Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: CN(C)C=O.[F:6][C:7]1[C:8]([CH3:26])=[C:9]2[C:14](=[CH:15][C:16]=1F)[N:13]([C@@H:18]1[CH2:20][C@@H:19]1[F:21])[CH:12]=[C:11]([C:22]([OH:24])=[O:23])[C:10]2=[O:25].Cl.Cl.[N:29]12[CH2:36][CH:33]([CH2:34][CH2:35]1)[NH:32][CH2:31][CH2:30]2>C(N(CC)CC)C>[N:29]12[CH2:36][CH:33]([CH2:34][CH2:35]1)[N:32]([C:16]1[CH:15]=[C:14]3[C:9]([C:10](=[O:25])[C:11]([C:22]([OH:24])=[O:23])=[CH:12][N:13]3[C@@H:18]3[CH2:20][C@@H:19]3[F:21])=[C:8]([CH3:26])[C:7]=1[F:6])[CH2:31][CH2:30]2
Reactant: Cc1c(F)c(F)cc2c1c(=O)c(C(=O)O)cn2[C@@H]1C[C@@H]1F
Reactant: C1CN2CCC(C2)N1
Agent: Cl
Solvent: CN(C)C=O
Solvent: CCN(CC)CC
Product: Cc1c(F)c(N2CCN3CCC2C3)cc2c1c(=O)c(C(=O)O)cn2[C@@H]1C[C@@H]1F
Temperature: 100 °C
Reaction time: 1 h
Yield: 50 %

Procedure:
To 6 ml of dried N,N-dimethylformamide were added 200 mg of 6,7-difluoro-1-[2-(S)-fluoro-1-(R)-cyclopropyl]-5-methyl-4-oxo-1,4-dihydroquinoline-3-carboxylic acid, 372 mg of 1,4-diazabicyclo[3.2.1]octane dihydrochloride, and 2 ml of triethylamine, and the mixture was stirred at 100° C. for 1 hour. After allowing to cool, the reaction mixture was concentrated under reduced pressure, and the residue was dissolved in a 1N sodium hydroxide aqueous solution under cooling with ice. The solution was neutralized with 1N hydrochloric acid and extracted with chloroform. The extract was dried over anhydrous sodium sulfate, and the solvent was removed under reduced pressure. The resulting crude crystals were recrystallized from a mixed solvent of ethanol and 28% aqueous ammonia, and the crystals were collected by filtration, washed with diethyl ether, and dried at 60° C. under reduced pressure overnight to yield 131 mg of the titled compound as a yellow powder.
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[CH2:13][CH2:12][CH:11](OS(C)(=O)=O)[CH2:10][CH2:9]1)=[O:7])([CH3:4])([CH3:3])[CH3:2].[CH3:19][S-:20].[Na+]>CN(C=O)C.O>[C:1]([O:5][C:6]([N:8]1[CH2:9][CH2:10][CH:11]([S:20][CH3:19])[CH2:12][CH2:13]1)=[O:7])([CH3:2])([CH3:3])[CH3:4]
Reactant: C[S-]
Reactant: CC(C)(C)OC(=O)N1CCC(OS(C)(=O)=O)CC1
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: O
Product: CSC1CCN(C(=O)OC(C)(C)C)CC1
Reaction time: 4 h
Yield: 71.4 %

Procedure:
Amine preparation: A mixture of 4-methanesulfonyloxy-piperidine-1-carboxylic acid tert-butyl ester (1.015 g), sodium thiomethoxide (635 mg) was heated to 80° C. in DMF (10 mL). After 4 h, the reaction mixture was diluted with water, extracted with ethyl acetate, dried (MgSO4), filtered and concentrated in vacuo and then purified by flash chromatography to give 4-methylsulfanyl-piperidine-1-carboxylic acid tert-butyl ester (600 mg). To a solution of 4-methylsulfanyl-piperidine-1-carboxylic acid tert-butyl ester (600 mg) in chloroform (15 mL) was added mCPBA (1.46 g). After stirring for 2 days, the reaction mixture was diluted with DCM, washed with sodium bicarbonate solution, dried (MgSO4) and the solvent removed in vacuo to yield 4-methanesulfonyl-piperidine-1-carboxylic acid tent-butyl ester (505 mg) as a white solid. Treatment of this compound with HCl in DCM/MeOH yielded the desired amine, isolated as the hydrochloride salt.
Reaction SMILES: [CH2:1]([O:8][C:9]1[CH:14]=[CH:13][C:12]([C:15](=[O:18])[CH2:16]Cl)=[CH:11][C:10]=1[NH:19][S:20]([CH3:23])(=[O:22])=[O:21])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[CH2:24]([NH:31][CH2:32][C:33]1[CH:38]=[CH:37][CH:36]=[CH:35][CH:34]=1)[C:25]1[CH:30]=[CH:29][CH:28]=[CH:27][CH:26]=1>CN(C)C=O>[CH2:1]([O:8][C:9]1[CH:14]=[CH:13][C:12]([C:15](=[O:18])[CH2:16][N:31]([CH2:24][C:25]2[CH:30]=[CH:29][CH:28]=[CH:27][CH:26]=2)[CH2:32][C:33]2[CH:38]=[CH:37][CH:36]=[CH:35][CH:34]=2)=[CH:11][C:10]=1[NH:19][S:20]([CH3:23])(=[O:22])=[O:21])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: CS(=O)(=O)Nc1cc(C(=O)CCl)ccc1OCc1ccccc1
Reactant: c1ccc(CNCc2ccccc2)cc1
Solvent: CN(C)C=O
Product: CS(=O)(=O)Nc1cc(C(=O)CN(Cc2ccccc2)Cc2ccccc2)ccc1OCc1ccccc1
Temperature: 25 °C
Reaction time: 8 h

