Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [Br:1]Br.[CH3:3][O:4][CH2:5][CH2:6][O:7][CH2:8][CH2:9][CH:10]([C:14]([OH:16])=[O:15])[C:11]([OH:13])=[O:12].S(S([O-])=O)([O-])(=O)=O.[Na+].[Na+]>Br.C(OCC)C>[Br:1][C:10]([CH2:9][CH2:8][O:7][CH2:6][CH2:5][O:4][CH3:3])([C:14]([OH:16])=[O:15])[C:11]([OH:13])=[O:12]
Reactant: BrBr
Reactant: COCCOCCC(C(=O)O)C(=O)O
Agent: Br
Agent: O=S([O-])S(=O)(=O)[O-]
Agent: [Na+]
Solvent: CCOCC
Product: COCCOCCC(Br)(C(=O)O)C(=O)O
Reaction time: 0.33 h
Yield: 78.9 %

Procedure:
HBr (4.1 M in acetic acid, two drops) and bromine (1.44 g, 9.01 mmol) was added to a stirred solution of [2-(2-methoxyethoxy)ethyl]malonic acid (Step 2) (1.75 g, 8.49 mmol) in diethyl ether. The reaction mixture was kept at ambient temperature for 20 minutes when most of the bromine colour had disappeared. Sodium pyrosulfite (5% in water) was added and the two phases were separated. The aqueous phase was extracted with diethyl ether two times. The organic extracts were combined and washed with water. The organic phase was dried over MgSO4 and concentrated in vacuo to give the title product as a colourless solid (1.91 g), 1H NMR (300 MHz, CDCl3) δ 6.91 (br s, 2H), 3.75 (t, 2H), 3.62 (m, 4H), 3.42 (s, 3H), 2.70 (t, 2H).
Reaction SMILES: [CH:1]1([N:7]=[C:8]=[N:9][CH:10]2[CH2:15][CH2:14][CH2:13][CH2:12][CH2:11]2)[CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1.C(N(CC)CC)C.N#N.C1C[O:28]CC1>>[CH:10]1([NH:9][C:8]([NH:7][CH:1]2[CH2:2][CH2:3][CH2:4][CH2:5][CH2:6]2)=[O:28])[CH2:15][CH2:14][CH2:13][CH2:12][CH2:11]1
Reactant: C1CCOC1
Reactant: C(=NC1CCCCC1)=NC1CCCCC1
Agent: N#N
Solvent: CCN(CC)CC
Product: O=C(NC1CCCCC1)NC1CCCCC1
Reaction time: 12 h

Procedure:
By mixing 0.1 g of polymer coupling agent from step 2, 0.15 g of 1,3-dicyclohexylcarbodiimide (DCC) in 2 g of THF, a 5 wt % polymer coupling agent solution is prepared. 20 μL of triethylamine is added into the mixture. The solution is then pumped into the capillary by N2 pressure. After 3 drops of the initiator solution come out of the other end of the capillary, both ends of the capillary are sealed with a silicon rubber septum. The reaction is allowed to proceed for 12.0 hour at room temperature. The capillary is then rinsed with acetone for 1.0 hour.
Reaction SMILES: [C:1]([CH:4]1[CH2:13][CH2:12][C:11]2[C:6](=[CH:7][CH:8]=[CH:9][CH:10]=2)[C:5]1=O)(=O)[CH3:2].Cl.[CH3:16][O:17][C:18]1[CH:23]=[CH:22][C:21]([NH:24][NH2:25])=[CH:20][CH:19]=1>C(O)C.O>[CH3:16][O:17][C:18]1[CH:23]=[CH:22][C:21]([N:24]2[C:5]3[C:6]4[CH:7]=[CH:8][CH:9]=[CH:10][C:11]=4[CH2:12][CH2:13][C:4]=3[C:1]([CH3:2])=[N:25]2)=[CH:20][CH:19]=1
Reactant: COc1ccc(NN)cc1
Reactant: CC(=O)C1CCc2ccccc2C1=O
Agent: Cl
Solvent: O
Solvent: CCO
Product: COc1ccc(-n2nc(C)c3c2-c2ccccc2CC3)cc1
Temperature: 80 °C

