])[CH3:18]
Reactant: O=c1[nH]c2ccc(Cl)cc2n1C1CCNCC1
Reactant: CC(=O)N1CCc2c(c(-c3ccc(Cl)c(C)c3)nn2C[C@@H]2CO2)C1
Solvent: CCO
Solvent: ClCCl
Product: CC(=O)N1CCc2c(c(-c3ccc(Cl)c(C)c3)nn2C[C@@H](O)CN2CCC(n3c(=O)[nH]c4ccc(Cl)cc43)CC2)C1
Temperature: 70 °C
Reaction time: 18 h
Yield: 11.7 %

Procedure:
(R)-1-[3-(4-Chloro-3-methyl-phenyl)-1-oxiranylmethyl-1,4,6,7-tetrahydro-pyrazolo[4,3-c]pyridin-5-yl]-ethanone (31 mg, 0.10 mmol) and 6-chloro-1-piperidin-4-yl-1,3-dihydro-benzoimidazol-2-one (36 mg, 0.17 mmol) were combined in EtOH (0.3 mL) and heated to 70° C. After 18 h the mixture was allowed to cool, diluted with CH2Cl2 and purified by preparative TLC (silica, 8% MeOH/CH2Cl2) to give 7 mg (12%) of the title compound. HPLC (reverse phase conditions), tR=3.49 min. MS (electrospray): m/z calculated for C30H3535Cl2N6O3 [M++H] 597.22. found 597.20. 1H NMR (CDCl3, 400 MHz, a mixture of amide rotamers): 9.16 (br d, J=10.1 Hz, 1H), 7.55 (br m, 1H), 7.40-7.28 (m, 2H), 7.18 (br s, 1H), 7.03 and 6.98 (A and B of ABX (with fine splittings), Jab=8.4 Hz, 2H), 4.85 and 4.74 (A and B of ABX (with fine splittings), Jab=15.7 Hz, 1H), 4.62 (s, 1H), 4.29-4.18 (m, 4H), 4.09-4.00 (m, 2H), 3.91-3.71 (m, 2H), 3.16-2.78 (m, 4H), 2.55-2.50 (m, 4H), 2.43 (s, 1.5H), 2.41 (s, 1.5H), 2.23 (m, 1H), 2.21 (s, 1.5H), 2.16 (s, 1.5H), 1.84 (br s, 2H).
Reaction SMILES: [CH3:1][S:2]([N:5]1[CH2:9][C@H:8]([S:10][C:11]([C:24]2[CH:29]=[CH:28][CH:27]=[CH:26][CH:25]=2)([C:18]2[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=2)[C:12]2[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=2)[CH2:7][C@H:6]1[CH2:30][OH:31])(=[O:4])=[O:3].[CH2:32](Br)[C:33]1[CH:38]=[CH:37][CH:36]=[CH:35][CH:34]=1.[H-].[Na+].C(Br)C1C=CC=CC=1.[H-].[Na+]>CN(C=O)C>[CH2:32]([O:31][CH2:30][C@@H:6]1[CH2:7][C@@H:8]([S:10][C:11]([C:12]2[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=2)([C:18]2[CH:19]=[CH:20][CH:21]=[CH:22][CH:23]=2)[C:24]2[CH:29]=[CH:28][CH:27]=[CH:26][CH:25]=2)[CH2:9][N:5]1[S:2]([CH3:1])(=[O:3])=[O:4])[C:33]1[CH:38]=[CH:37][CH:36]=[CH:35][CH:34]=1
Reactant: CS(=O)(=O)N1C[C@H](SC(c2ccccc2)(c2ccccc2)c2ccccc2)C[C@H]1CO
Reactant: BrCc1ccccc1
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: CS(=O)(=O)N1C[C@H](SC(c2ccccc2)(c2ccccc2)c2ccccc2)C[C@H]1COCc1ccccc1
Temperature: 0 °C
Yield: 59.1 %

