Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [CH3:1][N:2]([CH3:26])[CH2:3][CH2:4][O:5][C:6]1[CH:11]=[C:10]([S:12]([CH3:15])(=[O:14])=[O:13])[CH:9]=[CH:8][C:7]=1[N:16]1[C:20]2=[N:21][CH:22]=[N:23][C:24](O)=[C:19]2[CH:18]=[N:17]1.O=P(Cl)(Cl)[Cl:29].CN(C)C1C=CC=CC=1>>[Cl:29][C:24]1[N:23]=[CH:22][N:21]=[C:20]2[N:16]([C:7]3[CH:8]=[CH:9][C:10]([S:12]([CH3:15])(=[O:14])=[O:13])=[CH:11][C:6]=3[O:5][CH2:4][CH2:3][N:2]([CH3:26])[CH3:1])[N:17]=[CH:18][C:19]=12
Reactant: CN(C)CCOc1cc(S(C)(=O)=O)ccc1-n1ncc2c(O)ncnc21
Reactant: O=P(Cl)(Cl)Cl
Solvent: CN(C)c1ccccc1
Product: CN(C)CCOc1cc(S(C)(=O)=O)ccc1-n1ncc2c(Cl)ncnc21
Temperature: 100 °C
Reaction time: 1 h

Procedure:
In a reaction vial was placed a stir bar, 1-[2-(2-dimethylamino-ethoxy)-4-methanesulfonyl-phenyl]-1H-pyrazolo[3,4-d]pyrimidin-4-ol (50 mg), POCl3 (0.5 mL) and N,N-dimethylaniline (15 μl). The reaction mixture was stirred at 100° C. for 1 hour. Upon cooling the reaction mixture to the room temperature, a white precipitate formed. The mixture was left sealed over the weekend at room temperature. After concentrated under the vacuum, the residue was washed with Et2O and filtered to give {2-[2-(4-chloro-pyrazolo[3,4-d]pyrimidin-1-yl)-5-methanesulfonyl-phenoxy]-ethyl}-dimethyl-amine as a white solid. Exact mass calculated for C16H18ClN5O3S 395.08, found 396 (MH+).
Reaction SMILES: Cl[C:2]1[N:10]=[C:9]([CH:11]([OH:15])[CH2:12][CH2:13][CH3:14])[N:8]=[C:7]2[C:3]=1[N:4]=[CH:5][N:6]2[CH3:16].O.[NH3:18]>O1CCOCC1>[NH2:18][C:2]1[N:10]=[C:9]([CH:11]([OH:15])[CH2:12][CH2:13][CH3:14])[N:8]=[C:7]2[C:3]=1[N:4]=[CH:5][N:6]2[CH3:16]
Reactant: CCCC(O)c1nc(Cl)c2ncn(C)c2n1
Reactant: N
Solvent: O
Solvent: C1COCCO1
Product: CCCC(O)c1nc(N)c2ncn(C)c2n1
Temperature: 70 °C
Reaction time: 8 h

Procedure:
To the solution of 1-(6-chloro-9-methyl-9H-purin-2-yl)butan-1-ol (1.8 g, 7.47 mmol) in dioxane (10 ml) was added 30% w/w water solution of ammonia (20 ml). The reaction mixture was stirred overnight in an autoclave at 70° C. The solution was evaporated at atmospheric pressure at 50° C. and then under reduced pressure. The residue was purified by flash chromatography (DCM/MeOH: 95/5).
Reaction SMILES: [N:1]([CH:4]([CH2:9][C:10]([CH3:12])=[CH2:11])[C:5]([O:7][CH3:8])=[O:6])=[C:2]=[O:3].[N:13]1C=CC=CC=1.Cl.NO.C(OC)(OC)OC>C1COCC1.CO>[CH3:8][O:7][C:5]([CH:4]([NH:1][C:2]([NH2:13])=[O:3])[CH2:9][C:10]([CH3:12])=[CH2:11])=[O:6]
Reactant: C=C(C)CC(N=C=O)C(=O)OC
Reactant: c1ccncc1
Agent: Cl
Agent: NO
Solvent: CO
Solvent: COC(OC)OC
Solvent: C1CCOC1
Product: C=C(C)CC(NC(N)=O)C(=O)OC
Temperature: 25 °C
Reaction time: 2 h