Procedure:
To a solution of 2-acetyl-1-tetralone (329 mg, 1.75 mmol) in ethanol (12 mL) was added 4-methoxyphenyl hydrazine hydrochloride. The stirred suspension was heated to 80° C. overnight. The reaction was cooled to room temperature and diluted with water (100 mL) and extracted with EtOAc (2×50 mL). The combined organic layers were washed with water, 10% NaOH, 10% HCl, brine and dried over Na2SO4. The solvent was removed under reduced pressure and the residue purified on silica gel using a 5% EtOAc to 25% EtOAc in hexane gradient (yield 396 mg). LC-MS (C19H18N2O calculated 290) m/z 291 (M+H).
Reaction SMILES: [NH2:1][NH2:2].[C:3]([NH:7][C:8]([C:10]1[S:14][C:13]2[CH2:15][C:16]([CH3:19])([CH3:18])[CH2:17][C:12]=2[C:11]=1[CH:20]=O)=[O:9])([CH3:6])([CH3:5])[CH3:4]>C1COCC1>[C:3]([NH:7][C:8]([C:10]1[S:14][C:13]2[CH2:15][C:16]([CH3:19])([CH3:18])[CH2:17][C:12]=2[C:11]=1[CH:20]=[N:1][NH2:2])=[O:9])([CH3:6])([CH3:5])[CH3:4]
Reactant: NN
Reactant: CC1(C)Cc2sc(C(=O)NC(C)(C)C)c(C=O)c2C1
Solvent: C1CCOC1
Product: CC1(C)Cc2sc(C(=O)NC(C)(C)C)c(C=NN)c2C1
Temperature: 20 °C
Reaction time: 3 h
Yield: 95 %

Procedure:
To a solution of 85% aqueous hydrazine (10 mL) in THF (180 mL) was added 282f (5.6 g, 20.0 mmol) in anhydrous THF (20 mL) over a period of 5 minutes. It was stirred at 20° C. for 3 h. The reaction mixture was concentrated under reduced pressure to afford 282g as black solid (6.0 g, yield: 95%, purity: 95%). MS-ESI: [M+H]+ 294.0
Reaction SMILES: [Br:1][C:2]1[CH:9]=[CH:8][C:5]([CH:6]=O)=[CH:4][CH:3]=1.[C@@H:10]1([NH2:20])[C:19]2[C:14](=[CH:15][CH:16]=[CH:17][CH:18]=2)[CH2:13][CH2:12][CH2:11]1>>[Br:1][C:2]1[CH:9]=[CH:8][C:5]([CH2:6][NH:20][C@@H:10]2[C:19]3[C:14](=[CH:15][CH:16]=[CH:17][CH:18]=3)[CH2:13][CH2:12][CH2:11]2)=[CH:4][CH:3]=1
Reactant: N[C@H]1CCCc2ccccc21
Reactant: O=Cc1ccc(Br)cc1
Product: Brc1ccc(CN[C@H]2CCCc3ccccc32)cc1

Procedure:
4-Bromobenzaldehyde and (1S)-1,2,3,4-tetrahydro-1-naphthalenylamine were processed as described in Example 1A to provide the title compound.
Reaction SMILES: [F:1][C:2]1[CH:7]=[C:6]([F:8])[C:5]([F:9])=[CH:4][C:3]=1[CH:10]1[CH2:15][CH:14]([C:16]([O:18][CH3:19])=[O:17])[CH2:13][CH2:12][NH:11]1.CCN(C(C)C)C(C)C.[C:29](Cl)(=[O:32])[O:30][CH3:31]>C(Cl)Cl>[F:1][C:2]1[CH:7]=[C:6]([F:8])[C:5]([F:9])=[CH:4][C:3]=1[CH:10]1[CH2:15][CH:14]([C:16]([O:18][CH3:19])=[O:17])[CH2:13][CH2:12][N:11]1[C:29]([O:30][CH3:31])=[O:32]
Reactant: COC(=O)C1CCNC(c2cc(F)c(F)cc2F)C1
Reactant: COC(=O)Cl
Solvent: ClCCl
Solvent: CCN(C(C)C)C(C)C
Product: COC(=O)C1CCN(C(=O)OC)C(c2cc(F)c(F)cc2F)C1
Temperature: 25 °C
Reaction time: 1 h
Yield: 109.8 %

Procedure:
Methyl 2-(2,4,5-trifluorophenyl)piperidine-4-carboxylate (2.232 g, 8.17 mmol) was dissolved in DCM (50 mL) and DIPEA (1.707 mL, 9.80 mmol), then methyl carbonochloridate (0.965 mL, 12.25 mmol) was added. The solution was stirred at room temperature for 1 h. The reaction mixture was washed with 0.1 M HCl and satd NaHCO3, passed through a phase separator and evaporated to yield crude dimethyl 2-(2,4,5-trifluorophenyl)piperidine-1,4-dicarboxylate (2.971 g, quant.) as a brown oil. MS m/z 332 (M+H)+
Reaction SMILES: [C:1]([N:11]1[CH2:31][CH2:30][C:14]2[N:15]([C:23]3[CH:28]=[CH:27][C:26]([F:29])=[CH:25][CH:24]=3)[C:16]3[CH:17]=[CH:18][C:19]([F:22])=[CH:20][C:21]=3[C:13]=2[CH2:12]1)(OCC1C=CC=CC=1)=O.[F:32][C:33]1[CH:38]=[CH:37][C:36]([CH:39]2[CH2:43][CH2:42]C(O)[O:40]2)=[CH:35][CH:34]=1>>[CH:37]1[C:36]([CH:39]([OH:40])[CH2:43][CH2:42][CH2:1][N:11]2[CH2:12][C:13]3[C:21]4[CH:20]=[C:19]([F:22])[CH:18]=[CH:17][C:16]=4[N:15]([C:23]4[CH:24]=[CH:25][C:26]([F:29])=[CH:27][CH:28]=4)[C:14]=3[CH2:30][CH2:31]2)=[CH:35][CH:34]=[C:33]([F:32])[CH:38]=1
Reactant: OC1CCC(c2ccc(F)cc2)O1
Reactant: O=C(OCc1ccccc1)N1CCc2c(c3cc(F)ccc3n2-c2ccc(F)cc2)C1
Product: OC(CCCN1CCc2c(c3cc(F)ccc3n2-c2ccc(F)cc2)C1)c1ccc(F)cc1

