Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([S:8]([N:11]2[C:17]3[CH:18]=[CH:19][CH:20]=[CH:21][C:16]=3[CH2:15][CH2:14][CH2:13][CH2:12]2)(=[O:10])=[O:9])=[CH:4][C:3]=1[N:22]1[C:26]2=[N:27][C:28]([C:32](=[NH:35])[NH:33][OH:34])=[CH:29][C:30]([CH3:31])=[C:25]2[NH:24][C:23]1=[O:36].[C:37](N1C=CN=C1)(N1C=CN=C1)=[O:38].[H-].[Na+].Cl>CN(C)C=O.O>[Cl:1][C:2]1[CH:7]=[CH:6][C:5]([S:8]([N:11]2[C:17]3[CH:18]=[CH:19][CH:20]=[CH:21][C:16]=3[CH2:15][CH2:14][CH2:13][CH2:12]2)(=[O:9])=[O:10])=[CH:4][C:3]=1[N:22]1[C:26]2=[N:27][C:28]([C:32]3[NH:35][C:37](=[O:38])[O:34][N:33]=3)=[CH:29][C:30]([CH3:31])=[C:25]2[NH:24][C:23]1=[O:36]
Reactant: Cc1cc(C(=N)NO)nc2c1[nH]c(=O)n2-c1cc(S(=O)(=O)N2CCCCc3ccccc32)ccc1Cl
Reactant: O=C(n1ccnc1)n1ccnc1
Agent: Cl
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: O
Product: Cc1cc(-c2noc(=O)[nH]2)nc2c1[nH]c(=O)n2-c1cc(S(=O)(=O)N2CCCCc3ccccc32)ccc1Cl
Temperature: 25 °C
Reaction time: 1 h
Yield: 59.1 %

Procedure:
To a solution of 3-[2-chloro-5-(2,3,4,5-tetrahydro-1H-1-benzoazepin-1-ylsulfonyl)-phenyl]-5-hydroxycarbamimidoyl-7-methyl-1,3-dihydro-2H-imidazo[4,5-b]pyridin-2-one (0.1 g) in N,N-dimethylformamide (2 mL) was added 1,1′-carbonyldiimidazole (62 mg) at room temperature. To the mixture was added sodium hydride (55%, 38 mg) under ice-cooling, and the mixture was stirred at room temperature for 1 hour. To the reaction mixture was added water under ice-cooling, and the mixture was stirred for 30 minutes. The mixture was acidified by adding 1 mol/L hydrochloric acid, and the resulting mixture was extracted with ethyl acetate. The extract was washed with water and brine, and dried over anhydrous magnesium sulfate. The solvent was removed under reduced pressure to give the title compound (62 mg).
Reaction SMILES: [CH3:1][CH2:2][CH2:3][CH2:4][CH2:5]/[CH:6]=[CH:7]\[CH2:8]/[CH:9]=[CH:10]\[CH:11]=[CH:12]\[CH:13]=[CH:14]\[C@@H:15]1[O:17][C@H:16]1[CH2:18][CH2:19][CH2:20][C:21]([OH:23])=[O:22].CS(C)=[O:26]>>[CH3:1][CH2:2][CH2:3][CH2:4][CH2:5]/[CH:6]=[CH:7]\[CH2:8][C@@H:9]([OH:26])/[CH:10]=[CH:11]/[CH:12]=[CH:13]/[CH:14]=[CH:15]\[C@@H:16]([OH:17])[CH2:18][CH2:19][CH2:20][C:21]([OH:23])=[O:22]
Reactant: CCCCC/C=C\C/C=C\C=C\C=C\[C@@H]1O[C@H]1CCCC(=O)O
Reactant: CS(C)=O
Product: CCCCC/C=C\C[C@@H](O)/C=C/C=C/C=C\[C@@H](O)CCCC(=O)O
Reaction time: 0.03 h

