Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [CH2:1]([N:8]1[CH2:13][CH2:12][CH:11]([OH:14])[CH2:10][CH2:9]1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.C(N(CC)CC)C.[CH2:22]=[C:23]1[O:27][C:25](=[O:26])[CH2:24]1>C1COCC1>[CH2:1]([N:8]1[CH2:13][CH2:12][CH:11]([O:14][C:25](=[O:26])[CH2:24][C:23]([CH3:22])=[O:27])[CH2:10][CH2:9]1)[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: C=C1CC(=O)O1
Reactant: OC1CCN(Cc2ccccc2)CC1
Solvent: C1CCOC1
Solvent: CCN(CC)CC
Product: CC(=O)CC(=O)OC1CCN(Cc2ccccc2)CC1
Reaction time: 1.5 h
Yield: 50 %

Procedure:
To a solution of 10.0 g of 1-benzyl-4-hydroxypiperidine and a catalytic amount of triethylamine in 10 ml of THF was added dropwise 4.62 g of diketene over 15 minutes. After the addition, the reaction was effected at room temperature for 1.5 hours and then at 50°-60° C. for 4.5 hours. The reaction mixture was concentrated, and then distilled under reduced pressure to obtain 7.20 g of acetoacetic acid-N-benzyl-4-piperidinyl ester (yield: 50.0%), b.p. 146° C./0.13 mmHg.
Reaction SMILES: [ClH:1].[N:2]1([CH2:8][CH2:9][N:10]2[CH2:15][C:14]3[CH:16]=[C:17](/[CH:20]=[CH:21]/[C:22]([OH:24])=O)[CH:18]=[N:19][C:13]=3[NH:12][C:11]2=[O:25])[CH2:7][CH2:6][O:5][CH2:4][CH2:3]1.Cl.CN1CC2C=C(/C=C/C(O)=O)C=NC=2NC(=O)C1.[CH3:45][NH:46][CH2:47][C:48]1[S:52][C:51]2[CH:53]=[CH:54][CH:55]=[CH:56][C:50]=2[C:49]=1[CH3:57].CNCC1C=CC2C(=CC=CC=2)C=1CCC>>[ClH:1].[CH3:45][N:46]([CH2:47][C:48]1[S:52][C:51]2[CH:53]=[CH:54][CH:55]=[CH:56][C:50]=2[C:49]=1[CH3:57])[C:22](=[O:24])/[CH:21]=[CH:20]/[C:17]1[CH:18]=[N:19][C:13]2[NH:12][C:11](=[O:25])[N:10]([CH2:9][CH2:8][N:2]3[CH2:3][CH2:4][O:5][CH2:6][CH2:7]3)[CH2:15][C:14]=2[CH:16]=1
Reactant: O=C(O)/C=C/c1cnc2c(c1)CN(CCN1CCOCC1)C(=O)N2
Reactant: CNCc1sc2ccccc2c1C
Agent: CCCc1c(CNC)ccc2ccccc12
Agent: CN1CC(=O)Nc2ncc(/C=C/C(=O)O)cc2C1
Agent: Cl
Product: Cc1c(CN(C)C(=O)/C=C/c2cnc3c(c2)CN(CCN2CCOCC2)C(=O)N3)sc2ccccc12
Yield: 33 %

Procedure:
According to the procedure of Example 1, except substituting (E)-3-[3-(2-morpholin-4-yl-ethyl)-2-oxo-1,2,3,4-tetrahydro-pyrido[2,3-d]pyrimidin-6-yl]acrylic acid hydrochloride for the (E)-3-(4-methyl-2-oxo-2,3,4,5-tetrahydro-1H-pyrido[2,3-e][1,4]diazepin-7-yl)acrylic acid hydrochloride, and substituting methyl-(3-methyl-benzo[b]thiophen-2-ylmethyl)amine for the methyl-(1-propyl-naphthalen-2-ylmethyl)amine, the title compound (140 mg, 33%) was prepared as a off-white solid: 1H NMR (300 MHz, DMSO-d6) δ 10.45 (br s, 1H), 10.14 (s, 1H), 8.41-8.39 (m, 1H), 8.01 (s, 1H), 7.88-7.86 (m, 1H), 7.74-7.73 (m, 1H), 7.56-7.53 (m, 1H), 7.41-7.18 (m, 3H), 6.31 (br s, 1H), 5.11-4.88 (m, 2H), 4.57-4.55 (m, 2H), 3.99-3.96 (m, 2H), 3.75-3.71 (m, 4H), 3.57-3.55 (m, 2H), 3.39-3.37 (m, 2H), 3.1.5-2.94 (m, 5H), 2.42 (s, 3H); MS (ESI) m/e 506 (M+H)+.
Reaction SMILES: [CH3:1][O:2][N:3]=[C:4]([C:9]1[CH:14]=[CH:13][C:12]([O:15][CH3:16])=[CH:11][CH:10]=1)[CH2:5][C:6]([OH:8])=O.[NH2:17][C:18](=[N:21][C:22](=[O:28])[O:23][C:24]([CH3:27])([CH3:26])[CH3:25])[S:19][CH3:20].CCN=C=NCCCN(C)C.Cl.C(N(CC)CC)C>CN(C1C=CN=CC=1)C.ClCCl>[CH3:1][O:2][N:3]=[C:4]([C:9]1[CH:14]=[CH:13][C:12]([O:15][CH3:16])=[CH:11][CH:10]=1)[CH2:5][C:6]([NH:17][C:18](=[N:21][C:22](=[O:28])[O:23][C:24]([CH3:26])([CH3:25])[CH3:27])[S:19][CH3:20])=[O:8]
Reactant: CSC(N)=NC(=O)OC(C)(C)C
Reactant: CON=C(CC(=O)O)c1ccc(OC)cc1
Agent: CCN=C=NCCCN(C)C
Agent: CN(C)c1ccncc1
Agent: Cl
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CON=C(CC(=O)NC(=NC(=O)OC(C)(C)C)SC)c1ccc(OC)cc1
Temperature: 25 °C
Reaction time: 12 h
Yield: 88.6 %