Procedure:
A process of claim 6 which further comprises hydrogenation of said 2-carbobenzoxy-8-fluoro-5-(p-fluorophenyl)-2,3,4,5-tetrahydro-1H-pyrido[4,3-b]indole over a noble metal catalyst in the presence of substantially one molar equivalent of 2-(p-fluorophenyl)-5-hydroxytetrahydrofuran, at 0°-75° C. in a reaction-inert solvent to form flutroline.
Reaction SMILES: O[CH:2]=[C:3]1[C:11]2[C:6](=[CH:7][C:8]([C:12]([C:14]3[CH:15]=[C:16]([NH:20][C:21]([C:23]4[N:24]([CH3:30])[N:25]=[C:26]([CH3:29])[C:27]=4[Cl:28])=[O:22])[CH:17]=[CH:18][CH:19]=3)=[O:13])=[CH:9][CH:10]=2)[NH:5][C:4]1=[O:31].[CH3:32][N:33]1[CH2:38][CH2:37][N:36]([C:39]2[CH:44]=[CH:43][C:42]([NH2:45])=[CH:41][CH:40]=2)[CH2:35][CH2:34]1.CC(C)=O>C1COCC1>[CH3:32][N:33]1[CH2:34][CH2:35][N:36]([C:39]2[CH:44]=[CH:43][C:42]([NH:45][CH:2]=[C:3]3[C:11]4[C:10](=[CH:9][C:8]([C:12]([C:14]5[CH:15]=[C:16]([NH:20][C:21]([C:23]6[N:24]([CH3:30])[N:25]=[C:26]([CH3:29])[C:27]=6[Cl:28])=[O:22])[CH:17]=[CH:18][CH:19]=5)=[O:13])=[CH:7][CH:6]=4)[NH:5][C:4]3=[O:31])=[CH:41][CH:40]=2)[CH2:37][CH2:38]1
Reactant: CN1CCN(c2ccc(N)cc2)CC1
Reactant: Cc1nn(C)c(C(=O)Nc2cccc(C(=O)c3ccc4c(c3)NC(=O)C4=CO)c2)c1Cl
Solvent: CC(C)=O
Solvent: C1CCOC1
Product: Cc1nn(C)c(C(=O)Nc2cccc(C(=O)c3ccc4c(c3)NC(=O)C4=CNc3ccc(N4CCN(C)CC4)cc3)c2)c1Cl
Temperature: 65 °C
Reaction time: 24 h

Procedure:
A small screw cap test tube was charged with 4-Chloro-2,5-dimethyl-2H-pyrazole-3-carboxylic acid [3-(3-hydroxymethylene-2-oxo-2,3-dihydro-1H-indole-6-carbonyl)-phenyl]-amide (prepared below, 70 mg, 0.160 mmol) and THF (1.5 mL). To the resulting solution was added 4-(4-methyl-piperazin-1-yl)-phenylamine (30.6 mg, 0.160 mmol), and the mixture was stirred for 24 h at 65° C. Subsequently, the reaction mixture was cooled to room temperature and concentrated in vacuo. The crude residue was dissolved in EtOAc. The resulting solution was diluted with Hexanes to initiate the precipitation of the product. The solid precipitate that formed was filtered then washed with ˜3 mL of acetone yielding 58% (56.7 mg, 0.093 mmol) of the title compound.
Reaction SMILES: BrC1C=CC=C2C=1C(C1C(O)=CC3OCOC=3C=1)[C:5](=[O:16])N2CCCCC.[CH2:27]([O:29][C:30](=[O:53])[CH2:31][N:32]1[C:40]2[C:35](=[CH:36][C:37]([Cl:41])=[CH:38][CH:39]=2)[CH:34]([C:42]2[C:43]([OH:51])=[CH:44][C:45]3[O:49][CH2:48][CH2:47][C:46]=3[CH:50]=2)[C:33]1=[O:52])[CH3:28]>>[CH2:27]([O:29][C:30](=[O:53])[CH2:31][N:32]1[C:40]2[C:35](=[CH:36][C:37]([Cl:41])=[CH:38][CH:39]=2)[C:34]([C:42]2[C:43]([OH:51])=[CH:44][C:45]3[O:49][CH2:48][CH2:47][C:46]=3[CH:50]=2)([CH2:5][OH:16])[C:33]1=[O:52])[CH3:28]
Reactant: CCCCCN1C(=O)C(c2cc3c(cc2O)OCO3)c2c(Br)cccc21
Reactant: CCOC(=O)CN1C(=O)C(c2cc3c(cc2O)OCC3)c2cc(Cl)ccc21
Product: CCOC(=O)CN1C(=O)C(CO)(c2cc3c(cc2O)OCC3)c2cc(Cl)ccc21