Procedure:
Immediately before the assay, LTA4 was diluted to a concentration of 10 μM in assay buffer (without DMSO) and added to the reaction mixture to a final concentration of 2 μM to initiate the enzyme reaction. After incubation for 120 sec at room temperature, the reaction was stopped by ading 2 volumes of chilled quenching buffer, containing acetonitril with 1% acetic acid and 225 nM LTB4-d4 (Biomol). The samples were then kept at 4° C. over night to complete protein precipitation and centrifuged for 15 min at 1800 g. LTB4 formed was measured by LC-MS/MS using LTB4-d4 as an internal standard and an external LTB4 standard (Biomol) as reference. Briefly, the analyte was separated from LTB4 isomers formed by spontaneous hydrolysis of LTA4 using isocratic elution (modified protocol from Mueller et al. (1996), J. Biol. Chem. 271, 24345-24348) on a HPLC system (Waters, Milford, Mass.) and analyzed on a tandem quadrupole mass spectrometer (Waters). MRM transitions followed on 2 channels were 335.2>195.3 (LTB4) and 339.2>197.3 (LTB4-d4). Based on the amounts of LTB4 found at each inhibitor concentration, a dose-response curve was fitted to the data and an IC50 value was calculated.
Reaction SMILES: [C:1]1([C:7]([C:18]2[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=2)=[CH:8][S:9]([C:12]2[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=2)(=[O:11])=[O:10])[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.[Li]CCCC.[CH2:29]=[O:30]>C1COCC1>[C:1]1([C:7]([C:18]2[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=2)=[C:8]([S:9]([C:12]2[CH:13]=[CH:14][CH:15]=[CH:16][CH:17]=2)(=[O:10])=[O:11])[CH2:29][OH:30])[CH:2]=[CH:3][CH:4]=[CH:5][CH:6]=1
Reactant: O=S(=O)(C=C(c1ccccc1)c1ccccc1)c1ccccc1
Reactant: C=O
Agent: [Li]CCCC
Solvent: C1CCOC1
Product: O=S(=O)(C(CO)=C(c1ccccc1)c1ccccc1)c1ccccc1
Temperature: -78 °C
Reaction time: 0.5 h
Yield: 34 %

Procedure:
To a stirred solution of 1.25 g (3.90 mmol) of 2,2-diphenyl-1-(phenylsulfonyl) ethene in 20 mL of dry THF at -78° C., was added dropwise under a nitrogen atmosphere 2.8 mL of 1.4M n-BuLi (3.90 mmol). The dark black solution was stirred at -78° C. for 30 minutes. Gaseous fomaldehyde, generated by heating paraformaldehyde at 170° C., was passed through a 5-mm tube into the reaction mixture with the aid of a slow stream of nitrogen at -78° C. for 30 minutes. The mixture was allowed to come to room temperature over a period of 30 minutes while continuing to pass formaldehyde through the reaction mixture until a pale yellow color was observed. The mixture was stirred overnight at room temperature. The mixture was quenched with 50 mL of 5% HCl, and extracted with three 25-mL portions of CH2Cl2. The organic layer was dried over MgSO4, filtered, and the solvent removed in vacuo from a water bath at 45° C. The resulting crude oil was flash chromatographed on silica gel (230-400 mesh, 5×16-cm column) with 30% ether/Skelly B as eluant to give 0.47 g (34%) of the colorless alcohol. In a melting point capillary the compound does not melt but decomposes above 290° C. with blackening; IR (KBr) cm-1 3480, 3040, 1590, 1480, 1440, 1370, 1280, 1130, 1020, 960, 790, 730, 700, 680, 610; 1H NMR (CDCl3) δ 3.47 (t, 1H, OH), 4.61 (d, 2H, CH2O), 6.75-7.58 (m, 15H, phenyl).
Reaction SMILES: [C:1]1([NH:7][C:8]2([C:21]([O-:23])=[O:22])[CH2:13][CH2:12][N:11]([CH2:14][C:15]3[CH:20]=[CH:19][CH:18]=[CH:17][CH:16]=3)[CH2:10][CH2:9]2)[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.[Na+].[CH3:25]N(C)P(=O)(N(C)C)N(C)C.IC>CC1C=CC=CC=1>[C:1]1([NH:7][C:8]2([C:21]([O:23][CH3:25])=[O:22])[CH2:9][CH2:10][N:11]([CH2:14][C:15]3[CH:16]=[CH:17][CH:18]=[CH:19][CH:20]=3)[CH2:12][CH2:13]2)[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1
Reactant: CN(C)P(=O)(N(C)C)N(C)C
Reactant: O=C([O-])C1(Nc2ccccc2)CCN(Cc2ccccc2)CC1
Agent: [Na+]
Solvent: Cc1ccccc1
Solvent: CI
Product: COC(=O)C1(Nc2ccccc2)CCN(Cc2ccccc2)CC1
Temperature: 70 °C
Reaction time: 21 h