Procedure:
N-[2-Benzyloxy-5-(2-chloro-1-oxo-ethyl)-phenyl]-methanesulfonamide (EP 0 659 737) (17.0 g, 42.8 mmol) was dissolved in 200 mL of dimethylformamide and treated with dibenzylamine (22.0 g, 110 mmol). The mixture was stirred at room temperature overnight and then the solvent was removed. The residue was purified by silica gel chromatography using 20-50% ethyl acetate/hexanes as elute to give the title compound as a white solid; 1H NMR (300 MHz, CDCl3) δ 2.94 (s, 3H), 3.77 (s, 2H), 3.82 (s, 2H), 5.16 (s, 2H), 6.75 (brs, 1H), 6.96 (d, J=8.7 Hz, 1H), 7.20-7.50 (m, 15H), 7.67 (dd, J=8.7, 2.1Hz, 1H), 8.10 (d, J=2.1 Hz, 1H); MS (ES) m/z: 515.2 (M++H); HRMS Calcd. for C30H30N2O4S(M+): 514.1926. Found: 514.1927.
Reaction SMILES: [CH3:1][C:2]1[CH:22]=[CH:21][C:5]([C:6]([NH:8][NH:9][C:10](=O)[C:11]2[CH:16]=[CH:15][CH:14]=[C:13]([N+:17]([O-:19])=[O:18])[CH:12]=2)=O)=[CH:4][CH:3]=1.COC1C=CC(P2(SP(C3C=CC(OC)=CC=3)(=S)S2)=[S:32])=CC=1>C1C=CC=CC=1>[N+:17]([C:13]1[CH:12]=[C:11]([C:10]2[S:32][C:6]([C:5]3[CH:21]=[CH:22][C:2]([CH3:1])=[CH:3][CH:4]=3)=[N:8][N:9]=2)[CH:16]=[CH:15][CH:14]=1)([O-:19])=[O:18]
Reactant: Cc1ccc(C(=O)NNC(=O)c2cccc([N+](=O)[O-])c2)cc1
Reactant: COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1
Solvent: c1ccccc1
Product: Cc1ccc(-c2nnc(-c3cccc([N+](=O)[O-])c3)s2)cc1
Temperature: 60 °C

Procedure:
A mixture of 1-[(4-methyl)benzoyl]-2-(3-nitrobenzoyl)hydrazine (1.40 g, 4.68 mmol) and Lawesson's Reagent (0.95 g, 2.34 mmol) in benzene (25 ml) is slowly heated to 60° C. After 3 hours the solution is concentrated, quenched with 35 ml of water and heated to reflux for 12 hours. The mixture is then cooled to room temperature and the precpitate is collected by filtration. The precipitate is then taken up in chloroform (100 ml) and the insoluble portion is removed by filtration. The filtrate is then dried over MgSO4 and concentrated to yield 2-(3′-nitrophenyl)-5-(p-tolyl)-1,3,4-thiadiazole as a pale yellow solid. (0.67 g, 48%). 1H NMR (CDCl3): δ 2.45 (s, 3H), 7.35 (d, 2H), 7.73 (t, 1H), 7.92 (d, 2H), 8.38 (t, 2H), 8.81 (s, 1H).
Reaction SMILES: [OH:1][C:2]1[CH:3]=[C:4]([CH:9]=[C:10]([OH:13])[C:11]=1[CH3:12])[C:5]([O:7][CH3:8])=[O:6].C(=O)([O-])[O-].[K+].[K+].[CH2:20](Br)[C:21]1[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=1>CN(C=O)C>[CH2:20]([O:1][C:2]1[CH:3]=[C:4]([CH:9]=[C:10]([OH:13])[C:11]=1[CH3:12])[C:5]([O:7][CH3:8])=[O:6])[C:21]1[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=1
Reactant: BrCc1ccccc1
Reactant: COC(=O)c1cc(O)c(C)c(O)c1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Product: COC(=O)c1cc(O)c(C)c(OCc2ccccc2)c1
Temperature: 25 °C
Reaction time: 8 h