Procedure:
A solution of 0.1 mol of p-aminobenzaldehyde ethylene glycol acetal in 100 mL of anhydrous THF is added dropwise over 10 minutes to a solution of 0.1 mol of methyl 2-isocyanato-4-methyl-4-pentenoate and 0.35 mol pyridine in 100 mL THF at room temperature under N2. The reaction mixture is stirred at room temperature for 2 hours. After 2 hours the solvent is removed by rotary evaporator. A solution of 0.11 mmol hydroxylamine hydrochloride and 0.1 mol trimethyl orthoformate in CH3OH is added, and the reaction mixture is heated to reflux under N2 for 1 hour. The reaction mixture is reduced to about 1/4 volume by rotary evaporator, and water is added. The product, N-[4-(hydroxyiminomethyl)phenyl]-N'-[1-(1-methoxycarbonyl-3-methyl-3-butenyl]urea, is isolated by filtration and dried in vacuo.
Reaction SMILES: [CH3:1][O:2][C:3]([C:5]1[S:6][CH:7]=[C:8]([C:14]2[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=2)[C:9]=1[S:10]([NH2:13])(=[O:12])=[O:11])=[O:4].[CH3:20][O:21][C:22]1[CH:27]=[C:26]([O:28][CH3:29])[N:25]=[C:24]([N:30](C2C=CC=CC=2)[C:31](=O)[O-:32])[N:23]=1.N12CCCN=C1CCCCC2.CS(O)(=O)=O>O.C(#N)C>[CH3:1][O:2][C:3]([C:5]1[S:6][CH:7]=[C:8]([C:14]2[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=2)[C:9]=1[S:10]([NH:13][C:31]([NH:30][C:24]1[N:23]=[C:22]([O:21][CH3:20])[CH:27]=[C:26]([O:28][CH3:29])[N:25]=1)=[O:32])(=[O:12])=[O:11])=[O:4]
Reactant: COC(=O)c1scc(-c2ccccc2)c1S(N)(=O)=O
Reactant: COc1cc(OC)nc(N(C(=O)[O-])c2ccccc2)n1
Agent: CS(=O)(=O)O
Solvent: CC#N
Solvent: O
Solvent: C1CCC2=NCCCN2CC1
Product: COC(=O)c1scc(-c2ccccc2)c1S(=O)(=O)NC(=O)Nc1nc(OC)cc(OC)n1
Yield: 88.8 %

Procedure:
2.4 g (0.008 mol) of 2-methoxycarbonyl-4-phenylthiophen-3-ylsulfonamide, 2.2 g of N-(4,6-dimethoxypyrimidin-2-yl)phenylcarbamate, 1.2 g of 1,8-diazabicyclo[5.4.0]undec-7-ene and 30 ml of acetonitrile are stirred for 16 hours at room temperature. The reaction mixture is then poured into a mixture of ice and water and acidified with methanesulfonic acid. The resultant precipitate is filtered, washed with water and dried, affording 3.4 g (95%) of N-(2-methoxycarbonyl-4-phenylthiophen-3-ylsulfonyl)-N'-(4,6-dimethoxypyrimidin-2-yl)urea with a melting point of 225°-227° C.
Reaction SMILES: [NH2:1][C:2]1[CH:3]=[N:4][CH:5]=[CH:6][CH:7]=1.[Cl:8][C:9]1[C:14]([O:15][CH3:16])=[CH:13][C:12]([O:17][CH3:18])=[C:11]([Cl:19])[C:10]=1[C:20]1[C:29]2[N:28]=[C:27]([CH2:30][N:31]3[CH2:36][CH2:35][N:34]([CH2:37][CH3:38])[CH2:33][CH2:32]3)[CH:26]=[N:25][C:24]=2[C:23]([C:39](O)=[O:40])=[CH:22][CH:21]=1>C(Cl)Cl.CO>[N:4]1[CH:5]=[CH:6][CH:7]=[C:2]([NH:1][C:39]([C:23]2[C:24]3[N:25]=[CH:26][C:27]([CH2:30][N:31]4[CH2:36][CH2:35][N:34]([CH2:37][CH3:38])[CH2:33][CH2:32]4)=[N:28][C:29]=3[C:20]([C:10]3[C:9]([Cl:8])=[C:14]([O:15][CH3:16])[CH:13]=[C:12]([O:17][CH3:18])[C:11]=3[Cl:19])=[CH:21][CH:22]=2)=[O:40])[CH:3]=1
Reactant: Nc1cccnc1
Reactant: CCN1CCN(Cc2cnc3c(C(=O)O)ccc(-c4c(Cl)c(OC)cc(OC)c4Cl)c3n2)CC1
Solvent: CO
Solvent: ClCCl
Product: CCN1CCN(Cc2cnc3c(C(=O)Nc4cccnc4)ccc(-c4c(Cl)c(OC)cc(OC)c4Cl)c3n2)CC1
Temperature: 25 °C
Reaction time: 48 h