Procedure:
A mixture of 66.4 parts of sodium 4-(phenylamino)-1-(phenylmethyl)-4-piperidinecarboxylate in 375 parts of hexamethylphosphoric triamide is heated to 70° C. After cooling to 10° C, 31.2 parts of iodomethane are added (slightly exothermic reaction). The whole is stirred for 21 hours at room temperature. The reaction mixture is diluted with 360 parts of methylbenzene. The whole is washed with water and the layers are separated. The aqueous phase is washed with methylbenzene. The combined organic layers are washed successively once with 300 parts of a 10% sodium hydroxide solution and twice with 300 parts of water, dried, filtered and evaporated, yielding methyl 4-(phenylamino)-1 (phenylmethyl)-4-piperidinecarboxylate as a residue.
Reaction SMILES: [N+:1]([C:4]1[N:5]=[CH:6][N:7]([C@H:9]([CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH3:18])[C:10]([OH:12])=[O:11])[CH:8]=1)([O-:3])=[O:2].[CH3:19]C1C=CC(S(O)(=O)=O)=CC=1>CO.C(OCC)(=O)C>[CH3:19][O:11][C:10](=[O:12])[C@H:9]([N:7]1[CH:8]=[C:4]([N+:1]([O-:3])=[O:2])[N:5]=[CH:6]1)[CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH3:18]
Reactant: CCCCCC[C@H](C(=O)O)n1cnc([N+](=O)[O-])c1
Reactant: Cc1ccc(S(=O)(=O)O)cc1
Solvent: CO
Solvent: CCOC(C)=O
Product: CCCCCC[C@H](C(=O)OC)n1cnc([N+](=O)[O-])c1
Yield: 2813.6 %

Procedure:
(R)-2-(4-nitro-1H-imidazol-1-yl)-octanoic acid (16.0 g, 63.0 mmol) was dissolved in 1L of anhydrous methanol. To this solution was added pTsOH (300 mg). The reaction was then heated to reflux for 16 hours. Upon cooling, the solvent was removed in vacuo, to give an oil that was dissolved in 300 mL of ethyl acetate. The solution was washed (2×250 mL) with saturated NaHCO3 solution The organic was then dried (Na2SO4) and concentrated in vacuo to provide 13.2 g (78%) of (R)-methyl-2-(4-nitro-1H-imidazol-l-yl)-octanoate as an amber oil.
Reaction SMILES: [N:1]1([CH2:10][C:11]2[N:15]3[CH2:16][CH2:17][O:18][C:19]4[CH:24]=[CH:23][C:22](Br)=[CH:21][C:20]=4[C:14]3=[N:13][C:12]=2[C:26]([NH2:28])=[O:27])[C:5]2=[N:6][CH:7]=[CH:8][CH:9]=[C:4]2[CH:3]=[N:2]1.BrC1C=CC2OCCN3C(CN4C=CN=C4C)=C(C(N)=O)N=C3C=2C=1.N1C2C(=CC=NC=2)C=N1.[CH3:63][C:64]([OH:68])([C:66]#[CH:67])[CH3:65]>>[N:1]1([CH2:10][C:11]2[N:15]3[CH2:16][CH2:17][O:18][C:19]4[CH:24]=[CH:23][C:22]([C:67]#[C:66][C:64]([OH:68])([CH3:65])[CH3:63])=[CH:21][C:20]=4[C:14]3=[N:13][C:12]=2[C:26]([NH2:28])=[O:27])[C:5]2=[N:6][CH:7]=[CH:8][CH:9]=[C:4]2[CH:3]=[N:2]1
Reactant: C#CC(C)(C)O
Reactant: NC(=O)c1nc2n(c1Cn1ncc3cccnc31)CCOc1ccc(Br)cc1-2
Agent: Cc1nccn1Cc1c(C(N)=O)nc2n1CCOc1ccc(Br)cc1-2
Agent: c1cc2cn[nH]c2cn1
Product: CC(C)(O)C#Cc1ccc2c(c1)-c1nc(C(N)=O)c(Cn3ncc4cccnc43)n1CCO2
Yield: 40 %

