Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: C1(C[N:8]2[CH2:13][CH2:12][N:11]([C:14]3[CH:19]=[CH:18][C:17]([NH:20][C:21]([C:23]4[C:24]([C:29]5[CH:34]=[CH:33][C:32]([C:35]([F:38])([F:37])[F:36])=[CH:31][CH:30]=5)=[CH:25][CH:26]=[CH:27][CH:28]=4)=[O:22])=[CH:16][CH:15]=3)[CH2:10][CH2:9]2)C=CC=CC=1.[H][H]>CO.C1COCC1.[Pd]>[N:11]1([C:14]2[CH:15]=[CH:16][C:17]([NH:20][C:21]([C:23]3[C:24]([C:29]4[CH:34]=[CH:33][C:32]([C:35]([F:37])([F:36])[F:38])=[CH:31][CH:30]=4)=[CH:25][CH:26]=[CH:27][CH:28]=3)=[O:22])=[CH:18][CH:19]=2)[CH2:12][CH2:13][NH:8][CH2:9][CH2:10]1
Reactant: O=C(Nc1ccc(N2CCN(Cc3ccccc3)CC2)cc1)c1ccccc1-c1ccc(C(F)(F)F)cc1
Reactant: [H][H]
Agent: [Pd]
Solvent: CO
Solvent: C1CCOC1
Product: O=C(Nc1ccc(N2CCNCC2)cc1)c1ccccc1-c1ccc(C(F)(F)F)cc1
Yield: 49.5 %

Procedure:
A mixture of intermediate (5) (0.19 mole) in methanol (600 ml) and THF (600 ml) was hydrogenated overnight with Pd/C 10% (3 g) as a catalyst. After uptake of hydrogen (1 equivalent), the catalyst was filtered off and the filtrate was evaporated. The residue was triturated in DIPE. The precipitate was filtered off, dried, and dissolved in water. The mixture was alkalinized with Na2CO3 and then extracted with DCM. The organic layer was separated, dried, filtered and the solvent was evaporated. The residue was triturated in DIPE. The precipitate was filtered off and dried, yielding 40 g of N-[4-(1-piperazinyl)phenyl]-4′-(trifluoromethyl)-[1,1′-biphenyl]-2-carboxamide (intermediate 6).
Reaction SMILES: [C:1]1([OH:7])[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.[OH-].[Na+].Cl[C:11]1[N:16]=[C:15]([N:17]2[CH2:22][CH2:21][O:20][CH2:19][CH2:18]2)[N:14]=[C:13]([N:23]2[C:27]3[CH:28]=[CH:29][CH:30]=[CH:31][C:26]=3[N:25]=[C:24]2[CH:32]([F:34])[F:33])[N:12]=1.COCCOCCN(CCOCCOC)CCOCCOC>O.O1CCOCC1>[F:34][CH:32]([F:33])[C:24]1[N:23]([C:13]2[N:14]=[C:15]([N:17]3[CH2:18][CH2:19][O:20][CH2:21][CH2:22]3)[N:16]=[C:11]([O:7][C:1]3[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=3)[N:12]=2)[C:27]2[CH:28]=[CH:29][CH:30]=[CH:31][C:26]=2[N:25]=1
Reactant: Oc1ccccc1
Reactant: FC(F)c1nc2ccccc2n1-c1nc(Cl)nc(N2CCOCC2)n1
Agent: COCCOCCN(CCOCCOC)CCOCCOC
Agent: [Na+]
Agent: [OH-]
Solvent: O
Solvent: C1COCCO1
Product: FC(F)c1nc2ccccc2n1-c1nc(Oc2ccccc2)nc(N2CCOCC2)n1
Yield: 43.8 %