Procedure:
A mixture of 3-(methoxyimino)-3-(4-methoxyphenyl)propanoic acid (223 mg), tert-butyl amino(methylthio)methylenecarbamate (190 mg), EDAC.HCl (384 mg), DMAP (122 mg) and triethylamine (0.56 mL) in dichloromethane (3 mL) was stirred at room temperature for 12 h. The crude reaction mixture was purified directly by preparative TLC eluting with 35% ethyl acetate/75% hexanes to give the title compound as a yellowish oil (350 mg). HPLC retention time: 2.42 min (method A). MS (ESI) (M+Na)+ 418.18.
Reaction SMILES: [N:1]1[C:10]2[C:5](=[CH:6][CH:7]=[CH:8][C:9]=2[S:11][CH2:12][C:13]2[CH:21]=[CH:20][CH:19]=[CH:18][C:14]=2[C:15](O)=[O:16])[CH:4]=[CH:3][CH:2]=1.C(Cl)(=O)C([Cl:25])=O>C(Cl)Cl.CN(C=O)C>[N:1]1[C:10]2[C:5](=[CH:6][CH:7]=[CH:8][C:9]=2[S:11][CH2:12][C:13]2[CH:21]=[CH:20][CH:19]=[CH:18][C:14]=2[C:15]([Cl:25])=[O:16])[CH:4]=[CH:3][CH:2]=1
Reactant: O=C(O)c1ccccc1CSc1cccc2cccnc12
Reactant: O=C(Cl)C(=O)Cl
Solvent: CN(C)C=O
Solvent: ClCCl
Product: O=C(Cl)c1ccccc1CSc1cccc2cccnc12
Temperature: 25 °C

Procedure:
A solution of 1.0 eq. of 2-(quinolin-8-ylsulfanylmethyl)benzoic acid in CH2Cl2 was cooled to 0° C. To this was added 1.1 eq. of oxalyl chloride followed by one drop of DMF. The mixture was warmed to room temperature and stirred for a time sufficient for reaction completion. The mixture was concentrated to give 42 which was used directly.
Reaction SMILES: [Br:1][C:2]1[N:11]=[C:5]2[CH:6]=[C:7]([NH2:10])[CH:8]=[CH:9][N:4]2[N:3]=1.[CH2:12]([O:14][C:15]([C:17]1[CH:18]=[N:19][N:20]([CH3:25])[C:21]=1[C:22](O)=[O:23])=[O:16])[CH3:13].CCCP(=O)=O.C(N(CC)C(C)C)(C)C>O1CCCC1>[CH2:12]([O:14][C:15]([C:17]1[CH:18]=[N:19][N:20]([CH3:25])[C:21]=1[C:22](=[O:23])[NH:10][C:7]1[CH:8]=[CH:9][N:4]2[N:3]=[C:2]([Br:1])[N:11]=[C:5]2[CH:6]=1)=[O:16])[CH3:13]
Reactant: CCOC(=O)c1cnn(C)c1C(=O)O
Reactant: Nc1ccn2nc(Br)nc2c1
Agent: CCCP(=O)=O
Solvent: CCN(C(C)C)C(C)C
Solvent: C1CCOC1
Product: CCOC(=O)c1cnn(C)c1C(=O)Nc1ccn2nc(Br)nc2c1
Yield: 82.7 %