Procedure:
Similar to as described in General Procedure G, 3-((1H-pyrazolo[3,4-b]pyridin-1-yl)methyl)-10-bromo-5,6-dihydrobenzo[f]imidazo[1,2-d][1,4]oxazepine-2-carboxamide (prepared similarly as described in the synthesis of 10-bromo-3-((2-methyl-1H-imidazol-1-yl)methyl)-5,6-dihydrobenzo[f]imidazo[1,2-d][1,4]oxazepine-2-carboxamide replacing 2-methylimidazole with 6-azaindazole) was reacted with 2-methylbut-3-yn-2-ol to give the titled compound as a colorless solid (21 mg, 40%).
Reaction SMILES: C1(N=C=O)C=CC(N=C=O)=CC=1.[C:13]([C:15]1[CH:20]=[CH:19][CH:18]=[CH:17][C:16]=1[NH:21][C:22](=[O:24])[CH3:23])#[CH:14].[CH2:25]([O:27][C:28](=[O:37])[CH2:29][CH2:30][CH2:31][CH2:32][CH2:33][N+:34]([O-])=[O:35])[CH3:26].C(N(CC)CC)C>C1(C)C=CC=CC=1>[CH2:25]([O:27][C:28](=[O:37])[CH2:29][CH2:30][CH2:31][CH2:32][C:33]1[CH:14]=[C:13]([C:15]2[CH:20]=[CH:19][CH:18]=[CH:17][C:16]=2[NH:21][C:22](=[O:24])[CH3:23])[O:35][N:34]=1)[CH3:26]
Reactant: C#Cc1ccccc1NC(C)=O
Reactant: CCOC(=O)CCCCC[N+](=O)[O-]
Agent: O=C=Nc1ccc(N=C=O)cc1
Solvent: Cc1ccccc1
Solvent: CCN(CC)CC
Product: CCOC(=O)CCCCc1cc(-c2ccccc2NC(C)=O)on1
Yield: 116.6 %

Procedure:
Add 1,4-phenylenediisocyanate (5.15 g, 32.2 mmol) to a stirred solution of N-(2-ethynyl-phenyl)-acetamide (2.56 g, 16.1 mmol) and 6-nitro-hexanoic acid ethyl ester (4.56 g, 24.1 mmol) in toluene (200 mL, anhydrous) and stir under N2. Add triethylamine (4.5 mL, 32.2 mmol) and heat to reflux under N2 overnight. Filter mixture through a pad of Celite® and rinse with toluene. Concentrate to get 6.2 g yellow oil. Adsorb on SiO2 and purify the residue by flash chromatography on silica gel eluting with 0-60% EtOAc/hexanes to afford the title compound (4.02 g, 76%). Correct regioisomer is confirmed by NOESY. MS (IS) 331 (M+1)+.
Reaction SMILES: [H-].[Na+].[F:3][C:4]1[CH:9]=[CH:8][C:7]([C:10]2[C:14]([CH2:15][OH:16])=[C:13]([CH3:17])[O:12][N:11]=2)=[CH:6][CH:5]=1.Cl[C:19]1[CH:28]=[CH:27][C:22]([C:23]([O:25][CH3:26])=[O:24])=[CH:21][N:20]=1.[Cl-].[Na+]>C1COCC1>[CH3:26][O:25][C:23](=[O:24])[C:22]1[CH:27]=[CH:28][C:19]([O:16][CH2:15][C:14]2[C:10]([C:7]3[CH:6]=[CH:5][C:4]([F:3])=[CH:9][CH:8]=3)=[N:11][O:12][C:13]=2[CH3:17])=[N:20][CH:21]=1
Reactant: Cc1onc(-c2ccc(F)cc2)c1CO
Reactant: COC(=O)c1ccc(Cl)nc1
Agent: [Cl-]
Agent: [H-]
Agent: [Na+]
Solvent: C1CCOC1
Product: COC(=O)c1ccc(OCc2c(-c3ccc(F)cc3)noc2C)nc1
Temperature: 25 °C
Reaction time: 8 h
Yield: 43 %