Procedure:
Following the procedure as described in PREPARATION 1E, and making non-critical variations to replace 4-bromo-3-(6-hydroxy-1,3-benzodioxol-5-yl)-1-pentyl-1,3-dihydro-2H-indol-2-one with ethyl[5-chloro-3-(6-hydroxy-2,3-dihydro-1-benzofuran-5-yl)-2-oxo-2,3-dihydro-1H-indol-1-yl]acetate, the title compound was obtained (99%): MS (ES+) m/z 418.7 (M+1).
Reaction SMILES: [Br:1][C:2]1[CH:18]=[CH:17][C:5]([O:6][C:7]2[CH:8]=[C:9]([CH2:13][C:14]([OH:16])=[O:15])[CH:10]=[CH:11][CH:12]=2)=[C:4]([CH:19]=[O:20])[CH:3]=1.S(Cl)(Cl)=O.[OH-].[Na+].[CH3:27]O>>[CH3:27][O:15][C:14](=[O:16])[CH2:13][C:9]1[CH:10]=[CH:11][CH:12]=[C:7]([O:6][C:5]2[CH:17]=[CH:18][C:2]([Br:1])=[CH:3][C:4]=2[CH:19]=[O:20])[CH:8]=1
Reactant: O=Cc1cc(Br)ccc1Oc1cccc(CC(=O)O)c1
Reactant: CO
Agent: [Na+]
Agent: [OH-]
Solvent: O=S(Cl)Cl
Product: COC(=O)Cc1cccc(Oc2ccc(Br)cc2C=O)c1
Temperature: 65 °C
Reaction time: 8 h

Procedure:
To [3-(4-bromo-2-formyl-phenoxy)-phenyl]-acetic acid (1 g, 2.98 mmol) in MeOH (10 mL) was added thionyl chloride (0.43 mL, 5.97 mmol), and the reaction was heated to 65° C. for 2 hours, and then stirred overnight at room temperature. The mixture was neutralized with 1N aqueous NaOH and extracted three times with EtOAc. The combined organic layer was washed with H2O, dried, and concentrated, and the residue was purified by silica gel chromatography (20-40% EtOAc in hexanes) to give the title compound, as well as the corresponding acetal.
Reaction SMILES: [N:1]1[C:5]2[CH:6]=[CH:7][CH:8]=[CH:9][C:4]=2[NH:3][CH:2]=1.[H-].[Na+].Cl[CH2:13][C:14]1[S:15][CH:16]=[CH:17][CH:18]=1.O>CN(C)C=O>[S:15]1[CH:16]=[CH:17][CH:18]=[C:14]1[CH2:13][N:1]1[C:5]2[CH:6]=[CH:7][CH:8]=[CH:9][C:4]=2[N:3]=[CH:2]1
Reactant: c1ccc2[nH]cnc2c1
Reactant: ClCc1cccs1
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: O
Product: c1csc(Cn2cnc3ccccc32)c1
Reaction time: 0.5 h

Procedure:
To 11.81 g of benzimidazole in 50 ml of dimethylformamide was added 4.8 g of 50% sodium hydride in oil over 30 minutes. After stirring 30 minutes, 13.25 g of 2-chloromethylthiophene was added over a period of 30 minutes, and the reaction mixture stirred at room temperature overnight. The mixture was poured into water and the pH adjusted to 1.5. After extracting with ether, the pH was raised to 11 and precipitated product was filtered and dried, 19.9 g.
Reaction SMILES: [NH2:1][C:2]1[CH:3]=[N:4][C:5]2[C:10]([C:11]=1[NH2:12])=[CH:9][CH:8]=[CH:7][CH:6]=2.[F:13][C:14]([F:19])([F:18])[C:15](O)=O>>[F:13][C:14]([F:19])([F:18])[C:15]1[NH:12][C:11]2[C:10]3[CH:9]=[CH:8][CH:7]=[CH:6][C:5]=3[N:4]=[CH:3][C:2]=2[N:1]=1
Reactant: Nc1cnc2ccccc2c1N
Reactant: O=C(O)C(F)(F)F
Product: FC(F)(F)c1nc2cnc3ccccc3c2[nH]1