Procedure:
A mixture of 2-bromo-[1,2,4]triazolo[1,5-a]pyridin-7-amine (2.39 g, 11.2 mmol), 4-(ethoxycarbonyl)-1-methyl-1H-pyrazole-5-carboxylic acid (2.22 g, 11.2 mmol), propylphosphonic anhydride (50% in ethyl acetate, 16.5 ml, 28.0 mmol) and N,N-diisopropylethylamine (5.72 ml, 33.7 mmol) in tetrahydrofuran (80 ml) was refluxed for 18 hours under argon atmosphere. The solvent was evaporated and the resulting yellowish oil was triturated with sat. sodium hydrogencarbonate solution. The precipitated solid was filtered off, washed with water 4 times and dried in vacuo affording 5-(2-bromo-[1,2,4]triazolo[1,5-a]pyridin-7-ylcarbamoyl)-1-methyl-1H-pyrazole-4-carboxylic acid ethyl ester (3.64 g, 82.5%) as a light yellow solid. mp: 177-180° C., MS: m/z=393.0/395.0 (M+H+)
Reaction SMILES: [OH-].[Na+].CO.C([O:7][C:8]([C:10]1[C:14]([C:15]2[CH:20]=[CH:19][CH:18]=[CH:17][C:16]=2[O:21][CH3:22])=[CH:13][S:12][C:11]=1[N:23]1[C:31](=[O:32])[C:30]2[C:25](=[CH:26][CH:27]=[CH:28][CH:29]=2)[C:24]1=[O:33])=[O:9])C.Cl>O>[O:32]=[C:31]1[C:30]2[C:25](=[CH:26][CH:27]=[CH:28][CH:29]=2)[C:24](=[O:33])[N:23]1[C:11]1[S:12][CH:13]=[C:14]([C:15]2[CH:20]=[CH:19][CH:18]=[CH:17][C:16]=2[O:21][CH3:22])[C:10]=1[C:8]([OH:9])=[O:7]
Reactant: CCOC(=O)c1c(-c2ccccc2OC)csc1N1C(=O)c2ccccc2C1=O
Agent: Cl
Agent: [Na+]
Agent: [OH-]
Solvent: CO
Solvent: O
Product: COc1ccccc1-c1csc(N2C(=O)c3ccccc3C2=O)c1C(=O)O

Procedure:
To a solution of NaOH (1.4 mmol) in a 1:1 mixture of methanol:H2O (6 mL) is added 2-(1,3-dioxo-1,3-dihydro-isoindol-2-yl)-4-(2-methoxyphenyl)-thiophene-3-carboxylic acid ethyl ester (0.7 mmol, Example 17, Part C). The mixture is heated to reflux for 90 minutes, then diluted with water (12 mL), chilled in an ice bath, and acidified with concentrated HCl. The product that precipitates is collected by filtration, washed with water, and dried, affording the desired compound.
Reaction SMILES: I[CH2:2][CH2:3][CH2:4][N:5]1[C:9]2[CH:10]=[CH:11][CH:12]=[CH:13][C:8]=2[N:7]([CH3:14])[C:6]1=[O:15].[C:16]1([N:22]2[C:26]3([CH2:31][CH2:30][NH:29][CH2:28][CH2:27]3)[C:25](=[O:32])[NH:24][CH2:23]2)[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=1.C(=O)([O-])[O-].[Na+].[Na+]>CN(C)C=O>[CH3:14][N:7]1[C:8]2[CH:13]=[CH:12][CH:11]=[CH:10][C:9]=2[N:5]([CH2:4][CH2:3][CH2:2][N:29]2[CH2:28][CH2:27][C:26]3([N:22]([C:16]4[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=4)[CH2:23][NH:24][C:25]3=[O:32])[CH2:31][CH2:30]2)[C:6]1=[O:15]
Reactant: Cn1c(=O)n(CCCI)c2ccccc21
Reactant: O=C1NCN(c2ccccc2)C12CCNCC2
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: Cn1c(=O)n(CCCN2CCC3(CC2)C(=O)NCN3c2ccccc2)c2ccccc21
Temperature: 70 °C