Procedure:
The title compound was prepared in analogy to the procedure described in Step 14.1 but using 3-aminopyridine, 8-(2,6-dichloro-3,5-dimethoxy-phenyl)-2-(4-ethyl-piperazin-1-ylmethyl)-quinoxaline-5-carboxylic acid (Step 83.1) and stirring the reaction mixture for 2 days at rt. Title compound: ESI-MS: 581.0/583.2 [M+H]+; tR=3.04 min (System 1); TLC: Rf=0.33 (DCM/MeOH, 9:1).
Reaction SMILES: [N:1]1[CH:6]=[CH:5][CH:4]=[N:3][C:2]=1[N:7]1[CH2:12][CH2:11][NH:10][CH2:9][CH2:8]1.[Br:13]Br>Cl>[Br:13][C:5]1[CH:6]=[N:1][C:2]([N:7]2[CH2:12][CH2:11][NH:10][CH2:9][CH2:8]2)=[N:3][CH:4]=1
Reactant: BrBr
Reactant: c1cnc(N2CCNCC2)nc1
Agent: Cl
Product: Brc1cnc(N2CCNCC2)nc1
Temperature: 0 °C
Reaction time: 0.5 h
Yield: 59.6 %

Procedure:
This example serves to illustrate procedure B of Scheme 2. To an ice-cooled solution of 1-(2-pyrimidinyl)piperazine (16.4 g, 0.1 mole) in 1N HCl (100 mL) was added dropwise bromine (15.98 g, 0.1 mole). After stirring at 0° for 0.5 hr, the mixture was heated to 100° until dissipation of the red color had occurred. The mixture is filtered, cooled, made alkaline with 50% NaOH and extracted with ether. The dried extract (MgSO4) was concentrated in vacuo to provide 14.5 g (62%) of product, m.p. 73°-75°.
Reaction SMILES: [CH2:1]([C:6]1[CH2:11][CH2:10][CH:9]([C@H:12]2[CH2:17][CH2:16][C@H:15]([CH2:18][CH2:19][CH2:20][CH2:21][CH3:22])[CH2:14][CH2:13]2)[CH2:8][CH:7]=1)[CH2:2][CH2:3][CH2:4][CH3:5].C([C@H]1CC[C@H](C2CCC(=[O:40])CC2)CC1)CCCC>>[CH2:1]([C:6]1([OH:40])[CH2:11][CH2:10][CH:9]([C@H:12]2[CH2:17][CH2:16][C@H:15]([CH2:18][CH2:19][CH2:20][CH2:21][CH3:22])[CH2:14][CH2:13]2)[CH2:8][CH2:7]1)[CH2:2][CH2:3][CH2:4][CH3:5]
Reactant: CCCCC[C@H]1CC[C@H](C2CCC(=O)CC2)CC1
Reactant: CCCCCC1=CCC([C@H]2CC[C@H](CCCCC)CC2)CC1
Product: CCCCCC1(O)CCC([C@H]2CC[C@H](CCCCC)CC2)CC1

Procedure:
30.4 g of 1-pentyl-4-(trans-4-pentylcyclohexyl)-cyclohexene [obtainable by reacting 4-(trans-4-pentylcyclohexyl)-cyclohexanone with pentyl-MgBr, hydrolysing the product to give 1-pentyl-4-(trans-4-pentylcyclohexyl)-cyclohexanol and dehydrating the latter], 2.7 g of liquid HCN, 0.1 g of palladium bis-[2,3-0-isopropylidene-2,3-dihydroxy-1,4-bis-(diphenylphosphino)-butane] and 100 ml of acetonitrile are heated at 130° for 1 hour in an autoclave. The mixture is cooled, evaporated and worked up in the customary manner to give r-1-cyano-1-pentyl-cis-4-(trans-4-pentylcyclohexyl)-cyclohexane, m.p. 28°, c.p. 63°.
Reaction SMILES: [NH2:1][CH:2]1[N:8]=[C:7]([C:9]2[CH:14]=[CH:13][CH:12]=[CH:11][CH:10]=2)[C:6]2[CH:15]=[CH:16][CH:17]=[CH:18][C:5]=2[N:4]([CH2:19][C:20]([F:23])([F:22])[F:21])[C:3]1=[O:24].C1C([N+]([O-])=O)=CC=C([Cl-][C:35]([O-])=[O:36])C=1.C(N(CC)CC)C.Cl.Cl.[O:47]=[C:48]1[NH:56][C:51]2=[N:52][CH:53]=[CH:54][CH:55]=[C:50]2[N:49]1[CH:57]1[CH2:62][CH2:61][NH:60][CH2:59][CH2:58]1>O1CCCC1.CS(C)=O>[O:24]=[C:3]1[C@H:2]([NH:1][C:35]([N:60]2[CH2:61][CH2:62][CH:57]([N:49]3[C:50]4[C:51](=[N:52][CH:53]=[CH:54][CH:55]=4)[NH:56][C:48]3=[O:47])[CH2:58][CH2:59]2)=[O:36])[N:8]=[C:7]([C:9]2[CH:10]=[CH:11][CH:12]=[CH:13][CH:14]=2)[C:6]2[CH:15]=[CH:16][CH:17]=[CH:18][C:5]=2[N:4]1[CH2:19][C:20]([F:21])([F:23])[F:22]
Reactant: O=c1[nH]c2ncccc2n1C1CCNCC1
Reactant: NC1N=C(c2ccccc2)c2ccccc2N(CC(F)(F)F)C1=O
Agent: Cl
Solvent: CCN(CC)CC
Solvent: CS(C)=O
Solvent: C1CCOC1
Product: O=C(N[C@@H]1N=C(c2ccccc2)c2ccccc2N(CC(F)(F)F)C1=O)N1CCC(n2c(=O)[nH]c3ncccc32)CC1
Reaction time: 1 h
Yield: 70.8 %