Procedure:
Phenol (200 mg, 21 mmol) and NaOH (85 mg, 21 mmol) were combined in water to give a clear solution, which was then evaporated to dryness. 1-[4-Chloro-6-(4-morpholinyl)-1,3,5-triazin-2-yl]-2-(difluoromethyl)-1H-benzimidazole (184 mg, 0.5 mmol) and tris[2-(2-methoxyethoxy)ethyl]amine (TDA-1; 16 mg, 0.05 mmol) were added and the mixture was heated under reflux in dioxane (10 mL) for 2 hr. After cooling, the mixture was diluted with water to give a white solid, which was collected and recrystallised from MeOH to give 93 mg (44% yield) of 2-(difluoromethyl)-1-[4-(4-morpholinyl)-6-phenoxy-1,3,5-triazin-2-yl]-1H-benzimidazole: mp 228-231° C.; 1H NMR (CDCl3) δ 8.06 (d, J=8.2 Hz, 1H), 7.84 (d, J=7.8 Hz, 1H), 7.49 (br t, J=7.9 Hz, 2H), 7.36 (br t, J=7.5 Hz, 2H), 7.30 (dt, J=7.6, 1.1 Hz, 1H), 7.22 (m, 2H), 7.11 (t, JHF=53.6 Hz, 1H), 3.99-3.93 (m, 4H), 3.86-3.79 (m, 4H); Anal. Calc. for C21H18F2N6O2: C, 59.4; H, 4.3; N, 19.8. Found: C, 59.65; H, 4.2; N, 19.9%.
Reaction SMILES: [CH2:1]([O:8][C:9]1[C:10](=[O:32])[C:11]([C:28]([O:30]C)=[O:29])=[CH:12][N:13]2[CH2:18][CH2:17][N:16]([CH2:19][C:20]3[CH:25]=[CH:24][CH:23]=[C:22]([Cl:26])[CH:21]=3)[C:15](=[O:27])[C:14]=12)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1>O1CCCC1.O.[OH-].[Li+]>[CH2:1]([O:8][C:9]1[C:10](=[O:32])[C:11]([C:28]([OH:30])=[O:29])=[CH:12][N:13]2[CH2:18][CH2:17][N:16]([CH2:19][C:20]3[CH:25]=[CH:24][CH:23]=[C:22]([Cl:26])[CH:21]=3)[C:15](=[O:27])[C:14]=12)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: COC(=O)c1cn2c(c(OCc3ccccc3)c1=O)C(=O)N(Cc1cccc(Cl)c1)CC2
Agent: [Li+]
Agent: [OH-]
Solvent: O
Solvent: C1CCOC1
Product: O=C(O)c1cn2c(c(OCc3ccccc3)c1=O)C(=O)N(Cc1cccc(Cl)c1)CC2
Yield: 86.5 %

Procedure:
Methyl 9-benzyloxy-2-(3-chlorobenzyl)-1,8-dioxo-1,3,4,8-tetrahydro-2H-pyrido[1,2-a]pyrazine-7-carboxylate (420 mg) was dissolved in tetrahydrofuran (8 ml)-water (2 ml), and 4N aqueous lithium hydroxide solution (0.58 ml) was added with stirring. After stirring at 70° C. for 1 hr, the mixture was concentrated. Water (5 ml) and then 5% aqueous potassium hydrogen sulfate solution (15 ml) were added with stirring. The precipitated crystals were collected by filtration to give 9-benzyloxy-2-(3-chlorobenzyl)-1,8-dioxo-1,3,4,8-tetrahydro-2H-pyrido[1,2-a]pyrazine-7-carboxylic acid (352 mg).
Reaction SMILES: [NH2:1][CH2:2][CH2:3][C@H:4]([OH:21])[C@@H:5]([NH:13][C:14]([O:16][C:17]([CH3:20])([CH3:19])[CH3:18])=[O:15])[CH2:6][CH:7]1[CH2:12][CH2:11][CH2:10][CH2:9][CH2:8]1.[CH3:22][CH:23]([CH3:28])[CH2:24][C:25](Cl)=[O:26].C(N(CC)CC)C>C(Cl)Cl>[CH3:22][CH:23]([CH3:28])[CH2:24][C:25]([NH:1][CH2:2][CH2:3][C@H:4]([OH:21])[C@@H:5]([NH:13][C:14]([O:16][C:17]([CH3:18])([CH3:20])[CH3:19])=[O:15])[CH2:6][CH:7]1[CH2:8][CH2:9][CH2:10][CH2:11][CH2:12]1)=[O:26]
Reactant: CC(C)(C)OC(=O)N[C@@H](CC1CCCCC1)[C@@H](O)CCN
Reactant: CC(C)CC(=O)Cl
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CC(C)CC(=O)NCC[C@H](O)[C@H](CC1CCCCC1)NC(=O)OC(C)(C)C
Temperature: 0 °C
Reaction time: 1 h