Procedure:
Methyl 3,5-dihydroxy-4-methylbenzoate (3.5 g, 19.22 mmol, 1.0 eq) was dissolved in 300 ml of DMF. To this solution potassium carbonate (2.52 g, 18.26 mmol, 0.95 eq) was added. To this stirred suspension, benzyl bromide (3.12 g, 18.26 mmol, 0.95 eq) (diluted with 50 ml of DMF) was added dropwise over a period of 3 h. The solution was stirred overnight at ambient temperature. Then DMF was evaporated under reduced pressure. The residue was washed with water and the product was extracted thrice with DCM. The combined DCM layers was dried over sodium sulphate and evaporated under vacuum. The required product was purified by silica gel (240-400) column chromatography using 10% ethyl acetate/hexane as the eluent. Yield: 1.6 g (30%). 1H NMR (400 MHz, DMSO-d6): δ 2.07 (s, 3H), 3.81 (s, 3H), 5.14 (s, 2H), 7.08 (s, 1H), 7.14 (s, 1H), 7.33-7.35 (d, 1H, J=7.04 Hz), 7.39-7.42 (t, 2H, J=7.40 Hz), 7.46-7.48 (d, 2H, J=7.48 Hz), 9.78 (s, 1H).
Reaction SMILES: [NH2:1][CH2:2][C:3]1[CH:4]=[N:5][CH:6]=[C:7](Br)[CH:8]=1.[F:10][C:11]1[CH:20]=[C:19]2[C:14]([CH2:15][CH2:16][C:17](=[O:22])[N:18]2[CH3:21])=[CH:13][C:12]=1B1OC(C)(C)C(C)(C)O1>>[NH2:1][CH2:2][C:3]1[CH:8]=[C:7]([C:12]2[CH:13]=[C:14]3[C:19](=[CH:20][C:11]=2[F:10])[N:18]([CH3:21])[C:17](=[O:22])[CH2:16][CH2:15]3)[CH:6]=[N:5][CH:4]=1
Reactant: CN1C(=O)CCc2cc(B3OC(C)(C)C(C)(C)O3)c(F)cc21
Reactant: NCc1cncc(Br)c1
Product: CN1C(=O)CCc2cc(-c3cncc(CN)c3)c(F)cc21

Procedure:
In analogy to the procedure described for the preparation of example 45, reaction of 3-aminomethyl-5-bromopyridine and 7-fluoro-1-methyl-6-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-3,4-dihydro-1H-quinolin-2-one (intermediate A-22) gave the title compound as a light yellow solid. MS: 286.7 (M+H+).
Reaction SMILES: [N+:1]([C:4]1[CH:9]=[CH:8][CH:7]=[CH:6][C:5]=1[NH:10]N=C(C(=O)CC)CC)([O-:3])=[O:2].[OH-:19].[Na+]>>[CH3:6][C:5]1[C:6]2[C:5](=[C:4]([N+:1]([O-:3])=[O:2])[CH:9]=[CH:8][CH:7]=2)[NH:10][C:4]=1[C:9](=[O:19])[CH2:8][CH3:7]
Reactant: CCC(=O)C(CC)=NNc1ccccc1[N+](=O)[O-]
Reactant: [OH-]
Agent: [Na+]
Product: CCC(=O)c1[nH]c2c([N+](=O)[O-])cccc2c1C
Temperature: 80 °C
Reaction time: 8 h
Yield: 10 %

Procedure:
A mixture of hexane-3,4-dione (2-nitrophenyl)hydrazone (3.13 g) and polyphosphoric acid (50 g) was stirred at 80° C. overnight. The reaction mixture was poured into ice water, neutralized with 50% aqueous sodium hydroxide solution, and extracted with ethyl acetate. The ethyl acetate layer was washed with saturated brine, dried (MgSO4) and concentrated. The residue was subjected to silica gel column chromatography and the title compound (0.29 g, yield 10%) was obtained as yellow crystals from a fraction eluted with ethyl acetate-hexane (1:2, volume ratio). melting point>164° C. (decomposition).
Reaction SMILES: [CH:1]#[C:2][CH2:3][CH2:4][CH2:5][CH2:6][CH2:7]C.C1(C#C)C=CC=CC=1.[O:17]1[CH:21]=[CH:20][CH:19]=[C:18]1[C:22]#N>C(#N)C1C=CC=CC=1>[C:22]([C:18]1[O:17][CH:21]=[CH:20][CH:19]=1)#[C:1][CH2:2][CH2:3][CH2:4][CH2:5][CH2:6][CH3:7]
Reactant: N#Cc1ccco1
Reactant: C#CCCCCCC
Solvent: N#Cc1ccccc1
Solvent: C#Cc1ccccc1
Product: CCCCCCC#Cc1ccco1
Reaction time: 22 h
Yield: 62 %