Procedure:
To a suspension of sodium hydride (55% dispersion in mineral oil, 852 mg, 20 mmol) in THF (27 mL) was added a solution of [3-(4-fluoro-phenyl)-5-methyl-isoxazol-4-yl]-methanol (103 mg, 0.55 mmol) (3.68 g, 18 mmol) in THF (54 mL) at 0° C. and the reaction mixture warmed to room temperature over 30 min. Then a solution of methyl 6-chloronicotinate (3.35 g, 20 mmol) in THF (1.5 mL) was added dropwise at 0° C. and the reaction mixture was stirred at room temperature overnight. The reaction mixture was then poured into aqueous sodium chloride (saturated) and the mixture was extracted with ethyl acetate. The combined organic layers were then washed with water and brine and then dried over sodium sulfate, filtered and evaporated. Purification by chromatography (SiO2, heptane:ethyl acetate=7:3) afforded the title compound (81 mg, 47%) which was obtained as a light yellow solid. MS: m/e=343.3 [M+H]+.
Reaction SMILES: [H-].[Na+].[I-].[CH3:4][S+](C)(C)=O.[C:9]([C:13]1[CH:18]=[CH:17][C:16]([CH2:19][CH2:20][CH:21]=[O:22])=[CH:15][C:14]=1[NH:23][C:24](=[O:40])[CH2:25][CH:26]1[C:39]2[CH:38]=[CH:37][CH:36]=[CH:35][C:34]=2[O:33][C:32]2[C:27]1=[CH:28][CH:29]=[CH:30][CH:31]=2)([CH3:12])([CH3:11])[CH3:10]>O1CCCC1.C(OCC)(=O)C>[C:9]([C:13]1[CH:18]=[CH:17][C:16]([CH2:19][CH2:20][CH:21]2[CH2:4][O:22]2)=[CH:15][C:14]=1[NH:23][C:24](=[O:40])[CH2:25][CH:26]1[C:39]2[CH:38]=[CH:37][CH:36]=[CH:35][C:34]=2[O:33][C:32]2[C:27]1=[CH:28][CH:29]=[CH:30][CH:31]=2)([CH3:12])([CH3:10])[CH3:11]
Reactant: CC(C)(C)c1ccc(CCC=O)cc1NC(=O)CC1c2ccccc2Oc2ccccc21
Reactant: C[S+](C)(C)=O
Agent: [H-]
Agent: [I-]
Agent: [Na+]
Solvent: C1CCOC1
Solvent: CCOC(C)=O
Product: CC(C)(C)c1ccc(CCC2CO2)cc1NC(=O)CC1c2ccccc2Oc2ccccc21
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 64.7 %

Procedure:
A suspension of 690 mg (15.8 mmol) of sodium hydride (as a 55% w/w dispersion in mineral oil, which had previously been washed with hexane) in 10 ml of dimethyl sulfoxide was stirred for 30 minutes, after which 2.66 g (12.1 mmol) of trimethylsulfoxonium iodide were added. The resulting mixture was stirred for 1 hour at 40° C., and then a solution of 4.50 g (10.5 mmol) of N-[2-t-butyl-5-(3-oxopropyl)phenyl]-2-(9H-xanthen-9-yl)acetamide (prepared as described in Preparation 19) in 25 ml of tetrahydrofuran was added dropwise over a period of 5 minutes. The reaction mixture was then stirred for 1 hour, after which the reaction mixture was cooled to room temperature and then diluted with ethyl acetate. The diluted mixture was washed several times with water and once with a saturated aqueous solution of sodium chloride. The organic phase was dried over anhydrous magnesium sulfate, and the solvent was removed by distillation under reduced pressure. The resulting residue was purified by column chromatography through 250 g of silica gel, using a 9:1 by volume mixture of methylene chloride and ethyl acetate as the eluent, to give 3.00 g (yield 65%) of the title compound as crystals, melting at 156°-157° C. (after recrystallization from a mixture of ethyl acetate and hexane).
Reaction SMILES: [C:1]([NH:4][CH:5]1[CH2:14][CH2:13][C:12]2[C:7](=[CH:8][CH:9]=[CH:10][CH:11]=2)[C:6]1=[O:15])(=[O:3])[CH3:2].[BH4-].[Na+].C(O)(=O)C>C(O)C>[C:1]([NH:4][C@@H:5]1[CH2:14][CH2:13][C:12]2[C:7](=[CH:8][CH:9]=[CH:10][CH:11]=2)[C@H:6]1[OH:15])(=[O:3])[CH3:2]
Reactant: CC(=O)NC1CCc2ccccc2C1=O
Agent: [BH4-]
Agent: [Na+]
Solvent: CCO
Solvent: CC(=O)O
Product: CC(=O)N[C@@H]1CCc2ccccc2[C@H]1O
Temperature: 25 °C
Reaction time: 0.5 h