Procedure:
To (3S,4S)-1-amino-3-hydroxy-4-t-butyloxycarbonylamino-5-cyclohexylpentane (30.8 mg, 0.102 mmol) in dry methylene chloride (3 mL) at 0° C. was added 3-methyl-butyroyl chloride (0.123 mmol) and triethylamine (20.0 microliters, 0.143 mmol). The mixture was stirred at 0° C. for 1 hour, evaporated, taken up in methanol (3 mL) and treated with 1M NaOH (1 mL). After stirring for 1 hour, the mixture was diluted with ether, washed sequentially with 0.5M H3PO4, saturated NaHCO3 solution, and brine, and then dried over Na2SO4 and evaporated to afford the desired product.
Reaction SMILES: C(=O)([O-])[O-].[K+].[K+].Br[CH2:8][CH2:9][F:10].[C:11]([O:15][C:16]([N:18]1[CH2:23][CH2:22][NH:21][CH2:20][CH2:19]1)=[O:17])([CH3:14])([CH3:13])[CH3:12]>C(#N)C>[C:11]([O:15][C:16]([N:18]1[CH2:23][CH2:22][N:21]([CH2:8][CH2:9][F:10])[CH2:20][CH2:19]1)=[O:17])([CH3:14])([CH3:12])[CH3:13]
Reactant: CC(C)(C)OC(=O)N1CCNCC1
Reactant: FCCBr
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC#N
Product: CC(C)(C)OC(=O)N1CCN(CCF)CC1
Yield: 56.9 %

Procedure:
Potassium carbonate (1.85 g, 13.4 mmol) and 1-bromo-2-fluoroethane (440 PI, 5.9 mmol) were added to a solution of tert-butyl-1-piperazinecarboxylate (1 g, 5.4 mmol) in acetonitrile (12 ml). The reaction mixture was stirred at 65° C. for 3.5 hours after which time more 1-bromo-2-fluoroethane (160 μl, 2.1 mmol) was added. The reaction was heated for a further 3 hours then filtered to remove the inorganic solids. The filtrate was concentrated and the crude product was purified using column chromatography eluting with ethyl acetate to give 4-(2-fluoroethyl)-piperazine-1-carboxylic acid tert-butyl ester (714 mg, 57%).
Reaction SMILES: [CH:1]1[C:6](=[O:7])[C:5]([OH:8])=[CH:4][O:3][C:2]=1[CH2:9][OH:10].C(=O)([O-])[O-].[K+].[K+].[I-].[K+].Br[CH2:20][CH2:21][CH3:22]>CN(C)C=O>[OH:10][CH2:9][C:2]1[O:3][CH:4]=[C:5]([O:8][CH2:20][CH2:21][CH3:22])[C:6](=[O:7])[CH:1]=1
Reactant: O=c1cc(CO)occ1O
Reactant: CCCBr
Agent: O=C([O-])[O-]
Agent: [I-]
Agent: [K+]
Solvent: CN(C)C=O
Product: CCCOc1coc(CO)cc1=O
Temperature: 25 °C
Reaction time: 0.25 h

Procedure:
A mixture of kojic acid (28.4 g, 0.20 mole), 120 mL of N,N-dimethylformamide, potassium carbonate powder (27.6 g, 0.20 mole), potassium iodide (1.66 g, 0.01 mole), and 1-bromopropane (24.6 g, 0.20 mole) is stirred for 15 minutes at ambient temperature then stirred at 90° C. for 3 hours. The reaction mixture is cooled, evaporated to dryness in vacuo and then portioned between water and chloroform. The aqueous layer is extracted with chloroform (3×100 mL) and ethyl acetate (6×100 mL). The combined organics were dried with sodium sulfate and passed through a pad of magnesol and silica gel eluting with ethyl acetate. The eluate is evaporated in vacuo and crystallized with hexane/ethyl acetate (2/1) to give an off-white solid, 22.60 g, (61%); MS (ES+): m/z 185.3 (M+H).
Reaction SMILES: [CH3:1][N:2]([CH3:22])[C:3]1[CH:4]=[C:5]([CH:10]=[C:11]([N:19]([CH3:21])[CH3:20])[C:12]=1[N:13]1[CH2:18][CH2:17][CH2:16][CH2:15][CH2:14]1)[C:6](OC)=[O:7].O1CCCC1.[H-].[Al+3].[Li+].[H-].[H-].[H-]>C(OCC)(=O)C>[CH3:1][N:2]([CH3:22])[C:3]1[CH:4]=[C:5]([CH:10]=[C:11]([N:19]([CH3:21])[CH3:20])[C:12]=1[N:13]1[CH2:18][CH2:17][CH2:16][CH2:15][CH2:14]1)[CH2:6][OH:7]
Reactant: COC(=O)c1cc(N(C)C)c(N2CCCCC2)c(N(C)C)c1
Agent: [Al+3]
Agent: [H-]
Agent: [Li+]
Solvent: C1CCOC1
Solvent: CCOC(C)=O
Product: CN(C)c1cc(CO)cc(N(C)C)c1N1CCCCC1