Procedure:
Using the method of Example 144, 3,4-diaminoquinoline (from Example 39) was reacted with trifluoroacetic acid to provide 2-trifluoromethyl-1H-imidazo[4,5-c]quinoline, m.p. 252°-254° C. Analysis: Calculated for C11H6F3N3 : %C, 55.7; %H, 2.5; %N, 17.7; Found: %C, 55.3; %H, 2.3; %N, 18.2.
Reaction SMILES: [C:1]([O:5][C:6](=[O:36])[NH:7][C:8]1([C:12]2[CH:17]=[CH:16][C:15](C3C(=O)C4C(=CC=C(F)C=4)OC=3C3C=CC=CC=3)=[CH:14][CH:13]=2)[CH2:11][CH2:10][CH2:9]1)([CH3:4])([CH3:3])[CH3:2].[OH:37][CH2:38][CH2:39][N:40]1[CH:45]=[CH:44][C:43]2[C:46](=[O:57])[C:47](I)=[C:48]([C:50]3[CH:55]=[CH:54][CH:53]=[CH:52][CH:51]=3)[O:49][C:42]=2[C:41]1=[O:58]>>[C:1]([O:5][C:6](=[O:36])[NH:7][C:8]1([C:12]2[CH:13]=[CH:14][C:15]([C:47]3[C:46](=[O:57])[C:43]4[CH:44]=[CH:45][N:40]([CH2:39][CH2:38][OH:37])[C:41](=[O:58])[C:42]=4[O:49][C:48]=3[C:50]3[CH:55]=[CH:54][CH:53]=[CH:52][CH:51]=3)=[CH:16][CH:17]=2)[CH2:9][CH2:10][CH2:11]1)([CH3:4])([CH3:2])[CH3:3]
Reactant: O=c1c(I)c(-c2ccccc2)oc2c(=O)n(CCO)ccc12
Reactant: CC(C)(C)OC(=O)NC1(c2ccc(-c3c(-c4ccccc4)oc4ccc(F)cc4c3=O)cc2)CCC1
Product: CC(C)(C)OC(=O)NC1(c2ccc(-c3c(-c4ccccc4)oc4c(=O)n(CCO)ccc4c3=O)cc2)CCC1
Yield: 96 %

Procedure:
Following the procedure used to prepare {1-[4-(6-fluoro-4-oxo-2-phenyl-4H-chromen-3-yl)-phenyl]-cyclobutyl}-carbamic acid tert-butyl ester, 7-(2-hydroxy-ethyl)-3-iodo-2-phenyl-7H-pyrano[2,3-c]pyridine-4,8-dione was reacted to give the title compound (56 mg, 96%) as a colourless solid. LCMS (Method A): RT=4.41 min, [M+H]+=529.
Reaction SMILES: [OH:1][C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[C:8]1[N:12]=[C:11]([C:13]2[CH:18]=[CH:17][CH:16]=[CH:15][C:14]=2[OH:19])[N:10]([CH2:20][C:21](OCC)=[O:22])[N:9]=1.[NH:26]1[CH2:31][CH2:30][O:29][CH2:28][CH2:27]1>>[OH:1][C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[C:8]1[N:12]=[C:11]([C:13]2[CH:18]=[CH:17][CH:16]=[CH:15][C:14]=2[OH:19])[N:10]([CH2:20][C:21]([N:26]2[CH2:31][CH2:30][O:29][CH2:28][CH2:27]2)=[O:22])[N:9]=1
Reactant: CCOC(=O)Cn1nc(-c2ccccc2O)nc1-c1ccccc1O
Reactant: C1COCCN1
Product: O=C(Cn1nc(-c2ccccc2O)nc1-c1ccccc1O)N1CCOCC1