Procedure:
A mixture of 5 parts of 1,3-dihydro-1-(3-iodopropyl)-3-methyl-2H-benzimidazol-2-one, 3,4 parts of 1-phenyl-1,3,8-triazaspiro[4,5]decan-4-one, 2.65 parts of sodium carbonate and 22.5 parts of N,N-dimethylformamide is stirred and heated for 2 hours at 70° C. The reaction mixture is cooled and poured onto water, whereupon an oily precipitate is formed. The supernatant aqueous phase is decanted and the residual oil is dissolved in trichloromethane. The solution is dried, filtered and evaporated. The residue is purified by column-chromatography over silica gel using a mixture of trichloromethane and 5% of methanol as eluent. The pure fractions are collected and the eluent is evaporated, yielding 1 part of 8-[3-(1,3-dihydro-3-methyl-2-oxo-2H-benzimidazol-1-yl)propyl]-1-phenyl-1,3,8-triazaspiro[4,5]decan-4-one; mp. 164.4° C.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[C:6]([C:8]([F:11])([F:10])[F:9])[CH:5]=[C:4]([Cl:12])[C:3]=1[N:13]1[C:17]([CH2:18][CH3:19])=[C:16]([CH2:20][N:21]2[CH:30]([CH2:31][OH:32])[CH2:29][C:28]3[C:23](=[CH:24][CH:25]=[CH:26][CH:27]=3)[CH2:22]2)[C:15]([CH2:33][CH3:34])=[N:14]1.[H-].[Na+].[CH3:37]I>C1COCC1>[Cl:1][C:2]1[CH:7]=[C:6]([C:8]([F:9])([F:11])[F:10])[CH:5]=[C:4]([Cl:12])[C:3]=1[N:13]1[C:17]([CH2:18][CH3:19])=[C:16]([CH2:20][N:21]2[CH:30]([CH2:31][O:32][CH3:37])[CH2:29][C:28]3[C:23](=[CH:24][CH:25]=[CH:26][CH:27]=3)[CH2:22]2)[C:15]([CH2:33][CH3:34])=[N:14]1
Reactant: CCc1nn(-c2c(Cl)cc(C(F)(F)F)cc2Cl)c(CC)c1CN1Cc2ccccc2CC1CO
Reactant: CI
Agent: [H-]
Agent: [Na+]
Solvent: C1CCOC1
Product: CCc1nn(-c2c(Cl)cc(C(F)(F)F)cc2Cl)c(CC)c1CN1Cc2ccccc2CC1COC
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 26 %

Procedure:
A solution of 200 mg (0.39 mmol) of the compound of step A in 5 mL of THF was treated with 10 mg (0.42 mmol) of sodium hydride and stirred for 30 minutes at room temperature. Then 0.1 mL (1.6 mmol) of methyl iodide was added and the reaction mixture was stirred at room temperature for 24 hours. The reaction was quenched with water and the product was extracted into ethyl acetate which was dried and evaporated. The crude product was flash chromatographed on silica gel to give the desired product in 26% yield as a colorless oil. 1H-NMR (CDCl3) δ0.90 (3H, t, J=7), 1.20 (3H, t, J=7), 2.39 (2H, q, J=7), 2.65 (2H, q, J=7), 2.88-2.96 (1H, m), 3.16-3.20 (1H, m), 3.32 (3H, s), 3.55-3.78 7H, m), 6.90-7.24 (4H, m), 7.65 (2H, s).
Reaction SMILES: [CH2:1]([N:3]([CH2:19][CH3:20])[C:4](=[O:18])[C:5]1[CH:10]=[CH:9][C:8]([CH:11]=[CH2:12])=[CH:7][C:6]=1[O:13][C:14]([F:17])([F:16])[F:15])[CH3:2].[H][H]>[Pd].CO>[CH2:19]([N:3]([CH2:1][CH3:2])[C:4](=[O:18])[C:5]1[CH:10]=[CH:9][C:8]([CH2:11][CH3:12])=[CH:7][C:6]=1[O:13][C:14]([F:16])([F:15])[F:17])[CH3:20]
Reactant: C=Cc1ccc(C(=O)N(CC)CC)c(OC(F)(F)F)c1
Reactant: [H][H]
Agent: [Pd]
Solvent: CO
Product: CCc1ccc(C(=O)N(CC)CC)c(OC(F)(F)F)c1
Reaction time: 1 h
Yield: 83 %

Procedure:
To a stirring degassed solution of N,N-diethyl-4-ethenyl-2-(trifluoromethoxy)benzamide (1783 mg, 6.2 mmol) and 10% palladium on carbon (50 mg) in MeOH (30 mL) was added hydrogen (1 atm). The reaction was stirred for 1 h and then filtered. The filtrate was conc. in vacuo to a colorless oil. The oil was purified by flash chromatography (SiO2, 0-50% EtOAc in hexanes) to give 1489 mg of the desired product as a colorless oil. MS (ESI) 290 (M+H).
Reaction SMILES: [F:1][CH2:2][CH2:3][O:4][CH2:5][CH2:6][O:7][CH2:8][CH2:9][O:10][C:11]1[CH:23]=[C:22]2[C:14]([C:15]3[CH:16]=[CH:17][C:18]([NH2:24])=[CH:19][C:20]=3[NH:21]2)=[CH:13][CH:12]=1.[CH2:25]=O.C[O-].[Na+].[BH4-].[Na+]>CO>[F:1][CH2:2][CH2:3][O:4][CH2:5][CH2:6][O:7][CH2:8][CH2:9][O:10][C:11]1[CH:23]=[C:22]2[C:14]([C:15]3[CH:16]=[CH:17][C:18]([NH:24][CH3:25])=[CH:19][C:20]=3[NH:21]2)=[CH:13][CH:12]=1
Reactant: C=O
Reactant: Nc1ccc2c(c1)[nH]c1cc(OCCOCCOCCF)ccc12
Agent: C[O-]
Agent: [BH4-]
Agent: [Na+]
Solvent: CO
Product: CNc1ccc2c(c1)[nH]c1cc(OCCOCCOCCF)ccc12
Temperature: 25 °C
Yield: 56.7 %