Procedure:
To a solution of the 2-acetamido-3,4-dihydronaphthalen-1(2H)-one from Step A in absolute ethanol (150 ml) was added sodium borohydride (2.0 gms, 0.05 m) in portions. The reaction mixture was stirred at room temperature for 1/2 hour. Acetic acid was added dropwise to destroy the excess sodium borohydride. The reaction mixture was poured into water and extracted with ethyl acetate (3×150 ml). The ethyl acetate was washed with saturated aqueous sodium chloride (150 ml) and dried over anhydrous sodium sulfate. After filtration the solvent was removed under reduced pressure to yield 5.5 gms (54%, over Steps A and B), of product as a solid.
Reaction SMILES: CC(OC([NH:8][CH2:9][C:10]([OH:12])=[O:11])=O)(C)C.C(N=C=NC(C)C)(C)C.[CH3:22][CH2:23][C@@:24]1([OH:47])[C:29](=[O:30])[O:28][CH2:27][C:26]2[C:31]([N:33]3[C:45](=[CH:46][C:25]1=2)[C:44]1[N:43]=[C:42]2[C:37]([CH:38]=[CH:39][CH:40]=[CH:41]2)=[CH:36][C:35]=1[CH2:34]3)=[O:32]>C(Cl)Cl.CN(C)C1C=CN=CC=1.CS(C)=O>[CH3:22][CH2:23][C@@:24]1([OH:47])[C:29](=[O:30])[O:28][CH2:27][C:26]2[C:31]([N:33]3[C:45](=[CH:46][C:25]1=2)[C:44]1[N:43]=[C:42]2[C:37]([CH:38]=[CH:39][CH:40]=[CH:41]2)=[CH:36][C:35]=1[CH2:34]3)=[O:32].[NH2:8][CH2:9][C:10]([O-:12])=[O:11]
Reactant: CC(C)(C)OC(=O)NCC(=O)O
Agent: CC(C)N=C=NC(C)C
Agent: CC[C@@]1(O)C(=O)OCc2c1cc1n(c2=O)Cc2cc3ccccc3nc2-1
Agent: CN(C)c1ccncc1
Solvent: CS(C)=O
Solvent: ClCCl
Product: NCC(=O)[O-]
Temperature: 25 °C

Procedure:
All chemicals, unless otherwise indicated, were purchased from Sigma Chemical Co. (St. Louis, Mo.) or Fisher Scientific (Houston, Tex.) and used as received. t-boc-glycine (0.31 g, 1.71 mmol; Bachem, Bioscience Inc., King of Prussia, Pa.) was dissolved in 20 mL of anhydrous methylene chloride at room temperature. To this solution was added 1,3-diisopropylcarbodiimide (DIPC, 267.7 mL, 1.71 mmol), 4-dimethylamino-pyridine (DMAP, 0.14 g, 1.14 mmol) and camptothecin (CPT, 0.20149 g, 0.57 mmol) at 0° C. While CPT (Sigma Chemical Co., St. Louis, Mo.) was dissolved in dimethyl sulfoxide (DMSO) because of its low solubility, the concentration of DMSO in working solutions was less than 1.0%; a concentration which did not have a significant effect on cells. The reaction mixture was allowed to warm to room temperature and incubated overnight. The product was washed with 0.1 N HCl, dried and evaporated under reduced pressure to yield the sold product. The product was recrystallized from methanol to give CPT-glycinate. The t-boc protection group was removed by dissolving the CPT-glycinate in a mixture of methylene chloride and trifluoracetic acid (TFA) (50:50) and stirring at room temperature for 3 hours. Solvent was evaporated under reduced pressure and precipitated using ether to give CPT-glycinate-TFA salt. CPT-glycinate-TFA salt (34.0 mg or 50 mg) and PEG-NHS (100 mg; MW ˜3400; Shearwater Corporation, Huntsville, Ala.) were added to methylene chloride (5 ml) and DIEA (50 ml) was added to adjust the pH to basic. The reaction was stirred for 3 hours at room temperature. The product was recrystallized from cold ether and dried under vacuum overnight.
Reaction SMILES: [CH:1]([N:4]1[CH:8]=[CH:7][CH:6]=[N:5]1)([CH3:3])[CH3:2].[N+:9]([O-])([O-:11])=[O:10].[K+]>OS(O)(=O)=O>[CH:1]([N:4]1[CH:8]=[C:7]([N+:9]([O-:11])=[O:10])[CH:6]=[N:5]1)([CH3:3])[CH3:2]
Reactant: O=[N+]([O-])[O-]
Reactant: CC(C)n1cccn1
Agent: O=S(=O)(O)O
Agent: [K+]
Product: CC(C)n1cc([N+](=O)[O-])cn1
Temperature: 0 °C
Yield: 45.3 %