Procedure:
2.0 g of ethyl [3,5-bis(2-hydroxyphenyl)-[1,2,4]triazol-1-yl]acetate (Example 2) and 8 ml of morpholine are boiled under reflux for 1 h. The mixture is cooled, poured onto water and extracted with ethyl acetate. The combined organic phases are dried over sodium sulfate and concentrated on a rotary evaporator. The residue is crystallized from ethyl acetate/-hexane. After drying, 2-[3,5-bis(2-hydroxyphenyl)-[1,2,4]triazol-1-yl]-1-morpholin-4-ylethanone remains as colorless crystals of m.p. 149-151° C.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]2[C:8](=[CH:9][CH:10]=1)[NH:7][CH:6]=[C:5]2[CH2:11][CH2:12][NH:13][C:14](=[O:22])[C:15]1[CH:20]=[CH:19][CH:18]=[C:17](I)[CH:16]=1.[Cl:23][C:24]1[CH:25]=[C:26](B(O)O)[CH:27]=[CH:28][CH:29]=1.C(=O)([O-])[O-].[Na+].[Na+]>C(COC)OC.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>[Cl:23][C:24]1[CH:29]=[C:28]([C:17]2[CH:18]=[CH:19][CH:20]=[C:15]([C:14]([NH:13][CH2:12][CH2:11][C:5]3[C:4]4[C:8](=[CH:9][CH:10]=[C:2]([Cl:1])[CH:3]=4)[NH:7][CH:6]=3)=[O:22])[CH:16]=2)[CH:27]=[CH:26][CH:25]=1
Reactant: O=C(NCCc1c[nH]c2ccc(Cl)cc12)c1cccc(I)c1
Reactant: OB(O)c1cccc(Cl)c1
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: O
Solvent: COCCOC
Product: O=C(NCCc1c[nH]c2ccc(Cl)cc12)c1cccc(-c2cccc(Cl)c2)c1
Yield: 66.6 %

Procedure:
3′-chloro-N-(2-(5-chloro-1H-indol-3-yl)ethyl)biphenyl-3-carboxamide was prepared according to method B with N-(2-(5-chloro-1H-indol-3-yl)ethyl)-3-iodobenzamide (0.075 g; 0.176 mmol), 3-chlorophenylboronic acid (0.029 g; 0.180 mmol), tetrakis(triphenylphosphine)palladium (0.010 g; 0.009 mmol), sodium carbonate (0.037 g; 0.353 mmol), in dimethoxyethane (3 mL) and water (1 mL), irradiated in a microwave oven at 130° C. for 15 minutes. Flash chromatography on silica gel (eluent 10 to 80% ethyl acetate in heptane) furnished 0.048 g (66%) of 3′-chloro-N-(2-(5-chloro-1H-indol-3-yl)ethyl)biphenyl-3-carboxamide as a white solid.
Reaction SMILES: [F:1][CH:2]([F:29])[O:3][C:4]1[C:5]([O:23][CH2:24][C:25]([CH3:28])([CH3:27])[CH3:26])=[C:6](/[CH:10]=[CH:11]/[C:12]2[N:13]=[C:14]3[N:18]([C:19]=2[C:20](O)=[O:21])[CH:17]=[CH:16][S:15]3)[CH:7]=[CH:8][CH:9]=1.[CH:30]1([C:34]2[N:35]=[C:36]([NH2:39])[S:37][CH:38]=2)[CH2:33][CH2:32][CH2:31]1.CCN=C=NCCCN(C)C.Cl>CN(C1C=CN=CC=1)C.C1COCC1.CN(C=O)C>[CH3:27][C:25]([CH3:26])([CH3:28])[CH2:24][O:23][C:5]1[C:4]([O:3][CH:2]([F:1])[F:29])=[CH:9][CH:8]=[CH:7][C:6]=1/[CH:10]=[CH:11]/[C:12]1[N:13]=[C:14]2[N:18]([C:19]=1[C:20]([NH:39][C:36]1[S:37][CH:38]=[C:34]([CH:30]3[CH2:33][CH2:32][CH2:31]3)[N:35]=1)=[O:21])[CH:17]=[CH:16][S:15]2
Reactant: Nc1nc(C2CCC2)cs1
Reactant: CC(C)(C)COc1c(/C=C/c2nc3sccn3c2C(=O)O)cccc1OC(F)F
Agent: CCN=C=NCCCN(C)C
Agent: CN(C)c1ccncc1
Agent: Cl
Solvent: CN(C)C=O
Solvent: C1CCOC1
Product: CC(C)(C)COc1c(/C=C/c2nc3sccn3c2C(=O)Nc2nc(C3CCC3)cs2)cccc1OC(F)F

Procedure:
The title compound was prepared according to the general procedure (Method B) by coupling Intermediate 7A (100 mg, 0.236 mmol) with 4-(cyclobutyl)-1,3-thiazol-2-amine (40 mg, 0.260 mmol) in the presence of EDCI hydrochloride (90 mg, 0.472 mmol), DMAP (26 mg, 0.236 mmol) in a mixture of THF and DMF (1:1, 4 mL) to give 50 mg of the product as an off-white solid; 1H NMR (300 MHz, DMSO-d6) δ 1.07 (s, 9H), 1.84-1.90 (m, 2H), 1.95-2.05 (m, 1H), 2.15-2.30 (m, 4H), 3.58 (s, 2H), 6.73 (s, 1H), 7.18 (t, J=75.0 Hz, 1H), 7.20-7.30 (m, 2H), 7.38-7.44 (m, 1H), 7.66-7.72 (m, 1H), 7.83 (d, J=16.2 Hz, 1H), 8.10-8.18 (m, 1H), 8.62-8.68 (m, 1H), 12.87 (br s, 1H); ESI-MS (m/z) 559.22 (MH)+.
Reaction SMILES: [Br:1][C:2]1[CH:3]=[C:4]2[C:8](=[CH:9][CH:10]=1)[C:7](=[O:11])[CH2:6][CH2:5]2.CS(O)(=O)=O.[N-:17]=[N+]=[N-].[Na+]>C(Cl)Cl>[Br:1][C:2]1[CH:3]=[C:4]2[C:8](=[CH:9][CH:10]=1)[C:7](=[O:11])[NH:17][CH2:6][CH2:5]2
Reactant: O=C1CCc2cc(Br)ccc21
Reactant: [N-]=[N+]=[N-]
Agent: CS(=O)(=O)O
Agent: [Na+]
Solvent: ClCCl
Product: O=C1NCCc2cc(Br)ccc21
Temperature: 25 °C
Reaction time: 8 h
Yield: 42.9 %

