Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [OH:1][C:2]1[CH2:7][C:6]([CH2:14][CH2:15][C:16]2[CH:21]=[CH:20][CH:19]=[C:18]([OH:22])[CH:17]=2)([C:8]2[CH:13]=[CH:12][CH:11]=[CH:10][CH:9]=2)[O:5][C:4](=[O:23])[CH:3]=1.[C:24]([C:28]1[CH:33]=[C:32]([CH2:34][OH:35])[C:31]([CH3:36])=[CH:30][C:29]=1[S:37]S(C1C=CC(C)=CC=1)(=O)=O)([CH3:27])([CH3:26])[CH3:25].C([O-])([O-])=O.[K+].[K+]>CN(C=O)C>[C:24]([C:28]1[CH:33]=[C:32]([CH2:34][OH:35])[C:31]([CH3:36])=[CH:30][C:29]=1[S:37][C:3]1[C:4](=[O:23])[O:5][C:6]([CH2:14][CH2:15][C:16]2[CH:21]=[CH:20][CH:19]=[C:18]([OH:22])[CH:17]=2)([C:8]2[CH:9]=[CH:10][CH:11]=[CH:12][CH:13]=2)[CH2:7][C:2]=1[OH:1])([CH3:27])([CH3:26])[CH3:25]
Reactant: O=C1C=C(O)CC(CCc2cccc(O)c2)(c2ccccc2)O1
Reactant: Cc1ccc(S(=O)(=O)Sc2cc(C)c(CO)cc2C(C)(C)C)cc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Product: Cc1cc(SC2=C(O)CC(CCc3cccc(O)c3)(c3ccccc3)OC2=O)c(C(C)(C)C)cc1CO
Temperature: 25 °C
Reaction time: 8 h

Procedure:
The title compound was prepared as described in General Method 9 using 4-hydroxy-6-[2-(3-hydroxy-phenyl)-ethyl]-6-phenyl-5,6-dihydro-pyran-2-one (0.155 g, 0.5 mmol) from Example UU, toluene-4-thiosulfonic acid S-(2-tert-butyl-4-hydroxymethyl-5-methyl-phenyl) ester (prepared in Example FFF; 0.2 g, 0.55 mmol), K2CO3 (0.27 g, 1.95 mmol), and DMF (3 mL). The solution was stirred overnight at room temperature, concentrated and the residue partitioned between 1N HCI and EtOAc. The organic phase was dried (MgSO4), and concentrated. Purification by silica gel chromatography, eluting with MeOH:CHCl3 :hexane (5:90:10 to 10:90:10) gave the title compound, m.p. 132-135° C. 1H NMR (DMSO-d6) δ 1.45 (s, 9 H), 1.76 (s, 3 H), 2.08-2.24 (m, 3 H), 2.48 (m, 1 H), 3.41 (dd, 2 H), 4.32 (s, 2 H), 4.91 (br s, 1 H), 6.17 (s, 1 H), 6.46-6.55 (m, 3 H), 7.02 (t, 1 H), 7.22 (s, 1 H), 7.35-7.46 (m, 5 H), 9.23 (s, 1 H), 12.15 (bs, 1 H).
Reaction SMILES: [O:1]=[O+][O-].[CH2:4]([CH:8]1[CH2:16][C:15]2[C:10](=[CH:11][C:12]([O:17][CH3:18])=[CH:13][CH:14]=2)[C:9]1=[O:19])[CH:5]=CC>ClCCl.CO>[O:1]=[CH:5][CH2:4][CH:8]1[CH2:16][C:15]2[C:10](=[CH:11][C:12]([O:17][CH3:18])=[CH:13][CH:14]=2)[C:9]1=[O:19]
Reactant: O=[O+][O-]
Reactant: CC=CCC1Cc2ccc(OC)cc2C1=O
Solvent: CO
Solvent: ClCCl
Product: COc1ccc2c(c1)C(=O)C(CC=O)C2
Reaction time: 8 h
Yield: 50.9 %

Procedure:
Ozone (3 g ozone/hour) was conducted for 60 minutes while stirring through a solution, cooled to -70°, of 13.6 g of (RS)-2-(2-buten-1-yl)-6-methoxy-1-indanone in 200 ml of anhydrous dichloromethane and 400 ml of anhydrous methanol. Subsequently, the solution was flushed with oxygen and then 6.4 ml of dimethyl sulfide were added to the cold solution. The solution came to room temperature overnight and was evaporated in a vacuum. The residue was dissolved in 1600 ml of dichloromethane. The solution was treated with 600 g of silica gel and 100 ml of 10% oxalic acid solution and stirred overnight. Then, the mixture was filtered and the filtrate was concentrated in a vacuum. 6.5 g (51%) of (RS)-2-(2-oxoethyl)-6-methoxy-1-indanone were obtained as a yellow oil.