Procedure:
A mixture of 7-(2-(2-(2-fluoroethoxy)ethoxy)ethoxy)-9H-carbazol-2-amine (95 mg, 0.28 mmol), paraformaldehyde (43 mg, 1.43 mmol), and NaOMe (492 mg, 25% MeOH solution, 2.3 mmol) in 8 mL of MeOH was heated at reflux for 1.5 h under Ar atmosphere and cooled to rt. To this mixture was added NaBH4 (54 mg, 1.43 mmol) and the mixture was heated at reflux for 2 h. After cooling to rt, the mixture was quenched onto ice. It was extracted with ether (3×30 mL) and the combined organic phase was dried over MgSO4 and concentrated. The crude product was purified with chromatography (hexane/EtOAc) to afford 7-(2-(2-(2-fluoroethoxy)ethoxy)ethoxy)-N-methyl-9H-carbazol-2-amine (AD-CB-003P-WZ0141) as a light-brown solid (55 mg, 56%). 1H NMR (400 MHz, CDCl3) δ 7.76 (s, 1H), 7.77 (t, J=8.8 Hz, 2H), 6.78 (dd, J=8.0, 2.0 Hz, 1H), 6.77 (s, 1H), 6.53 (dd, J=8.4, 2.0 Hz, 1H), 6.46 (s, 1H), 4.62 9 m, 1H), 4.50 (m, 1H), 4.13 (t, J=5.2 Hz, 2H), 3.85 (t, J=5.2 Hz, 2H), 3.83 (s, 1H), 3.79-3.67 (m, 6H), 2.87 (s, 3H); MS (ESI) m/z 347 (M+H+).
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]2[C:9](=[CH:10][C:11]=1[C:12]([OH:14])=O)[N:8]=[CH:7][N:6]=[C:5]2[NH:15][CH:16]([C:18]1[NH:22][C:21]2[CH:23]=[CH:24][C:25]([Cl:27])=[CH:26][C:20]=2[N:19]=1)[CH3:17].FC1C(OC(N(C)C)=[N+](C)C)=C(F)C(F)=C(F)C=1F.F[P-](F)(F)(F)(F)F.C(N(C(C)C)CC)(C)C.[NH:63]1[CH2:68][CH2:67][CH:66]([C:69]([NH2:71])=[O:70])[CH2:65][CH2:64]1>CS(C)=O>[Cl:1][C:2]1[CH:3]=[C:4]2[C:9](=[CH:10][C:11]=1[C:12]([N:63]1[CH2:68][CH2:67][CH:66]([C:69]([NH2:71])=[O:70])[CH2:65][CH2:64]1)=[O:14])[N:8]=[CH:7][N:6]=[C:5]2[NH:15][CH:16]([C:18]1[NH:22][C:21]2[CH:23]=[CH:24][C:25]([Cl:27])=[CH:26][C:20]=2[N:19]=1)[CH3:17]
Reactant: NC(=O)C1CCNCC1
Reactant: CC(Nc1ncnc2cc(C(=O)O)c(Cl)cc12)c1nc2cc(Cl)ccc2[nH]1
Agent: CN(C)C(Oc1c(F)c(F)c(F)c(F)c1F)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CS(C)=O
Solvent: CCN(C(C)C)C(C)C
Product: CC(Nc1ncnc2cc(C(=O)N3CCC(C(N)=O)CC3)c(Cl)cc12)c1nc2cc(Cl)ccc2[nH]1

Procedure:
Prepared analogously to Example 37a from 6-chloro-4-[1-(5-chloro-1H-benzimidazol-2-yl)-ethylamino]-7-hydroxycarbonyl-quinazoline, pentafluorophenyl-tetramethyluronium-hexafluorophosphate (PFTU), diisopropylethylamine and piperidine-4-carboxylic acid amide in DMSO at ambient temperature.
Reaction SMILES: C(OC([NH:8][C@@H:9]([CH3:12])[CH2:10][OH:11])=O)(C)(C)C.[Cl:13][C:14]1[CH:15]=[C:16]([CH:21]=[CH:22][C:23]=1O)[C:17]([O:19][CH3:20])=[O:18].C1C=CC(P(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1.N(C(OC(C)C)=O)=NC(OC(C)C)=O>C1COCC1>[Cl:13][C:14]1[CH:15]=[C:16]([CH:21]=[CH:22][C:23]=1[O:11][CH2:10][C@@H:9]([NH2:8])[CH3:12])[C:17]([O:19][CH3:20])=[O:18]
Reactant: C[C@@H](CO)NC(=O)OC(C)(C)C
Reactant: COC(=O)c1ccc(O)c(Cl)c1
Agent: CC(C)OC(=O)N=NC(=O)OC(C)C
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: C1CCOC1
Product: COC(=O)c1ccc(OC[C@H](C)N)c(Cl)c1
Temperature: 25 °C
Reaction time: 1.5 h
Yield: 45.2 %