Procedure:
A solution of (3R) 3-amino-2-oxo-5-phenyl-1-(2,2,2-trifluorethyl)-2,3-dihydro-1H-1,4-benzodiazepine (Y.-J. Shi et al., Tetrahedron, 1999, 55, 909-918) (0.150 g, 0.45 mmol) and 4-nitrophenylchloroformate (0.091 g, 0.45 mmol) in dry tetrahydrofuran (2.5 mL) was cooled to 0° C. under argon. Triethylamine (0.063 mL, 0.45 mmol) was added and the reaction stirred for 1 h. A solution of 2-oxo-1-(4-piperidinyl)-2,3-dihydro-1H-imidazo[4,5-b]pyridine dihydrochloride (0.130 g, 0.45 mmol) and triethylamine (0.190 mL) in dimethylsulfoxide (2.5 mL) was added. The reaction was allowed to come to room temperature and stirred overnight. The crude product was purified by reverse phase HPLC (C-18, 5% to 95% 0.1% trifluoroacetic acid/acetonitrile in 0.1% aqueous trifluoroacetic acid gradient elution). The pure fractions were extracted with methylene chloride and saturated sodium bicarbonate. The organic layer was dried, filtered and evaporated. The product was taken up in methanol and treated with hydrogen chloride. The solvent was evaporated and the resulting solid was dried in vacuo, to yield the title compound (184 mg, 66% yield). MS 578.2118 (M+1) 1H NMR (500 MHz, C3OD) δ 8.02 (d, J=8 Hz, 1H), 8.00 (d, J=6 Hz, 1H), 7.80 (d, J=3 Hz, 2H), 7.60 (m, 3H), 7.50 (t, J=8 Hz, 2H), 7.45 (m, 1H), 7.39 (d, J=7 Hz, 1H), 7.34 (dd, J=6, 8 Hz, 1H), 5.55 (s, 1H), 5.26 (m, 1H), 4.61 (m, 2H), 4.35 (d, J=13 Hz, 2H), 3.08 (q, J=13 Hz, 2H), 2.40 (m, 2H), 1.91 (m, 2H).
Reaction SMILES: [F:1][C:2]([F:27])([F:26])[S:3]([O:6][C:7]1[CH:12]=[CH:11][C:10]([C:13]([C:15]2[CH:16]=[CH:17][C:18]3[O:22][C:21]([CH3:24])([CH3:23])[CH2:20][C:19]=3[CH:25]=2)=O)=[CH:9][CH:8]=1)(=[O:5])=[O:4].O.[NH2:29][NH2:30].C(O)(=O)C>C(O)C>[F:1][C:2]([F:27])([F:26])[S:3]([O:6][C:7]1[CH:12]=[CH:11][C:10]([C:13](=[N:29][NH2:30])[C:15]2[CH:16]=[CH:17][C:18]3[O:22][C:21]([CH3:24])([CH3:23])[CH2:20][C:19]=3[CH:25]=2)=[CH:9][CH:8]=1)(=[O:5])=[O:4]
Reactant: NN
Reactant: CC1(C)Cc2cc(C(=O)c3ccc(OS(=O)(=O)C(F)(F)F)cc3)ccc2O1
Solvent: CC(=O)O
Solvent: CCO
Solvent: O
Product: CC1(C)Cc2cc(C(=NN)c3ccc(OS(=O)(=O)C(F)(F)F)cc3)ccc2O1
Temperature: 25 °C
Yield: 96.5 %