Reaction SMILES: [N:1]1([CH2:6][CH2:7][O:8][C:9]2[CH:10]=[C:11]([NH2:19])[CH:12]=[CH:13][C:14]=2[C:15]([F:18])([F:17])[F:16])[CH2:5][CH2:4][CH2:3][CH2:2]1.[Cl:20][C:21]1[C:26]([C:27](Cl)=[O:28])=[CH:25][CH:24]=[CH:23][N:22]=1.C(N1CCC(OC2C=C(C(F)(F)F)C=C(NC(C3C(Cl)=NC=CC=3)=O)C=2)CC1)(OC(C)(C)C)=O>>[Cl:20][C:21]1[N:22]=[CH:23][CH:24]=[CH:25][C:26]=1[C:27]([NH:19][C:11]1[CH:12]=[CH:13][C:14]([C:15]([F:17])([F:18])[F:16])=[C:9]([O:8][CH2:7][CH2:6][N:1]2[CH2:5][CH2:4][CH2:3][CH2:2]2)[CH:10]=1)=[O:28]
Reactant: O=C(Cl)c1cccnc1Cl
Reactant: Nc1ccc(C(F)(F)F)c(OCCN2CCCC2)c1
Agent: CC(C)(C)OC(=O)N1CCC(Oc2cc(NC(=O)c3cccnc3Cl)cc(C(F)(F)F)c2)CC1
Product: O=C(Nc1ccc(C(F)(F)F)c(OCCN2CCCC2)c1)c1cccnc1Cl

Procedure:
2-Chloro-N-[3-(2-pyrrolidin-1-yl-ethoxy)-4-trifluoromethyl-phenyl]-nicotinamide was prepared from 3-(2-pyrrolidin-1-yl-ethoxy)-4-trifluoromethyl-phenylamine and 2-chloropyridine-3-carbonyl chloride by a procedure similar to that described in the preparation of 1-Boc-4-{3-[(2-chloro-pyridine-3-carbonyl)-amino]-5-trifluoromethyl-phenoxy}-piperidine.