Procedure:
To a solution of 1-isopropyl-1 H-pyrazole (5 g, 45.5 mmol) in conc.H2SO4 (50 mL) was added KNO3 (5.0 g, 50 mmol) portion wise at 0° C. After the addition, the resulting mixture was heated to 50 0° C. for 8 h. The reaction mixture was cooled to room temperature and poured into ice water, and the mixture was extracted with EtOAc. The combined organics were washed with saturated Na2CO3 solution, brine, and were dried over Na2SO4, and concentrated in vacuo. Chromatography on silica gel provided 1-isopropyl-4-nitro-1 H-pyrazole (3.2 g, 46% yield). 1H NMR (400 MHz, DMSO-d6): δ 8.99 (s, 1 H), 8.32 (s, 1 H), 4.65 (m, 1 H), 1.51 (d, J=6.8 Hz, 6H).
Reaction SMILES: Br[C:2]1[CH:7]=[CH:6][C:5]([Si:8]([CH3:11])([CH3:10])[CH3:9])=[CH:4][CH:3]=1.C([Li])CCC.[C:17](=[O:19])=[O:18]>C1COCC1>[CH3:9][Si:8]([CH3:11])([CH3:10])[C:5]1[CH:6]=[CH:7][C:2]([C:17]([OH:19])=[O:18])=[CH:3][CH:4]=1
Reactant: O=C=O
Reactant: C[Si](C)(C)c1ccc(Br)cc1
Agent: [Li]CCCC
Solvent: C1CCOC1
Product: C[Si](C)(C)c1ccc(C(=O)O)cc1
Temperature: -78 °C
Reaction time: 0.17 h

Procedure:
To 1-bromo-4-(trimethylsilyl)-benzene (Aldrich) (6.42 g, 28.04 mmol) in a clean, dry 250 mL round-bottom flask was added THF (100 mL) and the mixture was cooled to −78° C. with stirring for 10 minutes under nitrogen. Then, a 2.5M solution of n-butyllithium in hexanes (13.46 mL, 1.2 eq) was added slowly over about seven minutes. The resulting mixture was stirred at −78° C. for 1.5 hours (solution turned light yellow). Then, at −78° C. an excess of dry ice (4 large pieces) were added to the reaction mixture (solution turned color, then became clear) and the dry ice bath was removed and stirred for 15 minutes. TLC confirmed that the reaction was complete, and after stirring an additional 10 minutes at −78° C., the reaction was quenched with water (100 mL). Ethyl acetate (500 mL) was then added and with stirring 4N HCl was added to pH=2. The layers were separated and then washed the ethyl acetate layer with brine (1×250 mL) and finally the organic layer was dried over magnesium sulfate, filtered, concentrated and pumped to give 4-Trimethylsilanyl-benzoic acid as a white solid (5.49 g).
Reaction SMILES: [Cl:1][C:2]1[CH:10]=[C:9]2[C:5]([C:6]([C:11]([N:13]3[CH2:18][CH2:17][C:16]4([C:22]5[CH:23]=[CH:24][C:25]([F:27])=[CH:26][C:21]=5[C:20](=[O:28])[O:19]4)[CH2:15][CH2:14]3)=[O:12])=[CH:7][NH:8]2)=[CH:4][CH:3]=1.[CH3:29][N:30]1[C:34]([CH3:35])=[CH:33][C:32]([CH2:36]OS(C)(=O)=O)=[N:31]1>>[Cl:1][C:2]1[CH:10]=[C:9]2[C:5]([C:6]([C:11]([N:13]3[CH2:18][CH2:17][C:16]4([C:22]5[CH:23]=[CH:24][C:25]([F:27])=[CH:26][C:21]=5[C:20](=[O:28])[O:19]4)[CH2:15][CH2:14]3)=[O:12])=[CH:7][N:8]2[CH2:36][C:32]2[CH:33]=[C:34]([CH3:35])[N:30]([CH3:29])[N:31]=2)=[CH:4][CH:3]=1
Reactant: O=C1OC2(CCN(C(=O)c3c[nH]c4cc(Cl)ccc34)CC2)c2ccc(F)cc21
Reactant: Cc1cc(COS(C)(=O)=O)nn1C
Product: Cc1cc(Cn2cc(C(=O)N3CCC4(CC3)OC(=O)c3cc(F)ccc34)c3ccc(Cl)cc32)nn1C