Procedure:
The procedure was identical to Example 2, with the exception that 1-octyne (0.590 ml; 0.441 g; 4.00 mmol) was used as a substrate instead of phenylacetylene and 2-furonitrile (0.175 ml; 0.186 g; 2.00 mmol) was used as a substrate instead of benzonitrile. GC analysis of the organic phase of the hydrolyzed reaction sample after 22 h at 65° C. showed the presence of 1.24 mmol (62% yield) of 2-(1-octynyl)furan and no remaining 2-furonitrile in the reaction mixture.
Reaction SMILES: C(OC([NH:11][C@@H:12]([C:19](=[O:29])[NH:20][CH2:21][C:22]([O:24][C:25]([CH3:28])([CH3:27])[CH3:26])=[O:23])[C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1)=O)C1C=CC=CC=1>CCO.C1(C)C=CC=CC=1.[Pd]>[C:25]([O:24][C:22]([CH2:21][NH:20][C:19]([C@H:12]([NH2:11])[C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1)=[O:29])=[O:23])([CH3:28])([CH3:26])[CH3:27]
Reactant: CC(C)(C)OC(=O)CNC(=O)[C@H](NC(=O)OCc1ccccc1)c1ccccc1
Agent: [Pd]
Solvent: Cc1ccccc1
Solvent: CCO
Product: CC(C)(C)OC(=O)CNC(=O)[C@H](N)c1ccccc1
Reaction time: 5.5 h
Yield: 98.7 %

Procedure:
(R)-N-Benzyloxycarbonyl-α-[N-(t-butoxycarbonylmethyl)carbamoyl]benzylamine (Method 1; 12.8 g, 32.2 mmol) was dissolved in EtOH (99%, 200 ml) and toluene (50 ml). Pd/C (10%, 0.65 g) was added and hydrogenation was performed at atmospheric pressure for 5.5 hours at room temperature. The reaction mixture was filtered through diatomaceous earth and the solvents were evaporated to give the title compound (8.4 g, 99%). NMR (600 MHz, CDCl3): 1.45 (s, 9H), 3.93 (m, 2H), 4.54 (s, 1H), 7.31–7.42 (m, 5H), 7.51 (brs, 1H).
Reaction SMILES: Br[C:2]1[CH:3]=[C:4]2[C:8](=[C:9]([C:11]([NH2:13])=[O:12])[CH:10]=1)[NH:7][CH:6]=[C:5]2[CH:14]1[CH2:19][CH2:18][S:17](=[O:21])(=[O:20])[CH2:16][CH2:15]1.[C:22]1(B(O)O)[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=1.C([O-])([O-])=O.[K+].[K+]>O1CCOCC1.O.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:20]=[S:17]1(=[O:21])[CH2:18][CH2:19][CH:14]([C:5]2[C:4]3[C:8](=[C:9]([C:11]([NH2:13])=[O:12])[CH:10]=[C:2]([C:22]4[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=4)[CH:3]=3)[NH:7][CH:6]=2)[CH2:15][CH2:16]1
Reactant: OB(O)c1ccccc1
Reactant: NC(=O)c1cc(Br)cc2c(C3CCS(=O)(=O)CC3)c[nH]c12
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: C1COCCO1
Solvent: O
Product: NC(=O)c1cc(-c2ccccc2)cc2c(C3CCS(=O)(=O)CC3)c[nH]c12
Temperature: 150 °C
Yield: 28.9 %