Reaction SMILES: C[Si]([N-][Si](C)(C)C)(C)C.[Li+].F[C:12]1[C:17]([C:18]2[N:23]=[C:22]([CH3:24])[N:21]=[C:20]([N:25]([CH2:35][C:36]3[CH:41]=[CH:40][C:39]([O:42][CH3:43])=[CH:38][CH:37]=3)[CH2:26][C:27]3[CH:32]=[CH:31][C:30]([O:33][CH3:34])=[CH:29][CH:28]=3)[N:19]=2)=[CH:16][C:15]([C@H:44]([N:46]2[CH2:51][CH2:50][N:49]([S:52]([CH3:55])(=[O:54])=[O:53])[CH2:48][CH2:47]2)[CH3:45])=[CH:14][N:13]=1.[F:56][C:57]1[CH:58]=[C:59]([NH2:65])[CH:60]=[N:61][C:62]=1[O:63][CH3:64]>C1COCC1>[F:56][C:57]1[CH:58]=[C:59]([NH:65][C:12]2[C:17]([C:18]3[N:23]=[C:22]([CH3:24])[N:21]=[C:20]([N:25]([CH2:35][C:36]4[CH:37]=[CH:38][C:39]([O:42][CH3:43])=[CH:40][CH:41]=4)[CH2:26][C:27]4[CH:28]=[CH:29][C:30]([O:33][CH3:34])=[CH:31][CH:32]=4)[N:19]=3)=[CH:16][C:15]([C@H:44]([N:46]3[CH2:47][CH2:48][N:49]([S:52]([CH3:55])(=[O:53])=[O:54])[CH2:50][CH2:51]3)[CH3:45])=[CH:14][N:13]=2)[CH:60]=[N:61][C:62]=1[O:63][CH3:64]
Reactant: COc1ncc(N)cc1F
Reactant: COc1ccc(CN(Cc2ccc(OC)cc2)c2nc(C)nc(-c3cc([C@@H](C)N4CCN(S(C)(=O)=O)CC4)cnc3F)n2)cc1
Agent: C[Si](C)(C)[N-][Si](C)(C)C
Agent: [Li+]
Solvent: C1CCOC1
Product: COc1ccc(CN(Cc2ccc(OC)cc2)c2nc(C)nc(-c3cc([C@@H](C)N4CCN(S(C)(=O)=O)CC4)cnc3Nc3cnc(OC)c(F)c3)n2)cc1
Temperature: 0 °C
Reaction time: 1 h
Yield: 90.1 %

Procedure:
Lithium bis(trimethylsilyl)amide (1.0 M in hexane; 31.9 mL, 31.9 mmol) was added (dropwise over 10 min) to a mixture of (R)-4-(2-fluoro-5-(1-(4-(methylsulfonyl)piperazin-1-yl)ethyl)pyridin-3-yl)-N,N-bis(4-methoxybenzyl)-6-methyl-1,3,5-triazin-2-amine (Example 146, Step 6; 6.75 g, 10.62 mmol) and 5-fluoro-6-methoxypyridin-3-amine (Anichem, North Brunswick, N.J.; 2.264 g, 15.93 mmol) in THF (100 mL) at 0° C., and the resulting solution was stirred at 0° C. for 1 h. Excess LiHMDS was then quenched with saturated aqueous NH4Cl (140 mL) and the reaction mixture was partitioned between EtOAc (500 mL) and half-saturated aqueous NH4Cl (200 mL). The organic layer was separated, and the aqueous layer was extracted with EtOAc (2×200 mL). The combined organic extracts were sequentially washed with brine (300 mL), dried over sodium sulfate, filtered, and concentrated in vacuo. Chromatographic purification of the residue (silica gel, 0 to 100% EtOAc/hexanes) furnished (R)-4-(2-(5-fluoro-6-methoxypyridin-3-ylamino)-5-(1-(4-(methylsulfonyl)piperazin-1-yl)ethyl)pyridin-3-yl)-N,N-bis(4-methoxybenzyl)-6-methyl-1,3,5-triazin-2-amine (7.25 g, 90% yield) as a yellow solid. 1H NMR (400 MHz, CDCl3) δ 11.88 (1H, s), 8.72 (1H, d, J=2.0 Hz), 8.25 (1H, d, J=2.2 Hz), 8.06 (1H, dd, J=12.3, 1.6 Hz), 7.96 (1H, d, J=2.0 Hz), 7.21 (4H, t, J=8.2 Hz), 6.86 (4H, dd, J=14.1, 8.4 Hz), 4.70-4.96 (4H, m), 4.01 (3H, s), 3.81 (3H, s), 3.78 (3H, s), 3.55 (1H, q, J=6.7 Hz), 3.15 (4H, br s), 2.68 (3H, s), 2.59 (3H, s), 2.48-2.57 (4H, m), 1.38 (3H, d, J=6.7 Hz). 19F NMR (376 MHz, CDCl3) δ −139.13 (1 F, d, J=13.0 Hz). m/z (ESI, +ve) 758.3 (M+H)+.