Procedure:
Following the general procedure III as described above, the alkylation of 1′-[(6-chloro-1H-indol-3-yl)carbonyl]-5-fluoro-3H-spiro[2-benzofuran-1,4′-piperidin]-3-one (prepared according to example 19) with methanesulfonic acid 1,5-dimethyl-1H-pyrazol-3-ylmethyl ester (prepared by mesylation of commercially available methanesulfonic acid 1,5-dimethyl-1H-pyrazol-3-ylmethyl ester) gave the title compound. ES-MS m/e (%): 507.2 (M+H+).
Reaction SMILES: [NH2:1][C:2]1[N:7]=[C:6]([NH2:8])[CH:5]=[C:4]([Cl:9])[N:3]=1.C([OH:12])C.ClC1C=CC=C(C(OO)=O)C=1.[OH-].[Na+]>O>[NH2:1][C:2]1[N+:7]([O-:12])=[C:6]([NH2:8])[CH:5]=[C:4]([Cl:9])[N:3]=1
Reactant: Nc1cc(Cl)nc(N)n1
Reactant: CCO
Agent: O=C(OO)c1cccc(Cl)c1
Agent: [Na+]
Agent: [OH-]
Solvent: O
Product: Nc1cc(Cl)nc(N)[n+]1[O-]
Temperature: -10 °C
Reaction time: 7 h

Procedure:
75 g. of 2,4-diamino-6-chloropyrimidine are dissolved in 1500 ml. of ethanol at 35° C. The solution is cooled to -10° C. and a solution of 100 g. of 3-chloro-perbenzoic acid in 500 ml. of ethanol is slowly added dropwise in the course of 1 hour. The suspension is subsequently stirred at -10° C. for 7 hours and left to stand at 5° C. overnight. The suspension is neutralized with 24 g. of sodium hydroxide in 100 ml. of water. The solid material is filtered off and recrystallized from ethanol, there being obtained pure 2,4-diamino-6-chloropyrimidine-3-oxide.
Reaction SMILES: [Cl:1][C:2]1[CH:15]=[C:14]([N+:16]([O-])=O)[CH:13]=[CH:12][C:3]=1[O:4][CH2:5][CH2:6][N:7]([CH2:10][CH3:11])[CH2:8][CH3:9].ClCCl.CO>CO>[Cl:1][C:2]1[CH:15]=[C:14]([NH2:16])[CH:13]=[CH:12][C:3]=1[O:4][CH2:5][CH2:6][N:7]([CH2:8][CH3:9])[CH2:10][CH3:11]
Reactant: CCN(CC)CCOc1ccc([N+](=O)[O-])cc1Cl
Solvent: ClCCl
Solvent: CO
Product: CCN(CC)CCOc1ccc(N)cc1Cl

Procedure:
Prepared analogously to Example 3.1.b. from [2-(2-chloro-4-nitrophenoxy)ethyl]diethylamine in methanol in a reaction time of 4.5 hours. Yield: 36.12 g (81.8% of theory); C12H19ClN2O (M=242.75); calc.: molecular ion peak (M+H)+: 243/245; found: molecular ion peak (M+H)+: 243/245; Rf value: 0.36 (silica gel, dichloromethane/methanol (90:10)).
Reaction SMILES: [C:1]([CH:4]([CH2:17][CH2:18][CH2:19][CH:20]([OH:26])[CH2:21][CH2:22][CH2:23][CH2:24][CH3:25])[CH2:5][C:6]1[CH:16]=[CH:15][C:9]([CH:10]=[CH:11][C:12]([OH:14])=[O:13])=[CH:8][CH:7]=1)(=[O:3])[CH3:2].[H][H]>C(O)C.[Pd]>[C:1]([CH:4]([CH2:17][CH2:18][CH2:19][CH:20]([OH:26])[CH2:21][CH2:22][CH2:23][CH2:24][CH3:25])[CH2:5][C:6]1[CH:16]=[CH:15][C:9]([CH2:10][CH2:11][C:12]([OH:14])=[O:13])=[CH:8][CH:7]=1)(=[O:3])[CH3:2]
Reactant: CCCCCC(O)CCCC(Cc1ccc(C=CC(=O)O)cc1)C(C)=O
Reactant: [H][H]
Agent: [Pd]
Solvent: CCO
Product: CCCCCC(O)CCCC(Cc1ccc(CCC(=O)O)cc1)C(C)=O

Procedure:
p-(2-Acetyl-6-hydroxyundecyl)cinnamic acid (2.6 g., 0.0072 mole) in ethanol (30 ml.) is hydrogenated over 0.7 g. of a 5% Pd on charcoal catalyst at 1 atmosphere pressure and room temperature. The theoretical amount of hydrogen (0.0072 mole) is absorbed in 7 minutes. The catalyst is filtered off, solvent removed in vacuo, and the residue chromatographed on 45 g. of silica gel with 2% methanol in chloroform elution. The title compound is obtained as a colorless, viscous oil.