Procedure:
A solution of 25 g. of methyl 3,5-bis(dimethylamino)-4-piperidinobenzoate in 150 ml. of absolute tetrahydrofuran was added dropwise to a solution of lithium aluminum hydride in 300 ml. of absolute tetrahydrofuran, and the mixture was boiled under reflux for 3 hours. After cooling, the excess lithium aluminum hydride was cautiously decomposed with 100 ml. of ethyl acetate and then with 3 ml. of water and the solution evaporated to dryness. The residue was taken up in water, the oily product extracted with ethyl acetate and the ethyl acetate solution dried and evaporated. After recrystallization from high-boiling petroleum ether, there was obtained 3,5-bis(dimethylamino)-4-piperidinobenzyl alcohol having a melting point of 90°-92° C.
Reaction SMILES: [NH2:1][CH2:2][C:3]([CH3:7])([CH3:6])[CH2:4][OH:5].[CH2:8]([O:15][C:16](ON1C(=O)CCC1=O)=[O:17])[C:9]1[CH:14]=[CH:13][CH:12]=[CH:11][CH:10]=1.O>O1CCCC1>[CH2:8]([O:15][C:16]([NH:1][CH2:2][C:3]([CH3:7])([CH3:6])[CH2:4][OH:5])=[O:17])[C:9]1[CH:14]=[CH:13][CH:12]=[CH:11][CH:10]=1
Reactant: CC(C)(CN)CO
Reactant: O=C(OCc1ccccc1)ON1C(=O)CCC1=O
Solvent: C1CCOC1
Solvent: O
Product: CC(C)(CO)CNC(=O)OCc1ccccc1
Temperature: 25 °C
Reaction time: 8 h
Yield: 100 %

Procedure:
To a solution of 3-amino-2,2-dimethyl-1-propanol (2 g) in tetrahydrofuran (20 mL) was added N-(benzyloxycarbonyloxy)-succinimide (7.25 g), and the mixture was stirred at room temperature overnight. The reaction mixture was poured into water, and the resulting mixture was extracted with ethyl acetate. The extract was washed with water and brine, and dried over anhydrous sodium sulfate. The solvent was removed under reduced pressure, and the residue was purified by column chromatography on silica gel (eluent: n-hexane/ethyl acetate=3/1-1/1) to give 3-benzyloxycarbonylamino-2,2-dimethyl-1-propanol (4.6 g) To this material were added carbon tetrachloride (40 mL), acetonitrile (40 mL), water (48 mL), sodium periodate (11.6 g) and ruthenium trichloride (0.2 g) successively, and the mixture was stirred at room temperature overnight. To the reaction mixture were added sodium periodate (11.6 g) and ruthenium trichloride (0.2 g), and the mixture was stirred at room temperature for 3 days. The reaction mixture was diluted with water, and the resulting mixture was extracted with ethyl acetate. The extract was dried over anhydrous sodium sulfate. The solvent was removed under reduced pressure, and the residue was dissolved in a saturated aqueous potassium carbonate solution. The solution was washed with ethyl acetate, and the aqueous layer was acidified with 2 mol/L hydrochloric acid. The mixture was extracted with ethyl acetate, and the extract was washed with water and brine, and dried over anhydrous sodium sulfate. The solvent was removed under reduced pressure to give 3-benzyloxycarbonylamino-2,2-di(methyl)propionic acid (3.6 g). This material was dissolved in tetrahydrofuran (25 mL). To the solution was added 1,1′-carbonylbis-1H-imidazole (3.39 g), and the mixture was stirred at room temperature for 1 hour. To the reaction mixture was added 28% aqueous ammonia solution (25 mL), and the mixture was stirred at room temperature for 1 hour. The reaction mixture was diluted with water, and the resulting mixture was extracted with ethyl acetate. The extract was washed with 1 mol/L hydrochloric acid, water and brine, and dried over anhydrous sodium sulfate. The solvent was removed under reduced pressure to give 3-benzyloxycarbonylamino-2,2-di(methyl)-propionamide (3.35 g). The obtained 3-benzyloxycarbonylamino-2,2-di(methyl)propionamide (0.13 g) was dissolved in methanol (5 mL). To the solution was added 10% palladium-carbon powder (30 mg), and the mixture was stirred at room temperature under a hydrogen atmosphere for 2 hours. The insoluble material was removed by filtration, and the filtrate was concentrated under reduced pressure to give the title compound (61 mg).
Reaction SMILES: [C:1]([C:9]1[N:13]([CH3:14])[C:12]([CH2:15][C:16]([O:18][CH2:19][CH3:20])=[O:17])=[CH:11][C:10]=1[CH3:21])(=[O:8])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[H-].[Na+].[F:24][C:25]1[CH:26]=[C:27]([N+:32]([O-:34])=[O:33])[CH:28]=[CH:29][C:30]=1F>CN(C=O)C>[C:1]([C:9]1[N:13]([CH3:14])[C:12]([CH:15]([C:30]2[CH:29]=[CH:28][C:27]([N+:32]([O-:34])=[O:33])=[CH:26][C:25]=2[F:24])[C:16]([O:18][CH2:19][CH3:20])=[O:17])=[CH:11][C:10]=1[CH3:21])(=[O:8])[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: O=[N+]([O-])c1ccc(F)c(F)c1
Reactant: CCOC(=O)Cc1cc(C)c(C(=O)c2ccccc2)n1C
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: CCOC(=O)C(c1ccc([N+](=O)[O-])cc1F)c1cc(C)c(C(=O)c2ccccc2)n1C
Temperature: 0 °C
Yield: 83.7 %