Procedure:
A mixture of 1.6 grams (0.004 mole) of (4-trifluoromethylsulfonyloxyphenyl)(2,3-dihydro-2,2-dimethylbenzofuran-5-yl) ketone in 75 mL of ethanol was stirred, and 0.6 mL (0.0121 mole) of hydrazine hydrate followed by 0.5 mL of acetic acid were both added via syringe. Upon completion of addition the reaction mixture was heated at reflux for 7 hours and then was allowed to cool to ambient temperature where it was stirred for 18 hours. The reaction mixture was concentrated under reduced pressure, and the residue was stirred with diethyl ether and water. The mixture was placed in a separatory funnel, and the layers were separated. The organic layer was washed with aqueous 10% sodium hydroxide solution, two portions of water, and with a saturated, aqueous solution of sodium chloride. The organic layer was concentrated under reduced pressure to yield 1.6 grams of (4-trifluoromethylsulfonyloxyphenyl)(2,3-dihydro-2,2-dimethylbenzofuran-5-yl) ketone hydrazone as an oil. The nmr spectrum was consistent with the proposed structure.
Reaction SMILES: [CH:1]([C:3]1[CH:15]=[CH:14][C:6]([C:7]([O:9][C:10]([CH3:13])([CH3:12])[CH3:11])=[O:8])=[CH:5][CH:4]=1)=O.[N:16]([CH2:19][C:20]([O:22][CH3:23])=[O:21])=[N+]=[N-].C[O-].[Na+].N(C(=CC1C=CC=CC=1)C([O-])=O)=[N+]=[N-]>CO.O.C1(C)C(C)=CC=CC=1>[CH3:23][O:22][C:20]([C:19]1[NH:16][C:15]2[C:3]([CH:1]=1)=[CH:4][CH:5]=[C:6]([C:7]([O:9][C:10]([CH3:13])([CH3:12])[CH3:11])=[O:8])[CH:14]=2)=[O:21]
Reactant: CC(C)(C)OC(=O)c1ccc(C=O)cc1
Reactant: COC(=O)CN=[N+]=[N-]
Agent: C[O-]
Agent: [N-]=[N+]=NC(=Cc1ccccc1)C(=O)[O-]
Agent: [Na+]
Solvent: O
Solvent: Cc1ccccc1C
Solvent: CO
Product: COC(=O)c1cc2ccc(C(=O)OC(C)(C)C)cc2[nH]1
Temperature: 0 °C
Reaction time: 1 h
Yield: 42 %

Procedure:
A solution of t-butyl 4-formylbenzoate (8.52 g, 41 mmol) and methyl azidoacetate [M. S. Allen, L. K. Hamaker, A. J. La Loggia, J. M. Cook, Synth. Commun., 1992, 22, 2077-2102] (28.5 g, 248 mmol) in dry MeOH (200 mL) was added dropwise over 1 h to a solution of NaOMe (60 mL of a 3.3M solution in MeOH, 197 mmol) under nitrogen with cooling in an ice-salt bath. The yellow suspension was stirred for a further 1 h at 0° C., allowed to stand at 4° C. for 15 h, then diluted with water and the solid filtered off and dried in the dark. A solution of this crude azidocinnamate (8.76 g, 29 mmol) in dry xylene (400 mL) was added dropwise over 2 h to xylene (100 mL) at ref lux under nitrogen, the solution stirred at reflux for a further 1 h, then cooled and evaporated. Recrystallisation from MeOH gave t-butyl 2-(methoxycarbonyl)indole-6-carboxylate as a white solid (4.72 g, 42%), mp 189-190.5° C. 1H NMR [(CD3)2SO] δ12.26 (s, 1H, NH), 8.08 (s, 1H, H-3 or H-7), 7.73 (d, J=8.4 Hz, 1H, H-4), 7.61 (dd, J=8.4, 1.3 Hz, 1H, H-5), 7.21 (d, J=1.3 Hz, 1H, H-3 or H-7), 3.89 (s, 3H, CO2Me), 1.56 (s, 9H, CO2 tBu); 13C NMR δ165.5 (Co2 tBu), 161.4 (CO2Me), 136.5, 130.0, 129.9, 127.3 (C-2,6,8,9), 121.9, 120.3, 114.4, 107.5 (C-3,4,5,7), 80.4 (OCMe3), 52.1 (OCH3), 27.8 (tBu). Anal. (C15H17NO4) C,H,N.
Reaction SMILES: [F:1][C:2]1[CH:3]=[C:4]2[C:9](=[CH:10][CH:11]=1)[C@H:8]([CH:12]([CH3:14])[CH3:13])[C@:7]([CH2:16][CH2:17][NH:18][CH3:19])([OH:15])[CH2:6][CH2:5]2.[CH3:20][O:21][CH2:22][C:23]([CH2:32][O:33][CH3:34])([CH3:31])[C:24]([NH:26][CH2:27][CH2:28][CH:29]=O)=[O:25].C([BH3-])#N.[Na+]>C(Cl)Cl.CC(O)=O>[F:1][C:2]1[CH:3]=[C:4]2[C:9](=[CH:10][CH:11]=1)[C@H:8]([CH:12]([CH3:13])[CH3:14])[C@:7]([CH2:16][CH2:17][N:18]([CH3:19])[CH2:29][CH2:28][CH2:27][NH:26][C:24](=[O:25])[C:23]([CH2:32][O:33][CH3:34])([CH3:31])[CH2:22][O:21][CH3:20])([OH:15])[CH2:6][CH2:5]2
Reactant: CNCC[C@@]1(O)CCc2cc(F)ccc2[C@@H]1C(C)C
Reactant: COCC(C)(COC)C(=O)NCCC=O
Agent: [BH3-]C#N
Agent: [Na+]
Solvent: CC(=O)O
Solvent: ClCCl
Product: COCC(C)(COC)C(=O)NCCCN(C)CC[C@@]1(O)CCc2cc(F)ccc2[C@@H]1C(C)C
Temperature: 25 °C
Reaction time: 2 h
Yield: 91.8 %