Procedure:
5-bromo-2,3-dihydro-1H-inden-1-one (1K1) (9.48 mmol, 2 g) was dissolved in DCM (35 ml) and methane sulfonic acid (95 mmol, 9.11 g) was added. The reaction mixture was cooled to 0° C. before portionwise addition of sodium azide (28.4 mmol, 1.85 g). Once addition was complete the mixture was allowed to warm to room temperature and stirred overnight. The reaction mixture was partitioned between DCM and NaOH (2M, 50 ml). The phases were separated and the aqueous layer was extracted twice more with DCM. The combined organics were washed with water and brine, dried (MgSO4) and evaporated to dryness before purification on silica eluting with 75-100% EtOAc/heptane to give 6-bromo-3,4-dihydroisoquinolin-1(2H)-one (1K2) 919 mg (42%) 1H NMR (400 MHz, CDCl3) δ 7.93 (d, 1H) 7.49 (d, 1H) 7.40 (s, 1H) 6.36 (bs, 1H) 3.58 (t, 2H) 2.99 (t, 2H).
Reaction SMILES: [N+](C1C=CC(O[C:11](=[O:39])[NH:12][C:13]2[CH:18]=[C:17]([Cl:19])[CH:16]=[CH:15][C:14]=2[O:20][CH2:21][C:22]([N:24]2[CH2:29][CH2:28][N:27]([CH2:30][C:31]3[CH:36]=[CH:35][C:34]([F:37])=[CH:33][CH:32]=3)[CH2:26][C@H:25]2[CH3:38])=[O:23])=CC=1)([O-])=O.Cl.[CH3:41][O:42][C:43](=[O:47])[CH2:44][CH2:45][NH2:46].C(N(CC)CC)C>CO>[CH3:41][O:42][C:43](=[O:47])[CH2:44][CH2:45][NH:46][C:11]([NH:12][C:13]1[CH:18]=[C:17]([Cl:19])[CH:16]=[CH:15][C:14]=1[O:20][CH2:21][C:22]([N:24]1[CH2:29][CH2:28][N:27]([CH2:30][C:31]2[CH:36]=[CH:35][C:34]([F:37])=[CH:33][CH:32]=2)[CH2:26][C@H:25]1[CH3:38])=[O:23])=[O:39]
Reactant: COC(=O)CCN
Reactant: C[C@@H]1CN(Cc2ccc(F)cc2)CCN1C(=O)COc1ccc(Cl)cc1NC(=O)Oc1ccc([N+](=O)[O-])cc1
Agent: Cl
Solvent: CO
Solvent: CCN(CC)CC
Product: COC(=O)CCNC(=O)Nc1cc(Cl)ccc1OCC(=O)N1CCN(Cc2ccc(F)cc2)C[C@H]1C
Temperature: 25 °C
Reaction time: 8 h
Yield: 80 %

Procedure:
To a solution of (5-chloro-2-{2-[4-(4-fluoro-benzyl)-(2R)-2-methyl-piperazin-1-yl]-2-oxo-ethoxy}-phenyl)-carbamic acid 4-nitro-phenyl ester (0.10 g, 0.18 mmol) in methanol was added β-alanine methyl ester hydrochloride (0.038 g, 0.27 mmol) and triethylamine (0.038 mL, 0.27 mmol). The reaction was stirred at ambient temperature overnight. The reaction was concentrated and purified via chromatography on silica gel to give the title compound (0.075 g).
Reaction SMILES: [CH3:1][O:2][C:3](=[O:12])[C@H:4]([C:6]1[CH:11]=[CH:10][CH:9]=[CH:8][CH:7]=1)[NH2:5].[OH:13][CH:14]1[CH2:19][CH2:18][C:17](=O)[CH2:16][CH2:15]1.C(O[BH-](OC(=O)C)OC(=O)C)(=O)C.[Na+].O>ClCCCl>[OH:13][CH:14]1[CH2:19][CH2:18][CH:17]([NH:5][C@@H:4]([C:6]2[CH:11]=[CH:10][CH:9]=[CH:8][CH:7]=2)[C:3]([O:2][CH3:1])=[O:12])[CH2:16][CH2:15]1
Reactant: O=C1CCC(O)CC1
Reactant: COC(=O)[C@@H](N)c1ccccc1
Agent: CC(=O)O[BH-](OC(C)=O)OC(C)=O
Agent: [Na+]
Solvent: O
Solvent: ClCCCl
Product: COC(=O)[C@@H](NC1CCC(O)CC1)c1ccccc1
Temperature: 25 °C
Reaction time: 23 h
Yield: 35 %