Procedure:
Ethyl 5-benzoyl-1,4-dimethylpyrrole-2-acetate (5.0 g, 17.5 mmol) [prepared as in Example 1, Step (a)], was dissolved in DMF (50 ml) and the solution was cooled in an ice bath to 0° C. under an argon atmosphere. Sodium hydride, 50%/mineral oil, (1.3 g, 27.1 mmol) was added, and after 5 min 3,4-difluoronitrobenzene (3.36 g, 21.1 mmol) was added to the reaction mixture. After 1 h the reaction mixture was poured into 10% HCl/ice and the product was extracted into ethyl acetate. The organic phase was washed with water, dried over sodium sulfate, and evaporated to dryness. Purification on a Florisil® column (hexane-ethyl acetate, 9:1) gave ethyl 2-(5-benzoyl-1,4-dimethylpyrrol-2-yl)-2-(2-fluoro-4-nitrophenyl)acetate (6.22 g, 84%) as a solid. ##STR19##
Reaction SMILES: [Cl:1][C:2]1[CH:10]=[CH:9][C:5]2[O:6][CH2:7][O:8][C:4]=2[C:3]=1[NH:11][C:12]1[C:20]2[C:19]3[CH2:21][NH:22][CH2:23][CH2:24][C:18]=3[NH:17][C:16]=2[N:15]=[CH:14][CH:13]=1.CCN(C(C)C)C(C)C.[CH:34]1([C:37](Cl)=[O:38])[CH2:36][CH2:35]1>ClCCCl>[Cl:1][C:2]1[CH:10]=[CH:9][C:5]2[O:6][CH2:7][O:8][C:4]=2[C:3]=1[NH:11][C:12]1[C:20]2[C:19]3[CH2:21][N:22]([C:37]([CH:34]4[CH2:36][CH2:35]4)=[O:38])[CH2:23][CH2:24][C:18]=3[NH:17][C:16]=2[N:15]=[CH:14][CH:13]=1
Reactant: O=C(Cl)C1CC1
Reactant: Clc1ccc2c(c1Nc1ccnc3[nH]c4c(c13)CNCC4)OCO2
Solvent: ClCCCl
Solvent: CCN(C(C)C)C(C)C
Product: O=C(C1CC1)N1CCc2[nH]c3nccc(Nc4c(Cl)ccc5c4OCO5)c3c2C1
Temperature: 25 °C
Yield: 35.3 %

Procedure:
(5-Chloro-benzo[1,3]-dioxol-4-yl)-(6,7,8,9-tetrahydro-5H-dipyrido[2,3-b;3′,4′-d]pyrrol-4-yl)-amine (100 mg, 0.29 mmol) and DIEA (0.15 mL, 0.88 mmol) were dissolved in 1,2-dichloroethane (2 mL) and stirred at room temperature. Cyclopropanecarbonyl chloride (0.03 mL, 0.35 mmol) was added dropwise, and the reaction was stirred for 1 h at room temperature. The reaction was concentrated. The crude material was dissolved in DMSO (3 mL) and filtered. The filtrate was purified directly via prep-LC-MS to provide 68 (42 mg, 35% yield) as a white fluffy solid. LC-MS (M+H=411, obsd.=411).
Reaction SMILES: [CH3:1][C:2]1[S:3][C:4](/[CH:17]=[CH:18]/[CH:19]([OH:25])[CH2:20][CH2:21][CH2:22][CH2:23][CH3:24])=[C:5]([CH2:7][CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][C:13]([O:15][CH3:16])=[O:14])[N:6]=1.[C:26](OC(=O)C)(=[O:28])[CH3:27]>N1C=CC=CC=1.O>[CH3:1][C:2]1[S:3][C:4](/[CH:17]=[CH:18]/[CH:19]([O:25][C:26](=[O:28])[CH3:27])[CH2:20][CH2:21][CH2:22][CH2:23][CH3:24])=[C:5]([CH2:7][CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][C:13]([O:15][CH3:16])=[O:14])[N:6]=1
Reactant: CC(=O)OC(C)=O
Reactant: CCCCCC(O)/C=C/c1sc(C)nc1CCCCCCC(=O)OC
Solvent: O
Solvent: c1ccncc1
Product: CCCCCC(/C=C/c1sc(C)nc1CCCCCCC(=O)OC)OC(C)=O
Reaction time: 24 h