Procedure:
9.07 g (20 mmol) of (2S,4R)-(1-methanesulfonyl-4-tritylsulfanyl-pyrrolidin-2-yl)-methanol and 9.5 ml (80 mmol) of benzylbromide were dissolved in 660 ml DMF, cooled to 0° C. and treated with 1.4 g (32 mmol) of 55% NaH over 15 min in 4 portions. The reaction was warmed up over night and treated with 4.75 ml (40 mmol) benzylbromide/700 mg (16 mmol) 55% NaH and 6 h later again with the same amount of benzylbromide/NaH. After further 16 h at room temperature the reaction was quenched with saturated NH4Cl solution/EtOAc (3x). The organic phase was washed with aqueous 10% NaCl solution, dried over Na2SO4 and evaporated to give 25 g crude product. Flash-chromatography on silica gel (Hexane/EtOAc 4:1 to 1:4) gave 6.43 g (59%) of (2S,4R)-2-benzyloxymethyl-1-methanesulfonyl-4-tritylsulfanyl-pyrrolidine, MS: 544 (MH+). 6.4 g (11.77 mmol) (2S,4R)-2-benzyloxymethyl-1-methanesulfonyl-4-tritylsulfanyl-pyrrolidine were dissolved in 170 ml TFA and treated at 0° C. with 18.75 ml (117.7 mmol) of triethylsilane. After 18 h at 0° C., the mixture was evaporated and purified by flash-chromatography on silica gel (Hexane/EtOAc 4:1 to 1:4) to give 2.66 g (72%) of (3R,5S)-5-benzyloxymethyl-1-methanesulfonyl-pyrrolidine-3-thiol, MS: 302 (MH+).
Reaction SMILES: [N:1]1([CH2:6][CH2:7][N:8]2[CH:12]=[C:11]([CH2:13][CH2:14][C:15]([F:18])([F:17])[F:16])[N:10]=[C:9]2[CH:19]2[CH2:24][CH2:23][N:22](C(OC(C)(C)C)=O)[CH2:21][CH2:20]2)[CH2:5][CH2:4][CH2:3][CH2:2]1.[F:32][C:33]([F:38])([F:37])[C:34]([OH:36])=[O:35]>ClCCl>[F:32][C:33]([F:38])([F:37])[C:34]([OH:36])=[O:35].[F:32][C:33]([F:38])([F:37])[C:34]([OH:36])=[O:35].[F:32][C:33]([F:38])([F:37])[C:34]([OH:36])=[O:35].[F:18][C:15]([F:16])([F:17])[CH2:14][CH2:13][C:11]1[N:10]=[C:9]([CH:19]2[CH2:20][CH2:21][NH:22][CH2:23][CH2:24]2)[N:8]([CH2:7][CH2:6][N:1]2[CH2:2][CH2:3][CH2:4][CH2:5]2)[CH:12]=1
Reactant: CC(C)(C)OC(=O)N1CCC(c2nc(CCC(F)(F)F)cn2CCN2CCCC2)CC1
Solvent: ClCCl
Solvent: O=C(O)C(F)(F)F
Product: FC(F)(F)CCc1cn(CCN2CCCC2)c(C2CCNCC2)n1
Temperature: 0 °C
Reaction time: 1 h
Yield: 100 %

Procedure:
Combine tert-butyl 4-(1-(2-(pyrrolidin-1-yl)ethyl)-4-(3,3,3-trifluoropropyl)-1H-imidazol-2-yl)piperidine-1-carboxylate (0.73 g, 1.64 mmol) and dichloromethane (16.2 mL). Place under nitrogen and cool to 0° C. Add trifluoroacetic acid (16.2 mL). After 1 hour, concentrate in vacuo to give 4-(4-(3,3,3-trifluoropropyl)-1-(2-(pyrrolidin-1-yl)ethyl)-1H-imidazol-2-yl)piperidine tris(2,2,2-trifluoroacetate) (1.12 g, 100%). MS (ES) m/z=345 [M]+.
Reaction SMILES: C(N(CC)C(C)C)(C)C.Cl[C:11]([CH:13]1[CH2:16][N:15]([C:17]([O:19][CH2:20][C:21]2[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=2)=[O:18])[CH2:14]1)=[O:12].Cl.[NH2:28][CH2:29][C:30]1[C:35]([Cl:36])=[N:34][CH:33]=[CH:32][N:31]=1>ClCCl>[Cl:36][C:35]1[C:30]([CH2:29][NH:28][C:11]([CH:13]2[CH2:16][N:15]([C:17]([O:19][CH2:20][C:21]3[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=3)=[O:18])[CH2:14]2)=[O:12])=[N:31][CH:32]=[CH:33][N:34]=1
Reactant: O=C(Cl)C1CN(C(=O)OCc2ccccc2)C1
Reactant: NCc1nccnc1Cl
Agent: Cl
Solvent: ClCCl
Solvent: CCN(C(C)C)C(C)C
Product: O=C(NCc1nccnc1Cl)C1CN(C(=O)OCc2ccccc2)C1
Temperature: 25 °C
Reaction time: 2 h
Yield: 82.1 %