Reaction SMILES: [H-].[Na+].[CH3:3][O:4][C:5]1[CH:10]=[CH:9][C:8]([NH:11][C:12]([CH:14]2[CH2:16][CH2:15]2)=[O:13])=[CH:7][N:6]=1.O1CCCC1.Cl[CH2:23][O:24][CH2:25][CH2:26][O:27][CH3:28]>CCOCC>[CH3:23][O:24][CH2:25][CH2:26][O:27][CH2:28][N:11]([C:8]1[CH:9]=[CH:10][C:5]([O:4][CH3:3])=[N:6][CH:7]=1)[C:12]([CH:14]1[CH2:16][CH2:15]1)=[O:13]
Reactant: COCCOCCl
Reactant: COc1ccc(NC(=O)C2CC2)cn1
Agent: [H-]
Agent: [Na+]
Solvent: C1CCOC1
Solvent: CCOCC
Product: COCCOCN(C(=O)C1CC1)c1ccc(OC)nc1
Reaction time: 8 h
Yield: 61.2 %

Procedure:
Sodium hydride (0.33 g, 0.014 mol) and N-(2-methoxy-5-pyridyl)-cyclopropane carboxamide (92.5 g, 0.014 mol) were added to dry tetrahydrofuran (THF). This mixture was stirred under N2 for one hour when methoxyethyl chloromethyl ether (1.6 g, 0.014 mol) was added dropwise to the stirred mixture. The reaction was stirred overnight and diluted with ether and washed with water. The organic phase was dried over anhydrous magnesium sulfate, filtered, and evaporated in vacuo nto give 2.4 g of a yellow oil of the title compound. The structure was confirmed by mass spectroscopy (MS), IR and NMR analysis.
Reaction SMILES: [C:1]1([C:7]2[CH:12]=[CH:11][N:10]=[C:9]([N:13]3[CH2:20][CH:19]4[CH:15]([CH2:16][NH:17][CH2:18]4)[CH2:14]3)[N:8]=2)[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.[F:21][C:22]1[CH:23]=[CH:24][C:25]([C:31]2[N:36]=[CH:35][CH:34]=[CH:33][N:32]=2)=[C:26]([CH:30]=1)[C:27](O)=[O:28]>>[F:21][C:22]1[CH:23]=[CH:24][C:25]([C:31]2[N:32]=[CH:33][CH:34]=[CH:35][N:36]=2)=[C:26]([C:27]([N:17]2[CH2:16][CH:15]3[CH:19]([CH2:20][N:13]([C:9]4[N:8]=[C:7]([C:1]5[CH:2]=[CH:3][CH:4]=[CH:5][CH:6]=5)[CH:12]=[CH:11][N:10]=4)[CH2:14]3)[CH2:18]2)=[O:28])[CH:30]=1
Reactant: O=C(O)c1cc(F)ccc1-c1ncccn1
Reactant: c1ccc(-c2ccnc(N3CC4CNCC4C3)n2)cc1
Product: O=C(c1cc(F)ccc1-c1ncccn1)N1CC2CN(c3nccc(-c4ccccc4)n3)CC2C1

Procedure:
The title compound was prepared in a manner analogous to Example 15 utilizing Intermediate 26 and Intermediate 13. MS (ESI): mass calculated for C27H23FN6O, 466.52; m/z found 467.2 [M+H]+. 1H NMR (400 MHz, CDCl3): 8.72-8.66 (m, 2H), 8.44-8.29 (m, 2H), 8.16-8.02 (m, 2H), 7.53-7.45 (m, 3H), 7.21-7.14 (m, 1H), 7.10-7.06 (m, 1H), 7.01-6.98 (m, 1H), 6.87 (br s, 1H), 4.05-3.50 (m, 7H), 3.31-2.98 (m, 3H).