Procedure:
To the solution of 367 mg of 2-methyl-4-(6-carbomethoxy-hexyl)-5-(3-hydroxy-1-trans-octenyl)-thiazole (Ic, R1 = CH3) in 4 ml of anhydrous pyridine, 1 ml of acetic anhydride was added. The reaction mixture was allowed to stand for 24 hours at room temperature, diluted with 50 ml of water and extracted with 3 × 15 ml of ethyl acetate. The ethyl acetate extract was washed with water, dried over sodium sulphate and evaporated in vacuo. The obtained 403 mg of evaporation residue was purified by preparative thin layer chromatography, using a silica gel layer as adsorbent and a mixture of 40 % ethyl acetate and 60 % n-heptane as running solvent. Thus, 290 mg of 2-methyl-4-(6-carbomethoxyhexyl)-5-(3-acetoxy-1-trans-octenyl)-thiazole (Ie, R1 = CH3) of chromatographic purity were obtained.
Reaction SMILES: [NH:1]([C:15]([O:17][C:18]([CH3:21])([CH3:20])[CH3:19])=[O:16])[C@H:2]([C:12]([OH:14])=O)[CH2:3][O:4][CH2:5][C:6]1[CH:11]=[CH:10][CH:9]=[CH:8][CH:7]=1.C1C=CC2N(O)N=NC=2C=1.C1CCC(N=C=NC2CCCCC2)CC1.Cl.[CH3:48][O:49][C:50](=[O:54])[C@@H:51]([CH3:53])[NH2:52].CCN(CC)CC>CCOC(C)=O>[NH:1]([C:15]([O:17][C:18]([CH3:21])([CH3:20])[CH3:19])=[O:16])[C@H:2]([C:12]([NH:52][C@@H:51]([C:50]([O:49][CH3:48])=[O:54])[CH3:53])=[O:14])[CH2:3][O:4][CH2:5][C:6]1[CH:7]=[CH:8][CH:9]=[CH:10][CH:11]=1
Reactant: CC(C)(C)OC(=O)N[C@@H](COCc1ccccc1)C(=O)O
Reactant: COC(=O)[C@@H](C)N
Agent: C(=NC1CCCCC1)=NC1CCCCC1
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: CCN(CC)CC
Solvent: CCOC(C)=O
Product: COC(=O)[C@@H](C)NC(=O)[C@H](COCc1ccccc1)NC(=O)OC(C)(C)C
Temperature: 25 °C
Reaction time: 8 h
Yield: 49 %

Procedure:
To a solution of Boc-Ser(OBn) (4.12 g, 13.95 mmol) in EtOAc (100 mL) at 0° C. was added HOBT (2.35 g, 15.35 mmol) and DCC (3.17 g, 15.35 mmol). D-Alanine methyl ester hydrochloride (1.95 g, 13.95 mmol) was added followed by Et3N (2.14 mL, 15.35 mmol). The mixture was allowed to warm to room temperature and stirred overnight. The mixture was filtered, and the filtrate was washed with saturated aqueous NaHCO3, brine, dried (MgSO4), and concentrated. Flash chromatography (40% EtOAc/hexane) gave 2.60 g of the title compound as a colorless oil; CI-MS 381 (m+1).
Reaction SMILES: [C:1]([C:3]1[N:4]=[C:5]2[C:18](=[N:19][OH:20])[C:17]3[CH:16]=[CH:15][CH:14]=[CH:13][C:12]=3[C:6]2=[N:7][C:8]=1[C:9]([NH2:11])=[O:10])#[N:2].[C:21](Cl)(=[O:23])[CH3:22].O>N1C=CC=CC=1>[C:1]([C:3]1[N:4]=[C:5]2[C:18](=[N:19][O:20][C:21](=[O:23])[CH3:22])[C:17]3[CH:16]=[CH:15][CH:14]=[CH:13][C:12]=3[C:6]2=[N:7][C:8]=1[C:9]([NH2:11])=[O:10])#[N:2]
Reactant: N#Cc1nc2c(nc1C(N)=O)-c1ccccc1C2=NO
Reactant: CC(=O)Cl
Solvent: c1ccncc1
Solvent: O
Product: CC(=O)ON=C1c2ccccc2-c2nc(C(N)=O)c(C#N)nc21
Temperature: 25 °C
Reaction time: 16 h
Yield: 21.7 %