Procedure:
6.55 g of (1S,2S)-6-fluoro-1-isopropyl-2-(2-methylamino-ethyl)-1,2,3,4-tetrahydro-naphthalen-2-ol were dissolved in DCM (138 mL)/AcOH (15 mL). 5.36 g of 3-methoxy-2-methoxymethyl-2-methyl-N-(3-oxo-propyl)-propionamide and 6.39 g of sodium cyanoborohydride were added. The reaction mixture was stirred for 2 h at room temperature, quenched with sat.-NaHCO3 and extracted with DCM. The organic phase was washed with brine, dried over anh. Na2SO4 and concentrated in vacuo. The resulting crude material was purified by CC using DCM/MeOH/NEt3 from 100/0/1 to 40/1/0.4 as eluant to yield 10.57 g of N-(3-{[2-((1S,2S)-6-Fluoro-2-hydroxy-1-isopropyl-1,2,3,4-tetrahydro-naphthalen-2-yl)-ethyl]-methyl-amino}-propyl)-3-methoxy-2-methoxymethyl-2-methyl-propionamide as amber resin.
Reaction SMILES: [CH2:1]([NH:5][CH2:6][CH2:7][NH2:8])[CH2:2][CH2:3][CH3:4].[N:9]#[C:10][Br:11]>>[BrH:11].[CH2:1]([N:5]1[CH2:6][CH2:7][N:8]=[C:10]1[NH2:9])[CH2:2][CH2:3][CH3:4]
Reactant: N#CBr
Reactant: CCCCNCCN
Product: Br
Product: CCCCN1CCN=C1N
Yield: 57.6 %

Procedure:
Reaction of N-butylethylenediamine (10.7 g, 0.092 mol) with cyanogen bromide (9.76 g, 0.092 mol) as described in the preparation of intermediate 6 gave 11.77 g (57% yield) of the title compound as white crystals (ether-hexane). 1HNMR 400 MHz (CDCl3) δ (ppm): 0.96 (3H, t, J=7.2 Hz, CH3), 1.41 (2H, m, CH2), 1.60 (2H, m, CH2), 3.52 (2H, t, J=7.3 Hz, CH2), 3.64-3.74 (4H, m, 2×CH2), 7.58 and 7.7 (broad s, NH). MS (ESI+) m/e 142 [M+H+].
Reaction SMILES: Br[C:2]1[CH:11]=[C:10]2[C:5]([C:6](=[O:12])[CH2:7][CH2:8][O:9]2)=[CH:4][CH:3]=1.C(N(CC)CC)C.[CH:20]1([C:23]#[CH:24])[CH2:22][CH2:21]1.O>CN(C=O)C.[Cu]I>[CH:20]1([C:23]#[C:24][C:2]2[CH:3]=[CH:4][C:5]3[C:6](=[O:12])[CH2:7][CH2:8][O:9][C:10]=3[CH:11]=2)[CH2:22][CH2:21]1
Reactant: O=C1CCOc2cc(Br)ccc21
Reactant: C#CC1CC1
Agent: [Cu]I
Solvent: CN(C)C=O
Solvent: O
Solvent: CCN(CC)CC
Product: O=C1CCOc2cc(C#CC3CC3)ccc21
Temperature: 100 °C
Reaction time: 2 h
Yield: 88.3 %