Procedure:
To a cooled (0° C.) solution of (S)-2-(N-tert-butoxycarbonylamino)-1-propanol (1.05 g, 5.99 mmol), methyl 3-chloro-4-hydroxybenzoate (1.12 g, 6.00 mmol), and Ph3P (2.36 g, 9.00 mmol) in THF (20 mL) was added diisopropyl azodicarboxylate (DIAD) (1.77 mL, 8.99 mmol), and the resulting mixture was heated under reflux for 2 days. The solution was evaporated off and the residue was dissolved in CH2Cl2 (20 mL) and TFA (10 mL). The resulting mixture was stirred at room temp for 1.5 hr. The solution was concentrated in vacuo, and the residue was dissolved in CHCl3. The mixture was extracted with H2O, and the aqueous layer was made basic by the addition of sat. NaHCO3. This basic aqueous layer was extracted with CHCl3. The extract was washed with brine, dried over Na2SO4 and evaporated to give 660 mg (2 steps, 32%) methyl (S)-3-chloro-4-(2-amino-1-propoxy)benzoate as a colorless oil. 1H-NMR (CDCl3) δ 1.21 (d, 3 H, J=6.4 Hz), 3.41–3.48 (m, 1 H), 3.77–3.81 (m, 1 H), 3.89 (s, 3 H), 3.98–4.01 (m, 1 H), 6.91–6.94 (m, 1 H), 7.90–7.93 (m, 1 H), 8.05–8.06 (m, 1 H).
Reaction SMILES: Cl.[F:2][C:3]([F:35])([F:34])[C:4]1[CH:5]=[C:6]([CH:27]=[C:28]([C:30]([F:33])([F:32])[F:31])[CH:29]=1)[CH2:7][O:8][CH2:9][CH:10]([C:21]1[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=1)[CH2:11][NH:12][C:13]([CH:15]1[CH2:20][CH2:19][NH:18][CH2:17][CH2:16]1)=[O:14].Br[CH2:37][C:38]([O:40][C:41]([CH3:44])([CH3:43])[CH3:42])=[O:39].C(=O)([O-])[O-].[K+].[K+].CN(C=O)C>O>[F:35][C:3]([F:34])([F:2])[C:4]1[CH:5]=[C:6]([CH:27]=[C:28]([C:30]([F:32])([F:33])[F:31])[CH:29]=1)[CH2:7][O:8][CH2:9][CH:10]([C:21]1[CH:22]=[CH:23][CH:24]=[CH:25][CH:26]=1)[CH2:11][NH:12][C:13]([CH:15]1[CH2:20][CH2:19][N:18]([CH2:37][C:38]([O:40][C:41]([CH3:44])([CH3:43])[CH3:42])=[O:39])[CH2:17][CH2:16]1)=[O:14]
Reactant: O=C(NCC(COCc1cc(C(F)(F)F)cc(C(F)(F)F)c1)c1ccccc1)C1CCNCC1
Reactant: CC(C)(C)OC(=O)CBr
Agent: Cl
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Solvent: O
Product: CC(C)(C)OC(=O)CN1CCC(C(=O)NCC(COCc2cc(C(F)(F)F)cc(C(F)(F)F)c2)c2ccccc2)CC1
Temperature: 25 °C
Reaction time: 20 h
Yield: 92.7 %