Procedure:
N,N-diisopropylethylamine (109 mmol, 18.01 ml) and a solution of benzyl 3-(chlorocarbonyl)azetidine-1-carboxylate (5.53 g) in dichloromethane (32.5 ml) were added to a stirred suspension of 2-aminomethyl-3-chloropyrazine hydrochloride (content 77%; 21.80 mmol, 5.10 g) in dichloromethane (55 ml) at room temperature to give a dark brown solution. After stirring at room temperature for two hours the reaction mixture was quenched with water and filtered over decalite. Layers were separated and to the aqueous layer saturated aqueous sodium hydrogencarbonate solution was added and the layer was extracted three times with dichloromethane. The organic layers were combined, washed with brine, dried (sodium sulfate), and concentrated in vacuo. The residue was purified by column chromatography (silica gel, dichloromethane/methanol gradient 10/0 to 9/1) to give benzyl 3-((3-chloropyrazin-2-yl)methylcarbamoyl)azetidine-1-carboxylate (6.46 g).
Reaction SMILES: [Br:1][C:2]1[CH:7]=[CH:6][CH:5]=[C:4](I)[CH:3]=1.[C:9]1([C:15]#[CH:16])[CH:14]=[CH:13][CH:12]=[CH:11][CH:10]=1.C(NC(C)C)(C)C>C1(C)C=CC=CC=1.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.[Cu]I>[Br:1][C:2]1[CH:7]=[CH:6][CH:5]=[C:4]([C:16]#[C:15][C:9]2[CH:14]=[CH:13][CH:12]=[CH:11][CH:10]=2)[CH:3]=1
Reactant: Brc1cccc(I)c1
Reactant: C#Cc1ccccc1
Agent: [Cu]I
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Solvent: Cc1ccccc1
Solvent: CC(C)NC(C)C
Product: Brc1cccc(C#Cc2ccccc2)c1
Temperature: 25 °C
Reaction time: 8 h

Procedure:
1-bromo-3-iodobenzene (15.3 g, 54.0 mmol), phenylacetylene (5 g, 49.0 mmol), tetrakis(triphenylphosphine)palladium (2.8 g, 2.4 mmol) and copper(I) iodide (0.46 g, 2.4 mmol) were dissolved in dry toluene and diisopropylamine (35 mL, 196 mmol) under a nitrogen atmosphere. The reaction was stirred at room temperature overnight. The mixture was extracted with ethyl acetate and the organic layer was dried in vacuo to give the title compound as a residue that was used without further purification.
Reaction SMILES: Cl[C:2]1[C:7]([CH3:8])=[CH:6][C:5]([N+:9]([O-:11])=[O:10])=[CH:4][N:3]=1.[NH2:12][CH2:13][CH2:14][CH2:15][NH2:16].N1C=CC=CC=1>CO>[NH2:12][CH2:13][CH2:14][CH2:15][NH:16][C:2]1[C:7]([CH3:8])=[CH:6][C:5]([N+:9]([O-:11])=[O:10])=[CH:4][N:3]=1
Reactant: NCCCN
Reactant: Cc1cc([N+](=O)[O-])cnc1Cl
Solvent: CO
Solvent: c1ccncc1
Product: Cc1cc([N+](=O)[O-])cnc1NCCCN

Procedure:
2-Chloro-3-methyl-5-nitropyridine (15.5 g), 1,3-diaminopropane (30 ml) and pyridine (10 ml) were stirred together and, after the initial exotherm had subsided, the mixture was heated under reflux for 1.5 hr. On cooling the mixture was treated with methanol and the bulk of crystalline bi-product filtered off. The solution was stripped, the residue taken up in water and the pH adjusted to 6.5 with hydrochloric acid. After filtering through `Hyflo` the solution was extracted with chloroform. The pH was raised to 14, (NaOH) and extracted with ether. After drying (K2CO3), the ether extracts were stripped to give a yellow solid which was triturated with ether/pentane to give 2-(3-aminopropylamino)-3-methyl-5-nitropyridine, (12.9 g; 68%) m.p. 93°-95° C.
Reaction SMILES: [N:1]1(CC(N2CCNCC2=O)=O)[CH:9]=[C:7]([CH3:8])[C:5](=[O:6])[NH:4][C:2]1=[O:3].C(N(CC)CC)C>C(Cl)Cl.CN(C1C=CN=CC=1)C>[NH:1]1[CH:9]=[C:7]([CH3:8])[C:5](=[O:6])[NH:4][C:2]1=[O:3]
Reactant: Cc1cn(CC(=O)N2CCNCC2=O)c(=O)[nH]c1=O
Agent: CN(C)c1ccncc1
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: Cc1c[nH]c(=O)[nH]c1=O
Yield: 80 %