Procedure:
To a solution of 33 (1.0 g, 3.77 mmol) in dry pyridine (30 ml) cooled at 0° C., acetyl chloride (0.8 ml, 11.3 mmol) was added dropwise and the mixture was stirred 16 h at room temperature. Water (40 ml) was added and the precipitate was collected by filtration. The crude was purified by flash chromatography (CH2Cl2/acetone/MeOH 8:2:0.5) and triturated with Et2O/CH2Cl2/MeOH, affording 35 (251 mg, 21%) as yellow solid as single isomer. 1H NMR (300 MHz, DMSO d6): δ 8.12 (d, 1H), 7.91 (m, 2H), 7.77 (ddd, 1H), 7.43 (bs, 2H), 2.27 (s, 3H). ESI+MS: calcd for C15H9N5O3: 307.27; found: 308.1 (MH+).
Reaction SMILES: Br[C:2]1[C:3](C2C=CN=CC=2)=[N:4][N:5]([CH:7]2[CH2:12][CH2:11][N:10]([C:13]([O:15][CH2:16][C:17]3[CH:22]=[CH:21][CH:20]=[CH:19][CH:18]=3)=[O:14])[CH2:9][CH2:8]2)[CH:6]=1.[CH2:29]([O:36]/[N:37]=[C:38]1\[CH2:39][CH2:40][C:41]2[C:46]\1=[CH:45][CH:44]=[C:43](B(O)O)[CH:42]=2)[C:30]1[CH:35]=[CH:34][CH:33]=[CH:32][CH:31]=1.C(=O)([O-])[O-].[K+].[K+]>C(#N)C.O>[CH2:29]([O:36]/[N:37]=[C:38]1\[CH2:39][CH2:40][C:41]2[C:46]\1=[CH:45][CH:44]=[C:43]([C:2]1[CH:3]=[N:4][N:5]([CH:7]3[CH2:8][CH2:9][N:10]([C:13]([O:15][CH2:16][C:17]4[CH:22]=[CH:21][CH:20]=[CH:19][CH:18]=4)=[O:14])[CH2:11][CH2:12]3)[C:6]=1[C:7]1[CH:12]=[CH:11][N:10]=[CH:9][CH:8]=1)[CH:42]=2)[C:30]1[CH:35]=[CH:34][CH:33]=[CH:32][CH:31]=1
Reactant: O=C(OCc1ccccc1)N1CCC(n2cc(Br)c(-c3ccncc3)n2)CC1
Reactant: OB(O)c1ccc2c(c1)CC/C2=N\OCc1ccccc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC#N
Solvent: O
Product: O=C(OCc1ccccc1)N1CCC(n2ncc(-c3ccc4c(c3)CC/C4=N\OCc3ccccc3)c2-c2ccncc2)CC1
Temperature: 80 °C
Yield: 166.1 %