Procedure:
To 5-bromo-3-(1,1-dioxidotetrahydro-2H-thiopyran-4-yl)-1H-indole-7-carboxamide (80 mg, 0.216 mmol) in dioxane and water (4 mL/1 mL) was added phenylboronic acid (36 mg), Pd(PPh3)4 (25 mg) and K2CO3 (104 mg). The reaction mixture was heated to 150° C. for 20 minutes by microwave irradiation. The organic phase was separated, concentrated, and purified by HPLC to afford the title compound (23 mg).
Reaction SMILES: [CH:1]1([C:6]2[CH:36]=[CH:35][C:9]([CH2:10][O:11][C:12]3[CH:20]=[CH:19][C:18]4[N:17]5[CH2:21][CH2:22][CH:23]([CH2:24][C:25]([O:27]C(C)(C)C)=[O:26])[C:16]5=[C:15]([CH:32]5[CH2:34][CH2:33]5)[C:14]=4[CH:13]=3)=[CH:8][C:7]=2[C:37]([F:40])([F:39])[F:38])[CH2:5][CH2:4][CH2:3][CH2:2]1.NC(CS)C(O)=O>C(O)(C(F)(F)F)=O>[CH:1]1([C:6]2[CH:36]=[CH:35][C:9]([CH2:10][O:11][C:12]3[CH:20]=[CH:19][C:18]4[N:17]5[CH2:21][CH2:22][CH:23]([CH2:24][C:25]([OH:27])=[O:26])[C:16]5=[C:15]([CH:32]5[CH2:34][CH2:33]5)[C:14]=4[CH:13]=3)=[CH:8][C:7]=2[C:37]([F:40])([F:38])[F:39])[CH2:2][CH2:3][CH2:4][CH2:5]1
Reactant: CC(C)(C)OC(=O)CC1CCn2c1c(C1CC1)c1cc(OCc3ccc(C4CCCC4)c(C(F)(F)F)c3)ccc12
Agent: NC(CS)C(=O)O
Solvent: O=C(O)C(F)(F)F
Product: O=C(O)CC1CCn2c1c(C1CC1)c1cc(OCc3ccc(C4CCCC4)c(C(F)(F)F)c3)ccc12
Temperature: 25 °C
Reaction time: 0.25 h
Yield: 65 %

Procedure:
tert-Butyl 2-(7-(4-cyclopentyl-3-(trifluoromethyl)benzyloxy)-9-cyclopropyl-2,3-dihydro-1H-pyrrolo[1,2-a]indol-1-yl)acetate (9.2 mg, 0.017 mmol) was added to a solution of 2-amino-3-mercaptopropanoic acid (2.013 mg, 0.017 mmol) in TFA (1 mL) and the resulting mixture was stirred at room temperature for 15 min in a 20 mL sealed scintillation vial. After 15 min, the reaction mixture was poured into approximately 4 mL of ice water. A precipitate formed and was collected by vacuum filtration. The solid was washed with n-hexane (3×5 mL) and dried (vacuum oven) to give the title compound as a off-white solid (5.5 mg). LCMS m/z=498.4 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ ppm 0.35-0.43 (m, 1H), 0.55-0.64 (m, 1H), 0.74-0.88 (m, 2H), 1.55-1.78 (m, 5H), 1.79-1.89 (m, 2H), 1.94-2.05 (m, 2H), 2.19-2.30 (m, 1H), 2.42-2.48 (m, 1H), 2.69-2.81 (m, 1H), 2.93 (dd, J=15.92, 3.79 Hz, 1H), 3.20-3.30 (m, 1H), 3.54-3.65 (m, 1H), 3.84-3.94 (m, 1H), 3.97-4.07 (m, 1H), 5.15 (s, 2H), 6.76 (dd, J=8.59, 2.27 Hz, 1H), 7.05 (d, J=2.27 Hz, 1H), 7.14 (d, J=8.59 Hz, 1H), 7.62 (d, J=8.33 Hz, 1H), 7.67-7.77 (m, 2H), 12.28 (bs, 1H).
Reaction SMILES: [CH:1]1([C:7]([NH:9][C:10]2[S:11][C:12]3[CH2:23][CH2:22][CH2:21][CH2:20][C:13]=3[C:14]=2[C:15](OCC)=[O:16])=[O:8])[CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1.[CH3:24][N:25]([CH3:29])[CH2:26][CH2:27][NH2:28]>>[CH:1]1([C:7]([NH:9][C:10]2[S:11][C:12]3[CH2:23][CH2:22][CH2:21][CH2:20][C:13]=3[C:14]=2[C:15]([NH:28][CH2:27][CH2:26][N:25]([CH3:29])[CH3:24])=[O:16])=[O:8])[CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1
Reactant: CCOC(=O)c1c(NC(=O)C2CCCCC2)sc2c1CCCC2
Reactant: CN(C)CCN
Product: CN(C)CCNC(=O)c1c(NC(=O)C2CCCCC2)sc2c1CCCC2