Procedure:
A mixture of Compound 4 produced in Example 32 (1.26 g, 2.4 mmol), tert-butyl bromoacetate (0.38 mL, 2.6 mmol), potassium carbonate (1.00 g, 7.2 mmol) and DMF (10 mL) was stirred for 20 hours at room temperature. Water was added to the reaction mixture followed by extracting with ethyl acetate. The organic layers were combined, washed with water and a saturated saline solution and dried over anhydrous sodium sulfate. The solvent was evaporated therefrom in vacuo to give Compound 79 (1.34 g, 93%).
Reaction SMILES: [NH:1]1[CH:5]=[C:4]([C:6]2[C:7]3[CH:14]=[CH:13][N:12]([CH2:15][O:16][CH2:17][CH2:18][Si:19]([CH3:22])([CH3:21])[CH3:20])[C:8]=3[N:9]=[CH:10][N:11]=2)[CH:3]=[N:2]1.[CH:23]1([C:28]#[C:29][C:30]#[N:31])[CH2:27][CH2:26][CH2:25][CH2:24]1.CN(C)C=O.C(=O)([O-])[O-].[K+].[K+]>>[CH:23]1(/[C:28](/[N:1]2[CH:5]=[C:4]([C:6]3[C:7]4[CH:14]=[CH:13][N:12]([CH2:15][O:16][CH2:17][CH2:18][Si:19]([CH3:22])([CH3:21])[CH3:20])[C:8]=4[N:9]=[CH:10][N:11]=3)[CH:3]=[N:2]2)=[CH:29]/[C:30]#[N:31])[CH2:27][CH2:26][CH2:25][CH2:24]1
Reactant: N#CC#CC1CCCC1
Reactant: C[Si](C)(C)CCOCn1ccc2c(-c3cn[nH]c3)ncnc21
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Product: C[Si](C)(C)CCOCn1ccc2c(-c3cnn(/C(=C\C#N)C4CCCC4)c3)ncnc21
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 82.6 %

Procedure:
To a stirred solution of 4-(1H-pyrazol-4-yl)-7-{[2-(trimethylsilyl)ethoxy]methyl}-7H-pyrrolo[2,3-d]pyrimidine (17, 7.260 g, 23.01 mmol) and 3-cyclopentylprop-2-ynenitrile (8, 6.140 g, 34.52 mmol, 1.5 equiv) in N,N-Dimethylformamide (DMF, 40.0 mL, 516 mmol) at room temperature was added solid potassium carbonate (K2CO3, 318 mg, 2.30 mmol, 0.1 equiv). The resulting reaction mixture was stirred at room temperature for 30 min. When LCMS showed the reaction was deemed complete, the reaction mixture was quenched with water (80 mL), extracted with EtOAc (2×150 mL). The combined organic layers were washed with water (80 mL) and brine (50 mL), dried over magnesium sulfate (MgSO4), filtered and concentrated under reduced pressure. The residue was purified by flash chromatography (SiO2, 0-30% EtOAc/hexane gradient elution) to give (Z)-3-cyclopentyl-3-(4-(7-((2-(trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl)acrylonitrile (19, 8.256 g, 10.0 g theoretical, 82.6% yield) as a colorless syrup. For 19: 1HNMR (CDCl3, 300 MHz) δ ppm 9.15 (bs, 1H), 8.96 (s, 1H), 8.56 (s, 1H), 7.51 (d, 1H, J=3.5 Hz), 6.93 (d, 1H, J=3.5 Hz), 5.75 (s, 2H), 5.29 (s, 1H), 3.62 (m, 1H), 3.60 (t, 2H, J=8.2 Hz), 2.16 (m, 2H), 1.81 (m, 4H), 1.59 (m, 2H), 0.98 (t, 2H, J=8.2 Hz), 0.00 (s, 9H); C23H30N6OSi (MW, 434.61), LCMS (EI) m/e 435.2 (M++H).
Reaction SMILES: F[C:2]1[CH:11]=[C:10]2[C:5]([CH:6]=[CH:7][C:8](=[O:14])[N:9]2[CH2:12][CH3:13])=[CH:4][N:3]=1.[N:15]1([C:21]2[CH:27]=[CH:26][C:24]([NH2:25])=[CH:23][CH:22]=2)[CH2:20][CH2:19][O:18][CH2:17][CH2:16]1.C([N-]C(C)C)(C)C.[Li+]>C1COCC1.C(O)(=O)C>[CH2:12]([N:9]1[C:10]2[C:5](=[CH:4][N:3]=[C:2]([NH:25][C:24]3[CH:23]=[CH:22][C:21]([N:15]4[CH2:20][CH2:19][O:18][CH2:17][CH2:16]4)=[CH:27][CH:26]=3)[CH:11]=2)[CH:6]=[CH:7][C:8]1=[O:14])[CH3:13]
Reactant: CCn1c(=O)ccc2cnc(F)cc21
Reactant: Nc1ccc(N2CCOCC2)cc1
Agent: CC(C)[N-]C(C)C
Agent: [Li+]
Solvent: C1CCOC1
Solvent: CC(=O)O
Product: CCn1c(=O)ccc2cnc(Nc3ccc(N4CCOCC4)cc3)cc21
Reaction time: 8 h
Yield: 52 %