Procedure:
To a solution of 7-bromochroman-4-one (2.0 g, 8.8 mmol) in DMF (10 mL) was added CuI (380 mg, 1.7 mmol), Pd(PPh3)Cl2 (540 mg, 0.8 mmol) and triethylamine (5 mL) under nitrogen at rt. The suspension was warmed to 100° C. and then cyclopropylacetylene (1.1 g, 17.6 mmol) was added dropwise. The mixture was stirred at 100° C. under nitrogen for 2 h. The reaction mixture was cooled to rt, poured into water, and extracted with EtOAc. Organics were separated and washed with brine, dried (Na2SO4), and concentrated. The residue was purified by silica gel chromatography to give 1.65 g (88%) of the title compound as a tan solid. 1H NMR (300 MHz, CDCl3): δ 0.83-0.93 (4H, m), 1.44-1.49 (1H, m), 2.79 (2H, t, J=6.6 Hz), 4.52 (2H, t, J=6.6 Hz), 6.96-7.00 (2H, m), 7.79 (1H, d, J=7.8 Hz). [M+H] calc'd for C14H12O, 213; found 213.
Reaction SMILES: [NH2:1][C:2]1[CH:16]=[CH:15][C:14]([Cl:17])=[CH:13][C:3]=1[C:4](=[N:11][OH:12])[C:5]1[CH:10]=[CH:9][CH:8]=[CH:7][CH:6]=1.CCOCC.[Cl:23][CH:24]([F:28])[C:25](Cl)=[O:26]>O>[Cl:23][CH:24]([F:28])[C:25]([NH:1][C:2]1[CH:16]=[CH:15][C:14]([Cl:17])=[CH:13][C:3]=1[C:4](=[N:11][OH:12])[C:5]1[CH:6]=[CH:7][CH:8]=[CH:9][CH:10]=1)=[O:26]
Reactant: Nc1ccc(Cl)cc1C(=NO)c1ccccc1
Reactant: O=C(Cl)C(F)Cl
Solvent: O
Solvent: CCOCC
Product: O=C(Nc1ccc(Cl)cc1C(=NO)c1ccccc1)C(F)Cl
Reaction time: 0.5 h
Yield: 88 %

Procedure:
Water, 250 ml, was added to a solution of 50 g (0.203 mole) of 2-amino-5-chlorobenzophenone oxime (mixture of isomers) in 1 l. of ether, and the mixture was stirred rapidly and cooled to 5°. Solutions of (A) 100 ml of 10% sodium hydroxide in water and (B) 33.5 g (0.228 mole) of chlorofluoroacetyl chloride made up to 100 ml with ether were simultaneously added at the same rate over 30 min., keeping the temperature of the reaction mixture at about 10° with cooling. The reaction mixture was stirred for 30 min. after the addition, and the ether layer was separated, washed with water, dried (MgSO4), and evaporated to dryness under reduced pressure. The residue was recrystallized from benzene to give 61.2 g (88%) of 2-(chlorofluoroacetamido)-5-chlorobenzophenone oxime (mixture of isomers) as light yellow crystals, mp 110°-129°. The 19F nmr (acetone-d6) indicates a mixture of two isomers in a 70:30 ratio: δ -143.2 ppm (d, d, J=50, 2.5 Hz, 30%) and δ -144.3 ppm (d, d, J=50, 2.5 Hz, 70%).
Reaction SMILES: Br[C:2]1[CH:7]=[CH:6][C:5]([Br:8])=[CH:4][N:3]=1.[Li]CCCC.[F:14][CH:15]([F:19])[C:16]([O-])=[O:17]>C1(C)C=CC=CC=1.[NH4+].[Cl-]>[Br:8][C:5]1[CH:6]=[CH:7][C:2]([C:16](=[O:17])[CH:15]([F:19])[F:14])=[N:3][CH:4]=1
Reactant: O=C([O-])C(F)F
Reactant: Brc1ccc(Br)nc1
Agent: [Cl-]
Agent: [Li]CCCC
Agent: [NH4+]
Solvent: Cc1ccccc1
Product: O=C(c1ccc(Br)cn1)C(F)F
Temperature: 25 °C
Reaction time: 8 h

Procedure:
To a solution of 2,5-dibromopyridine (16 g, 67 mmol) in toluene (150 mL) was added 2.5 N solution of n-BuLi (27 mL, 67 mmol) dropwise at −78° C. The resulting solution was stirred at −78° C. for 1 hour before the addition of 2,2-difluoroacetate (10 g, 80 mmol). After stirred at ambient temperature overnight, the reaction solution was diluted with saturated aqueous NH4Cl solution (80 mL) at 0° C., and then extracted with ethyl acetate (2×100 mL). All the organic solution was dried over sodium sulfate, filtered and concentrated in vacuo. The crude residue was purified by flash column chromatography with 5-10% ethyl acetate in hexane to afford the title compound as a white solid. 1H NMR (300 MHz, CDCl3) δ 8.82 (s, 1H), 8.08 (d, J=6.0 Hz, 1H), 8.03 (d, J=6.0 Hz, 1H), 7.05 (t, J=54.4 Hz, 1H).
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[CH2:25][CH2:24][CH2:23][C@@:10]2([O:14][C:13](=[O:15])[N:12]([C:16]3[CH:17]=[N:18][C:19]([NH2:22])=[CH:20][CH:21]=3)[CH2:11]2)[CH2:9]1)=[O:7])([CH3:4])([CH3:3])[CH3:2].[CH3:26][N:27]([CH3:45])[C:28]([C:30]1[N:39]([CH:40]2[CH2:44][CH2:43][CH2:42][CH2:41]2)[C:33]2[N:34]=[C:35](Cl)[N:36]=[CH:37][C:32]=2[CH:31]=1)=[O:29]>>[C:1]([O:5][C:6]([N:8]1[CH2:25][CH2:24][CH2:23][C@@:10]2([O:14][C:13](=[O:15])[N:12]([C:16]3[CH:17]=[N:18][C:19]([NH:22][C:35]4[N:36]=[CH:37][C:32]5[CH:31]=[C:30]([C:28](=[O:29])[N:27]([CH3:26])[CH3:45])[N:39]([CH:40]6[CH2:44][CH2:43][CH2:42][CH2:41]6)[C:33]=5[N:34]=4)=[CH:20][CH:21]=3)[CH2:11]2)[CH2:9]1)=[O:7])([CH3:4])([CH3:2])[CH3:3]
Reactant: CC(C)(C)OC(=O)N1CCC[C@@]2(C1)CN(c1ccc(N)nc1)C(=O)O2
Reactant: CN(C)C(=O)c1cc2cnc(Cl)nc2n1C1CCCC1
Product: CN(C)C(=O)c1cc2cnc(Nc3ccc(N4C[C@]5(CCCN(C(=O)OC(C)(C)C)C5)OC4=O)cn3)nc2n1C1CCCC1
Yield: 64 %