Procedure:
The product of Example 13 and N,N-dimethylethylenediamine were processed as in Examples 29A, 29B and 5B to afford the title compound. 1H NMR (300 MHz, CD3OD) δ ppm 1.16-1.57 (m, 5H), 1.68-1.77 (m, 1H), 1.78-1.89 (m, 6H), 1.90-2.00 (m, 2H), 2.34-2.45 (m, 1H), 2.36 (s, 3H), 2.61-2.79 (m, 4H), 3.00 (s, 6H), 3.38 (t, J=5.9 Hz, 2H), 3.75 (t, J=5.9 Hz, 2H), 7.22 (d, J=8.1 Hz, 2H), 7.66-7.72 (m, 2H); MS (DCI/NH3) m/z 378 (M+H)+; anal. calculated for C20H31N3O2S.C7H8O3S.1.2H2O: C, 56.76; H, 7.30; N, 7.35. Found: C, 56.86; H, 7.45; N, 7.05.
Reaction SMILES: Br[C:2]1[CH2:6][CH2:5][CH2:4][C:3]=1[C:7]1[CH:12]=[CH:11][C:10]([S:13][CH3:14])=[CH:9][CH:8]=1.[F:15][C:16]1[CH:21]=[CH:20][C:19](B(O)O)=[C:18]([CH3:25])[CH:17]=1>>[F:15][C:16]1[CH:21]=[CH:20][C:19]([C:2]2[CH2:6][CH2:5][CH2:4][C:3]=2[C:7]2[CH:12]=[CH:11][C:10]([S:13][CH3:14])=[CH:9][CH:8]=2)=[C:18]([CH3:25])[CH:17]=1
Reactant: CSc1ccc(C2=C(Br)CCC2)cc1
Reactant: Cc1cc(F)ccc1B(O)O
Product: CSc1ccc(C2=C(c3ccc(F)cc3C)CCC2)cc1
Yield: 88.2 %

Procedure:
Following the synthetic procedure outlined in Step 3 of Example 1, 500 mg (1.9 mmol) of 1-(2-bromocyclopenten-1-yl)-4-(methylthio)benzene (Example 1, Step 2) was reacted with 590 mg (3.8 mmol) of 4-fluoro-2-methylphenylboronic acid (Step 1). Purification by silica gel chromatography (MPLC) with hexane gave 500 mg (95% ) of 1-[2-(4-fluoro-2-methylphenyl)cyclopenten-1-yl]-4-(methylthio)benzene as a colorless solid: mp 67°-68° C.; NMR (CDCl3) δ 2.00-2.11 (m, 2H), 2.05 (s, 3H), 2.41 (s, 3H), 2.69-2.77 (m, 2H), 2.86-2.95 (m, 2H), 6.80-7.07 (m, 7H) .
Reaction SMILES: S(Cl)(Cl)=O.[CH3:5][O:6][C:7]1[C:8]([O:19][CH2:20][CH2:21][CH2:22][N:23]2[CH2:28][CH2:27][O:26][CH2:25][CH2:24]2)=[CH:9][C:10]([N+:16]([O-:18])=[O:17])=[C:11]([CH:15]=1)[C:12](O)=[O:13].C[N:30](C=O)C>>[CH3:5][O:6][C:7]1[C:8]([O:19][CH2:20][CH2:21][CH2:22][N:23]2[CH2:28][CH2:27][O:26][CH2:25][CH2:24]2)=[CH:9][C:10]([N+:16]([O-:18])=[O:17])=[C:11]([CH:15]=1)[C:12]([NH2:30])=[O:13]
Reactant: COc1cc(C(=O)O)c([N+](=O)[O-])cc1OCCCN1CCOCC1
Reactant: CN(C)C=O
Solvent: O=S(Cl)Cl
Product: COc1cc(C(N)=O)c([N+](=O)[O-])cc1OCCCN1CCOCC1
Temperature: 50 °C