Procedure:
5.5 g, of N-(thymin-1-ylacetyl)-piperazinone (20.6 mmol) was suspended in 200 mL of dry DCM and treated with 3.77 g (1.5 eq, 30.9 mmol) DMAP, 11.23 g (51.5 mmol, 2.5 eq) Boc-anhydride and 7.2 mL (51.5 mmol, 2.5 eq) of triethylamine. The reaction also results in protection of the secondary amino group on the thymine. The reaction mixture was stirred at room temperature for 3-4 hours, while following the reaction progress by TLC. Upon completion, the reaction mixture was concentrated by rotary evaporation, and the resulting oil was resuspended in DCM. The organic phase was washed successively with 0.1 N HCl solution (2×25 mL), water (2×100 mL) and dried over sodium sulfate. Concentration and purification by recrystallization from diethyl ether afforded 6 g of the Boc-protected thymine PNA precursor (80% yield) as a white solid.
Reaction SMILES: [F:1][CH:2]([CH:8]([O:11][C:12](=[O:16])[C:13]([CH3:15])=[CH2:14])[CH2:9][CH3:10])[C:3]([O:5]CC)=[O:4].[OH-].C[N+](C)(C)C>C1COCC1>[F:1][CH:2]([CH:8]([O:11][C:12](=[O:16])[C:13]([CH3:15])=[CH2:14])[CH2:9][CH3:10])[C:3]([OH:5])=[O:4]
Reactant: C=C(C)C(=O)OC(CC)C(F)C(=O)OCC
Agent: C[N+](C)(C)C
Agent: [OH-]
Solvent: C1CCOC1
Product: C=C(C)C(=O)OC(CC)C(F)C(=O)O
Temperature: 25 °C
Reaction time: 5 h
Yield: 89.9 %

Procedure:
Under a nitrogen atmosphere, 5.81 g (25 mmol) of the ethyl 2-fluoro-3-(methacryloyloxy)pentanoate, and 250 mL of THF were cooled in a 1 L reaction vessel on an ice bath to an ice temperature, and thereto was added 250 g of a 2.38% by mass aqueous tetramethylammoniumhydroxide solution. The temperature of the mixture was elevated to the room temperature, followed by stirring the mixture at a room temperature for 5 hrs. After disappearance of the raw material was confirmed by thin layer chromatography, the solvent of the reaction liquid was distilled off under a reduced pressure. Water was added to the reaction mixture thus obtained, and the mixture was extracted three times with ethyl acetate. The organic layer was washed with water twice, and the solvent was distilled off under a reduced pressure to obtain 4.59 g of 2-fluoro-3-(methacryloyloxy)pentanoic acid represented by the following formula (yield: 90%).
Reaction SMILES: C(O)=O.[CH:4]([NH2:6])=[O:5].[C:7]1([CH2:13][C:14](=O)[CH2:15][CH3:16])[CH:12]=[CH:11][CH:10]=[CH:9][CH:8]=1>O>[CH2:13]([CH:14]([NH:6][CH:4]=[O:5])[CH2:15][CH3:16])[C:7]1[CH:12]=[CH:11][CH:10]=[CH:9][CH:8]=1
Reactant: NC=O
Reactant: CCC(=O)Cc1ccccc1
Solvent: O=CO
Solvent: O
Product: CCC(Cc1ccccc1)NC=O
Temperature: 167.5 °C
Yield: 80 %