Procedure:
Following general N—C coupling procedure 1, (R)-3-(6-amino-pyridin-3-yl)-2-oxo-1-oxa-3,7-diaza-spiro[4.5]decane-7-carboxylic acid tert-butyl ester was combined with 2-Chloro-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidine-6-carboxylic acid dimethylamide which gave (R)-3-[6-(7-Cyclopentyl-6-dimethylcarbamoyl-7H-pyrrolo[2,3-d]pyrimidin-2-ylamino)-pyridin-3-yl]-2-oxo-1-oxa-3,7-diaza-spiro[4.5]decane-7-carboxylic acid tert-butyl ester as a white solid (0.175 g, 0.275 mmol) in 64% yield. 1H NMR (400 MHz, CDCl3) δ ppm 1.47 (s, 9H) 1.55-1.68 (m, 2H) 1.68-1.85 (m, 3H) 1.88-2.18 (m, 8H) 2.50-2.68 (m, 2H) 3.13-3.21 (m, 6H) 3.21-3.32 (m, 1H) 3.37-3.58 (m, 1H) 3.61-3.72 (m, 1H) 3.75 (d, J=8.53 Hz, 2H) 3.86 (d, J=8.53 Hz, 2H) 4.72-4.95 (m, J=8.91, 8.91, 8.78, 8.53 Hz, 1H) 6.48 (s, 1H) 8.14 (dd, J=9.29, 2.76 Hz, 1H) 8.31 (br. s., 1H) 8.53 (d, J=9.54 Hz, 1H) 8.76 (s, 1H). MS m/z 605.5 (M+H)+.
Reaction SMILES: [CH3:1][S:2][CH:3]([S:8][CH3:9])[CH2:4][CH2:5][S:6][CH3:7].C([Li])CCC.[C:15](=[O:17])=[O:16].[OH-].[K+]>CCCCCC.C1COCC1>[CH3:1][S:2][C:3]([S:8][CH3:9])([CH2:4][CH2:5][S:6][CH3:7])[C:15]([OH:17])=[O:16]
Reactant: CSCCC(SC)SC
Reactant: O=C=O
Agent: [K+]
Agent: [Li]CCCC
Agent: [OH-]
Solvent: CCCCCC
Solvent: C1CCOC1
Product: CSCCC(SC)(SC)C(=O)O
Reaction time: 2 h

Procedure:
In a three-neck flask under a protective gas atmosphere, 1,1,3-tris(methylthio)propane (2) (3.65 g, 20 mmol) was dissolved in 50 ml of abs. THF. Subsequently, at −20° C., a butyllithium solution in n-hexane (14 ml, 1.6 M) was slowly added dropwise with stirring. In the course of this, the solution turned bright yellow. After stirring had been continued at this temperature for 2 h, gaseous dry CO2 was passed through via a frit at −70° C. over a period of 30 minutes. The reaction solution was thawed slowly until a temperature of 20° C. was attained, at which a 10% aqueous KOH solution (80 ml) was added. After phase separation, the organic phase was washed with 10% aqueous KOH solution (2×50 ml). The combined KOH phases were washed with diethyl ether (3×30 ml) and then adjusted cautiously to pH 1 with conc. HCl while cooling. The product was extracted with diethyl ether (3×50 ml). The combined ether phases were subsequently dried over Na2SO4 and, after filtration, concentrated on a rotary evaporator. 2,2,4-tris(methylthio)butanoic acid (4) was obtained as a yellowish oil (4.1 g, yield=90%), which crystallized slowly when left to stand. The NMR characterization gave the same data as in Example 3.