Procedure:
Thionyl chloride (15 ml) and DMF (0.05 ml) were added to 5-methoxy-4-(3-morpholinopropoxy)-2-nitrobenzoic acid (7.54 g). The mixture was heated at 50° C. for 1 hour, the excess thionyl chloride was removed by evaporation and by azeotroping with toluene (×2). The resulting solid was suspended in THF (200 ml) and ammonia was bubbled through the mixture for 30 minutes. The precipitate was removed by filtration and washed with THF. After concentration of the filtrate by evaporation, the product crystallised and was collected by filtration to give 5-methoxy-4-(3-morpholinopropoxy)-2-nitrobenzamide (5.25 g) as light yellow crystals which were used without further purification.
Reaction SMILES: C(OC(=O)CCNC(=O)C1C=CC(CN)=CC=1)C.C1C2(CCCCC2)CCC(=O)C1.[CH2:31]([O:33][C:34](=[O:59])[CH2:35][CH2:36][NH:37][C:38](=[O:58])[C:39]1[CH:44]=[CH:43][C:42]([CH2:45][NH:46][CH:47]2[CH2:52][CH2:51][C:50]3([CH2:57][CH2:56][CH2:55][CH2:54][CH2:53]3)[CH2:49][CH2:48]2)=[CH:41][CH:40]=1)[CH3:32].C(N(C(C)C)CC)(C)C.[F:69][C:70]1[CH:71]=[C:72]([CH:76]=[C:77]([C:79]([F:82])([F:81])[F:80])[CH:78]=1)[C:73](Cl)=[O:74]>C(#N)C>[CH2:31]([O:33][C:34](=[O:59])[CH2:35][CH2:36][NH:37][C:38](=[O:58])[C:39]1[CH:44]=[CH:43][C:42]([CH2:45][NH:46][CH:47]2[CH2:52][CH2:51][C:50]3([CH2:53][CH2:54][CH2:55][CH2:56][CH2:57]3)[CH2:49][CH2:48]2)=[CH:41][CH:40]=1)[CH3:32].[CH2:31]([O:33][C:34](=[O:59])[CH2:35][CH2:36][NH:37][C:38](=[O:58])[C:39]1[CH:44]=[CH:43][C:42]([CH2:45][N:46]([C:73](=[O:74])[C:72]2[CH:76]=[C:77]([C:79]([F:80])([F:81])[F:82])[CH:78]=[C:70]([F:69])[CH:71]=2)[CH:47]2[CH2:52][CH2:51][C:50]3([CH2:53][CH2:54][CH2:55][CH2:56][CH2:57]3)[CH2:49][CH2:48]2)=[CH:41][CH:40]=1)[CH3:32]
Reactant: O=C(Cl)c1cc(F)cc(C(F)(F)F)c1
Agent: CCOC(=O)CCNC(=O)c1ccc(CN)cc1
Agent: CCOC(=O)CCNC(=O)c1ccc(CNC2CCC3(CCCCC3)CC2)cc1
Agent: O=C1CCC2(CCCCC2)CC1
Solvent: CCN(C(C)C)C(C)C
Solvent: CC#N
Product: CCOC(=O)CCNC(=O)c1ccc(CN(C(=O)c2cc(F)cc(C(F)(F)F)c2)C2CCC3(CCCCC3)CC2)cc1
Reaction time: 1 h
Yield: 200.2 %

Procedure:
3-[4-(Spiro[5.5]undec-3-ylaminomethyl)benzoylamino]propionic acid ethyl ester was prepared by reductive alkylation of 3-(4-aminomethyl-benzoylamino)propionic acid ethyl ester with spiro[5.5]undecan-3-one. 3-[4-(Spiro[5.5]undec-3-ylaminomethyl)benzoylamino]propionic acid ethyl ester (200 mg, 499 μmol) was dissolved in acetonitrile (5 mL) and diisopropylethylamine (170 μL) and cooled on an ice bath. Commercially available 3-fluoro-5-(trifluoromethyl)benzoylchloride (136 mg, 602 μmol) dissolved in acetonitrile (5 mL) was added dropwise. The reaction was complete within one hour as shown by HPLC. The solvent was evaporated and water (10 mL) was added to the residue followed by saturated sodium bicarbonate (10 mL). The product was extracted using ethyl acetate (2×50 mL). The combined ethyl acetate extracts were washed with water (20 mL) and brine (20 mL). Drying the organic phases over MgSO4 and evaporation of the solvent afforded 3-(4-{[(3-fluoro-5-trifluoromethylbenzoyl)spiro[5.5]undec-3-yl-amino]methyl}benzoylamino)propionic acid ethyl ester (295 mg) which was hydrolyzed using sodium hydroxide to afford the title compound.
Reaction SMILES: [N:1]([CH:4]1[CH2:23][N:8]2[C:9]3[C:14]([C:15]([CH2:16][C:17]([O:19]CCC)=[O:18])=[C:7]2[CH2:6][CH2:5]1)=[CH:13][CH:12]=[CH:11][CH:10]=3)=[N+:2]=[N-:3].[Br:24][C:25]1[CH:30]=[CH:29][C:28]([CH:31]([OH:34])[C:32]#[CH:33])=[CH:27][CH:26]=1>>[Br:24][C:25]1[CH:26]=[CH:27][C:28]([CH:31]([OH:34])[C:32]2[N:1]([CH:4]3[CH2:23][N:8]4[C:9]5[C:14]([C:15]([CH2:16][C:17]([OH:19])=[O:18])=[C:7]4[CH2:6][CH2:5]3)=[CH:13][CH:12]=[CH:11][CH:10]=5)[N:2]=[N:3][CH:33]=2)=[CH:29][CH:30]=1
Reactant: C#CC(O)c1ccc(Br)cc1
Reactant: CCCOC(=O)Cc1c2n(c3ccccc13)CC(N=[N+]=[N-])CC2
Product: O=C(O)Cc1c2n(c3ccccc13)CC(n1nncc1C(O)c1ccc(Br)cc1)CC2