Procedure:
To benzyl 4-(4-bromo-3-(pyridin-4-yl)-1H-pyrazol-1-yl)piperidine-1-carboxylate (0.32 g; Example 5, Step 1) in 10 mL acetonitrile and 3 mL water was added 0.315 g (E)-1-(benzyloxyimino)-2,3-dihydro-1H-inden-5-ylboronic acid (prepared as described in example 2, step 4) and 0.30 g potassium carbonate. The reaction mixture was purged with nitrogen and 84 mg tetrakis(triphenyphosphine)palladium(0) catalyst was added. The reaction mixture heated to 80° C. for 2 hours, filtered through celite, and the filter cake was washed with acetonitrile. The filtrate was evaporated under vacuum to yield crude product. The residue was purified by chromatography, eluting with ethyl acetate to afford 0.36 g (83% yield) product as a colorless oil. 1H NMR (CDCl3) was consistent with the desired structure. LC/MS showed one peak with a M+1 molecular ion of m/z 598.3 by positive ESI.
Reaction SMILES: C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.CC(OC(/N=N/C(OC(C)C)=O)=O)C.[Cl:34][C:35]1[CH:36]=[C:37]([OH:46])[C:38]([CH3:45])=[C:39]([CH:44]=1)[C:40]([O:42][CH3:43])=[O:41].[CH2:47]([NH:54][C:55]([C@H:57]1[CH2:62][CH2:61][C@@H:60](O)[CH2:59][CH2:58]1)=[O:56])[C:48]1[CH:53]=[CH:52][CH:51]=[CH:50][CH:49]=1>C1COCC1>[CH2:47]([NH:54][C:55]([C@H:57]1[CH2:62][CH2:61][C@H:60]([O:46][C:37]2[C:38]([CH3:45])=[C:39]([CH:44]=[C:35]([Cl:34])[CH:36]=2)[C:40]([O:42][CH3:43])=[O:41])[CH2:59][CH2:58]1)=[O:56])[C:48]1[CH:53]=[CH:52][CH:51]=[CH:50][CH:49]=1
Reactant: O=C(NCc1ccccc1)[C@H]1CC[C@@H](O)CC1
Reactant: COC(=O)c1cc(Cl)cc(O)c1C
Agent: CC(C)OC(=O)/N=N/C(=O)OC(C)C
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: C1CCOC1
Product: COC(=O)c1cc(Cl)cc(O[C@H]2CC[C@H](C(=O)NCc3ccccc3)CC2)c1C
Temperature: 25 °C
Reaction time: 0.25 h

Procedure:
To a cooled (0° C. ice bath) solution of triphenylphosphine (392 mg, 1.495 mmol) in THF (10 mL) was added DIAD (0.291 mL, 1.495 mmol). The reaction was stirred for 15 minutes (became a suspension). To this suspension with stirring was added a solution of methyl 5-chloro-3-hydroxy-2-methylbenzoate (250 mg, 1.246 mmol) and (cis)-N -benzyl-4-hydroxycyclohexanecarboxamide (350 mg, 1.500 mmol) in THF (5 mL) in one portion. The reaction was allowed to warm to room temperature and stirred overnight, at which time the reaction was concentrated in vacuo. The residue was purified by silica gel chromatography (Analogix, SF25-60 g, 10 to 60% EtOAc in hexanes). The resulting solid was triturated with 10% methanol in water, filtered, washed with water, and dried under vacuum to give methyl 3-(((trans)-4-(benzylcarbamoyl)cyclohexyl)oxy)-5-chloro-2-methylbenzoate (180 mg, 0.433 mmol, 34.7% yield) as a white solid. 1H NMR (400 MHz, DMSO-d6) δ 8.33 (t, J=5.94 Hz, 1H), 7.38 (d, J=2.02 Hz, 1H), 7.27-7.35 (m, 3H), 7.16-7.27 (m, 3H), 4.37-4.49 (m, 1H), 4.27 (d, J=5.81Hz, 2H), 3.82 (s, 3H), 2.25 (s, 3H), 1.97-2.16 (m, 3H), 1.75-1.89 (m, 2H), 1.53-1.69 (m, 2H), 1.30-1.47 (m, 2H). MS(ES) [M+H]+ 259.0 (weak).
Reaction SMILES: [C:1]1(=[O:13])[CH2:12][CH2:11][CH2:10][CH2:9][CH2:8][CH2:7][CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1.[C:14](=O)([O-])[O-:15].[K+].[K+].C=O>C(#N)C.O>[OH:15][CH2:14][CH:2]1[CH2:3][CH2:4][CH2:5][CH2:6][CH2:7][CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][C:1]1=[O:13]
Reactant: O=C([O-])[O-]
Reactant: O=C1CCCCCCCCCCC1
Agent: C=O
Agent: [K+]
Solvent: CC#N
Solvent: O
Product: O=C1CCCCCCCCCCC1CO
Temperature: 40 °C
Reaction time: 4 h

Procedure:
To a solution of cyclododecanone (1) (5.0 g, 27.47 mmol, 1 equiv) and potassium carbonate (0.06 g, 0.41 mmol, 0.015 equiv) in acetonitrile (20 mL) and water (2 mL) was added formaldehyde (37% in water) (4.2 mL, 52.20 mmol, 1.9 equiv) at 40° C. dropwise. The reaction was stirred at 40° C. for 4 hours, then cooled to room temperature and extracted with diethyl ether (3×50 mL). The combined organic layers were dried over sodium sulfate, filtered, concentrated under reduced pressure. The crude product was purified on an AnaLogix system using a gradient of 0 to 30% ethyl acetate in heptanes to give the desired product as a clear oil, which slowly solidifies to a white solid (2.5 g, 43% yield).