Procedure:
A stirred solution of (XV, where R2 is ethyl) (100 mg, 0.52 mmol), 4-(4-morpholinyl)aniline (0.26 g, 1.1 mmol) in THF (5.0 mL) under nitrogen at -78° C. was treated with a solution (0.8 mL, 1.2 mmol) of lithium diisopropylamide (1.5 M in cyclohexane), then the temperature was allowed to rise slowly to 20° C. overnight. The resulting solution was treated with 3 drops of glacial acetic acid and concentrated to a dark residue that was purified that purified by silica gel chromatography eluting with EtOAc. The product fractions were pooled and concentrated to a solid that was crystallized to give 1-ethyl-7-(4-(morpholin-4-yl)phenylamino)-1H-[1,6]naphthyridin-2-one (94 mg, 52%): mp (2-propanol/hexanes) 219-223° C.
Reaction SMILES: [CH2:1]([C:3](=[CH:8][CH3:9])[CH:4]=[CH:5][CH2:6][NH2:7])[CH3:2].ClCCl.[CH3:13][N:14]([CH3:19])[S:15](Cl)(=[O:17])=[O:16]>C(N(CC)CC)C>[CH3:13][N:14]([CH3:19])[S:15]([NH:7][CH2:6][CH:5]=[CH:4][C:3]([CH2:1][CH3:2])=[CH:8][CH3:9])(=[O:17])=[O:16]
Reactant: CC=C(C=CCN)CC
Reactant: CN(C)S(=O)(=O)Cl
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CC=C(C=CCNS(=O)(=O)N(C)C)CC
Reaction time: 0.5 h

Procedure:
A mixture of N-(4-ethyl-2,4-hexadien-1-yl)phthalimide (3.0 g), hydrazine monohydrate (0.88 g), and ethanol (30 ml) was refluxed for 40 minutes under nitrogen atmosphere. After cooling, the precipitate was filtered and washed with ethanol. Evaporation of the filtrate gave a crystalline residue which was dissolved in 1N sodium hydroxide solution and extracted with dichloromethane. The organic extract was washed with water and brine, dried over anhydrous sodium sulfate, and evaporated to give 4-ethyl-2,4-hexadien-1-ylamine as an oil. To a mixture of crude 4-ethyl-2,4-hexadien-1-ylamine, triethylamine (1.79 g), and dichloromethane (30 ml) at 0° C. was added dropwise dimethylsulfamoyl chloride (2.03 g) during 10 minutes. After 30 minutes, triethylamine (0.6 g) and dimethylsulfamoyl chloride (0.85 g) were added to the reaction mixture. After 1 hour at 0° C., the reaction mixture was washed with water and aqueous sodium hydrogen carbonate solution, dried over anhydrous magnesium sulfate, and evaporated in vacuo. The residue was chromatographed on silica gel (dichloromethane-hexane, 7:3) to give N,N-dimethyl-N'-(4-ethyl-2,4-hexadien-1-yl)sulfamide (924 mg) as an oil.
Reaction SMILES: [O:1]=[C:2]1[C@@H:8]([NH:9]C(=O)OCC2C=CC=CC=2)[CH2:7][CH2:6][S:5][C@H:4]2[CH2:20][CH2:21][C@H:22](C(F)(F)F)[CH2:23][N:3]12.NC([C:35]([F:38])([F:37])[F:36])CCCCO.N[C@H]1CCS[C@H]2CC[C@H](C(F)(F)F)CN2C1=O>>[NH2:9][C@H:8]1[CH2:7][CH2:6][S:5][C@H:4]2[CH2:20][CH2:21][CH2:22][C@H:23]([C:35]([F:38])([F:37])[F:36])[N:3]2[C:2]1=[O:1]
Reactant: NC(CCCCO)C(F)(F)F
Reactant: O=C(N[C@H]1CCS[C@H]2CC[C@H](C(F)(F)F)CN2C1=O)OCc1ccccc1
Agent: N[C@H]1CCS[C@H]2CC[C@H](C(F)(F)F)CN2C1=O
Product: N[C@H]1CCS[C@H]2CCC[C@H](C(F)(F)F)N2C1=O

Procedure:
(4S,7R,10aS)-4-Amino-7-(trifluoromethyl)hexahydro-2H-pyrido[2,1-b][1,3]thiazepin-5(7H)-one (39 mg, 0.15 mmol) was synthesized as described for the preparation of Intermediate 58 using 5-amino-6,6,6-trifluorohexan-1-ol in step A followed by the preparation of Intermediate 60. Anal. Calcd. for C10H15F3N2OS m/z 268.3. found: 269.0 (M+H)+; 1H NMR (400 MHz, CDCl3) δ ppm 5.29 (dd, J=4.4, 2.8 Hz, 1H), 5.13-4.99 (m, 1H), 3.95 (dd, J=10.6, 3.6 Hz, 1H), 3.07 (ddd, J=14.5, 10.0, 3.3 Hz, 1H), 2.74 (ddd, J=14.6, 6.7, 3.3 Hz, 1H), 2.48-2.29 (m, 2H), 2.24 (ddt, J=13.8, 6.9, 3.4 Hz, 1H), 2.16-2.02 (m, 2H), 1.94-1.69 (m, 5H).