Procedure:
The title compound was prepared using procedures described in EXAMPLE 3 from propyl (7-azido-6,7,8,9-tetrahydropyrido[1,2-α]indol-10-yl)acetate and 1-(4-bromophenyl)prop-2-yn-1-ol. MS (+ESI) m/z: 483.0.
Reaction SMILES: Br[C:2]1[CH:3]=[C:4]([CH:27]=[CH:28][CH:29]=1)[C:5]([NH:7][C:8]1[C:17]2[C:12](=[CH:13][CH:14]=[CH:15][CH:16]=2)[C:11]([O:18][CH2:19][CH2:20][N:21]2[CH2:26][CH2:25][O:24][CH2:23][CH2:22]2)=[CH:10][CH:9]=1)=[O:6].[F:30][C:31]1[CH:36]=[CH:35][CH:34]=[CH:33][C:32]=1B(O)O>>[N:21]1([CH2:20][CH2:19][O:18][C:11]2[C:12]3[C:17](=[CH:16][CH:15]=[CH:14][CH:13]=3)[C:8]([NH:7][C:5]([C:4]3[CH:3]=[C:2]([C:32]4[CH:33]=[CH:34][CH:35]=[CH:36][C:31]=4[F:30])[CH:29]=[CH:28][CH:27]=3)=[O:6])=[CH:9][CH:10]=2)[CH2:26][CH2:25][O:24][CH2:23][CH2:22]1
Reactant: O=C(Nc1ccc(OCCN2CCOCC2)c2ccccc12)c1cccc(Br)c1
Reactant: OB(O)c1ccccc1F
Product: O=C(Nc1ccc(OCCN2CCOCC2)c2ccccc12)c1cccc(-c2ccccc2F)c1

Procedure:
Compound is prepared from 3-bromo-N-[4-(2-morpholin-4-yl-ethoxy)-naphthalen-1-yl]-benzamide and 2-fluorophenyl boronic acid according to conditions described in general procedure K. 1H NMR 300 MHz (CDCl3) δ 8.3(d, 1H), 8.15(s, 1H), 7.18-8.05(m, 11H), 6.8(d, 1H, J=10 Hz), 4.3(t, 2H), 3.75(m, 4H), 3.0(t, 2H), 2.6(m, 4H).
Reaction SMILES: [CH3:1][C:2]1[CH2:7][CH2:6][CH:5]([C:8](Cl)=[O:9])[CH2:4][CH:3]=1.[OH-:11].[Na+]>CO.O1CCCC1>[CH3:1][C:2]1[CH2:7][CH2:6][CH:5]([C:8]([OH:9])=[O:11])[CH2:4][CH:3]=1
Reactant: [OH-]
Reactant: CC1=CCC(C(=O)Cl)CC1
Agent: [Na+]
Solvent: C1CCOC1
Solvent: CO
Product: CC1=CCC(C(=O)O)CC1

Procedure:
To a solution of 4-methylcyclohex-3-enecarbonyl chloride (2 ml) in a mixture of methanol (20 ml) and tetrahydrofuran (20 ml) was added aqueous sodium hydroxide (4N, 20 ml). The resultant mixture was stirred at ambient temperature for 1 hour, and evaporated. The residue was taken up into a mixture of water and ethyl acetate and adjusted pH to around 1. The organic layer was separated, washed with brine, dried over magnesium sulfate, and evaporated under reduced pressure to give 4-methylcyclohex-3-enecarboxylic acid, which was used without further purification.
Reaction SMILES: [O:1]1[CH:5]=[CH:4][CH:3]=[C:2]1[C:6]1[NH:14][C:13]([NH2:15])=[N:12][C:11]2[C:7]=1[N:8]=[CH:9][N:10]=2.[CH2:16]([N:20]=[C:21]=[O:22])[CH2:17][CH2:18][CH3:19]>CN(C1C=CN=CC=1)C.CN(C=O)C>[NH2:15][C:13]1[N:12]=[C:11]2[C:7]([N:8]=[CH:9][N:10]2[C:21]([NH:20][CH2:16][CH2:17][CH2:18][CH3:19])=[O:22])=[C:6]([C:2]2[O:1][CH:5]=[CH:4][CH:3]=2)[N:14]=1
Reactant: Nc1nc2ncnc-2c(-c2ccco2)[nH]1
Reactant: CCCCN=C=O
Agent: CN(C)c1ccncc1
Solvent: CN(C)C=O
Product: CCCCNC(=O)n1cnc2c(-c3ccco3)nc(N)nc21
Temperature: 65 °C
Reaction time: 1 h
Yield: 98.6 %

Procedure:
A solution of 6-(2-furyl)-1H-purine-2-amine (0.050 g, 0.25 mmol) and DMAP (5 mg, 0.03 mmol) in anhydrous DMF (1 μL) was treated with n-butylisocyanate (0.029 g, 0.30 mmol), shaken at 65° C. for 1 h, poured onto ice-cold water (10 mL), cooled at 0° C. for 15 min and the resulting precipitate filtered and dried in vacuo over P2O5 to give the title compound (74 mg, 100%) as a white solid.