Procedure:
(S)-(+)-2-Phenylglycine methyl ester (commercially available from Sigma-Aldrich, Milwaukee, Wis., 433 g, 2.146 mol) was added to a solution of 4-hydroxycyclohexanone (245 g, 2.146 mol) in DCE (8.5 L). Sodium triacetoxyborohydride was added (910 g, 4.292 mol), and the mixture was stirred at room temperature under nitrogen for 23 hours. Water (3 L) was added to quench the reaction, and the organic layer was separated. The aqueous phase was extracted with DCM (4 L×2) and the organic layers were combined, dried, filtered and concentrated. The residue was purified by column chromatography (gradient elution with 100% DCM to DCM/MeOH=25:1) to afford (S)-methyl 2-((4-hydroxycyclohexyl)amino)-2-phenylacetate (197 g, 35%) (mixture of cis and trans). m/z (ESI) 264 (M+H)+.
Reaction SMILES: [C:1]([O:4][CH:5]1[C:9]2=[N:10][CH:11]=[C:12]([NH2:28])[C:13]([N:14]3[CH2:19][CH2:18][CH2:17][C@H:16]([NH:20][C:21]([O:23][C:24]([CH3:27])([CH3:26])[CH3:25])=[O:22])[CH2:15]3)=[C:8]2[CH2:7][CH2:6]1)(=[O:3])[CH3:2].[F:29][C:30]1[CH:35]=[C:34]([S:36]([CH3:38])=[O:37])[CH:33]=[C:32]([F:39])[C:31]=1[C:40]1[N:45]=[C:44]([C:46](O)=[O:47])[CH:43]=[CH:42][C:41]=1[F:49].CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.CCN(C(C)C)C(C)C>CN(C=O)C>[C:1]([O:4][CH:5]1[C:9]2=[N:10][CH:11]=[C:12]([NH:28][C:46]([C:44]3[CH:43]=[CH:42][C:41]([F:49])=[C:40]([C:31]4[C:32]([F:39])=[CH:33][C:34]([S:36]([CH3:38])=[O:37])=[CH:35][C:30]=4[F:29])[N:45]=3)=[O:47])[C:13]([N:14]3[CH2:19][CH2:18][CH2:17][C@H:16]([NH:20][C:21]([O:23][C:24]([CH3:27])([CH3:26])[CH3:25])=[O:22])[CH2:15]3)=[C:8]2[CH2:7][CH2:6]1)(=[O:3])[CH3:2]
Reactant: CS(=O)c1cc(F)c(-c2nc(C(=O)O)ccc2F)c(F)c1
Reactant: CC(=O)OC1CCc2c1ncc(N)c2N1CCC[C@H](NC(=O)OC(C)(C)C)C1
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: CC(=O)OC1CCc2c1ncc(NC(=O)c1ccc(F)c(-c3c(F)cc(S(C)=O)cc3F)n1)c2N1CCC[C@H](NC(=O)OC(C)(C)C)C1
Temperature: 25 °C
Reaction time: 16 h
Yield: 14.1 %

Procedure:
A mixture of 3-amino-4-{(3S)-3-[(tert-butoxycarbonyl)amino]piperidin-1-yl}-6,7-dihydro-5H-cyclopenta[b]pyridin-7-yl acetate (12.0 mg, 0.031 mmol), 6-[2,6-difluoro-4-(methylsulfinyl)phenyl]-5-fluoropyridine-2-carboxylic acid (11.6 mg, 0.037 mmol), HATU (29.2 mg, 0.077 mmol) in DMF (0.07 mL) and DIPEA (11.9 mg, 0.092 mmol) was stirred at room temperature for 16 h. The reaction mixture was filtered, concentrated under reduced pressure and purified by preparative LC-MS (XBridge™ preparative C18 5 μm OBD™ column, 30×10 mm, 60 mL/min., eluting with a gradient of MeCN and water with 0.1% NH4OH) to give the sub-title compound as a colorless gum (3.0 mg, 14%). LCMS calc. for C33H37F3N5O6S (M+H)+: m/z=688.2. Found: 688.2.