Procedure:
To a stirred solution of formic acid (250 ml) and formamide (500 ml) was added 1-phenyl-2-butanone (25 g, 0.168 mols); the reaction was then heated to 165-170° C. for four hours. The reaction was then cooled and poured into water (1 l). The aqueous phase was then extracted with ethyl acetate (3×100 ml). The organic phase was washed with saturated sodium bicarbonate (2×200 ml) and dried over magnesium sulfate. Evaporation of the solvent yielded an oil (24.1 g, 80%).
Reaction SMILES: [Br:1][C:2]1[C:3]([CH2:9][N:10]2[C@@H:14]([CH3:15])[C@@H:13]([C:16]3[CH:21]=[C:20]([C:22]([F:25])([F:24])[F:23])[CH:19]=[C:18]([F:26])[CH:17]=3)[O:12][C:11]2=[O:27])=[N:4][C:5](Cl)=[CH:6][CH:7]=1.Cl.[F:29][C:30]1([F:34])[CH2:33][NH:32][CH2:31]1.C(N(CC)CC)C>C1COCC1>[Br:1][C:2]1[C:3]([CH2:9][N:10]2[C@@H:14]([CH3:15])[C@@H:13]([C:16]3[CH:21]=[C:20]([C:22]([F:25])([F:24])[F:23])[CH:19]=[C:18]([F:26])[CH:17]=3)[O:12][C:11]2=[O:27])=[N:4][C:5]([N:32]2[CH2:33][C:30]([F:34])([F:29])[CH2:31]2)=[CH:6][CH:7]=1
Reactant: C[C@H]1[C@@H](c2cc(F)cc(C(F)(F)F)c2)OC(=O)N1Cc1nc(Cl)ccc1Br
Reactant: FC1(F)CNC1
Agent: Cl
Solvent: C1CCOC1
Solvent: CCN(CC)CC
Product: C[C@H]1[C@@H](c2cc(F)cc(C(F)(F)F)c2)OC(=O)N1Cc1nc(N2CC(F)(F)C2)ccc1Br

Procedure:
(4S,5R)-3-[(3-bromo-6-chloropyridin-2-yl)methyl]-5-[3-fluoro-5-(trifluoromethyl)phenyl]-4-methyl-1,3-oxazolidin-2-one (1.0721 g, 2.293 mmol), 3,3-difluoroazetidine hydrochloride (1.336 g, 10.32 mmol), triethylamine (3.20 ml, 22.93 mmol) and THF (10 ml) were sealed in a microwave vessel and subject to microwave irradiation at 150° C. for 8 hrs. Volatiles were removed under reduced pressure. The resulting pot residue was worked up with brine/ethyl acetate. The combined extracts were dried over Na2SO4, filtered and evaporated to afford a dark mixture. This dark mixture was purified by flash chromatography (SiO2, Biotage SNAP Cartridge, silica gel, KP-Sil, 100 g cartridge). The column was eluted by an ethyl acetate/hexanes mixture (0% to 40% ethyl acetate). Related fractions were pooled and evaporated under reduced pressure to afford a light amber glass of 530.8 mg as the titled compound. LCMS calc.=523.03. found=525.99.
Reaction SMILES: [OH:1][C:2]1[CH:14]=[CH:13][C:12]2[NH:11][C:10]3[CH:9]=[C:8](I)[C:7]4[C:16](=[O:20])[NH:17][C:18](=[O:19])[C:6]=4[C:5]=3[C:4]=2[CH:3]=1.[CH3:21][O:22][C:23]1[CH:28]=[C:27](B2OC(C)(C)C(C)(C)O2)[CH:26]=[CH:25][C:24]=1[OH:38]>>[OH:1][C:2]1[CH:14]=[CH:13][C:12]2[NH:11][C:10]3[CH:9]=[C:8]([C:27]4[CH:26]=[CH:25][C:24]([OH:38])=[C:23]([O:22][CH3:21])[CH:28]=4)[C:7]4[C:16](=[O:20])[NH:17][C:18](=[O:19])[C:6]=4[C:5]=3[C:4]=2[CH:3]=1
Reactant: COc1cc(B2OC(C)(C)C(C)(C)O2)ccc1O
Reactant: O=C1NC(=O)c2c1c(I)cc1[nH]c3ccc(O)cc3c21
Product: COc1cc(-c2cc3[nH]c4ccc(O)cc4c3c3c2C(=O)NC3=O)ccc1O
Yield: 58 %

Procedure:
The reaction of 9-hydroxy-4-iodopyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione, prepared as in example 7, with 2-methoxy-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenol according to the procedure described in example 8 gave 9-hydroxy-4-(4-hydroxy-3-methoxyphenyl)pyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione (23) (I, Ar=4-hydroxy-3-methoxyphenyl) in a 58% yield; mp 290–295° C. (dec). 1H NMR δ [(CD3)2SO] 11.67 (br s, 1H), 10.97 (br s, 1H), 9.22 (br s, 1H), 9.15 (s, 1H), 8.33 (d, J=2.4 Hz, 1H), 7.57 (s, 1H), 7.41 (d, J=8.6 Hz, 1H), 7.23 (d, J=2.0 Hz, 1H), 7.04 (m, 2H), 6.86 (d, J=8.1 Hz, 1H), 3.82 (s, 3H). FABMS found [M+H]+: 375.0973. C21H15N2O5 requires 375.0981.