Reaction SMILES: [NH:1]1[CH2:7][CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1.CN(C)C=O.F[C:14]1[CH:19]=[CH:18][C:17]([C:20]([F:23])([F:22])[F:21])=[CH:16][C:15]=1[N+:24]([O-:26])=[O:25]>O>[N+:24]([C:15]1[CH:16]=[C:17]([C:20]([F:21])([F:22])[F:23])[CH:18]=[CH:19][C:14]=1[N:1]1[CH2:7][CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1)([O-:26])=[O:25]
Reactant: O=[N+]([O-])c1cc(C(F)(F)F)ccc1F
Reactant: C1CCCNCC1
Solvent: CN(C)C=O
Solvent: O
Product: O=[N+]([O-])c1cc(C(F)(F)F)ccc1N1CCCCCC1
Temperature: 25 °C
Reaction time: 1 h
Yield: 97.5 %

Procedure:
Hexahydro-1H-azepine (682 μl, 6.05 mmol, commercially available product) was added at 0° C. to an N,N-dimethylformamide (DMF; 2 ml) solution of 1-fluoro-2-nitro-4-(trifluoromethyl)benzene (506 mg, 2.42 mmol, commercially available product). The resulting mixture was warmed to room temperature and stirred for one hour. Water was added to the mixture, and the resulting mixture was extracted three times with ethyl acetate. The obtained organic layer was washed with a saturated sodium chloride solution, dried over anhydrous sodium sulfate, filtered, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (20 g, hexane/ethyl acetate=7/1). Thus, hexahydro-1-[2-nitro-4-(trifluoromethyl)phenyl]-1H-azepine (680 mg, 97.5%) was yielded as an orange-colored solid.
Reaction SMILES: Cl.Cl.Cl.[NH2:4][C:5]1[N:10]=[CH:9][N:8]=[C:7]2[N:11]([CH:15]([C:17]3[CH:18]=[C:19]([Cl:34])[C:20]([C:32]#[N:33])=[C:21]4[C:27]=3[O:26][CH2:25][CH2:24][N:23]([CH:28]3[CH2:31][NH:30][CH2:29]3)[CH2:22]4)[CH3:16])[N:12]=[C:13]([CH3:14])[C:6]=12.C(N(CC)C(C)C)(C)C.[C:44](OC(=O)C)(=[O:46])[CH3:45]>CN(C)C=O>[C:44]([N:30]1[CH2:31][CH:28]([N:23]2[CH2:22][C:21]3=[C:20]([C:32]#[N:33])[C:19]([Cl:34])=[CH:18][C:17]([CH:15]([N:11]4[C:7]5=[N:8][CH:9]=[N:10][C:5]([NH2:4])=[C:6]5[C:13]([CH3:14])=[N:12]4)[CH3:16])=[C:27]3[O:26][CH2:25][CH2:24]2)[CH2:29]1)(=[O:46])[CH3:45]
Reactant: Cc1nn(C(C)c2cc(Cl)c(C#N)c3c2OCCN(C2CNC2)C3)c2ncnc(N)c12
Reactant: CC(=O)OC(C)=O
Agent: Cl
Solvent: CN(C)C=O
Solvent: CCN(C(C)C)C(C)C
Product: CC(=O)N1CC(N2CCOc3c(C(C)n4nc(C)c5c(N)ncnc54)cc(Cl)c(C#N)c3C2)C1
Reaction time: 1 h
Yield: 29.9 %

Procedure:
The crude 9-[1-(4-amino-3-methyl-1H-pyrazolo[3,4-d]pyrimidin-1-yl)ethyl]-4-azetidin-3-yl-7-chloro-2,3,4,5-tetrahydro-1,4-benzoxazepine-6-carbonitrile trishydrochloride (0.015 g, 0.0278 mmol) was dissolved in N,N-dimethylformamide (2 mL) and cooled in an ice bath, and then N,N-diisopropylethylamine (0.0142 g, 0.112 mmol) and acetic anhydride (0.0032 mL, 0.033 mmol) were added. After stirring for 1 h, the product was purified without work up, by prep HPLC on a C-18 column eluting water:acetonitrile gradient buffered pH 10 to give 4-(1-acetylazetidin-3-yl)-9-[1-(4-amino-3-methyl-1H-pyrazolo[3,4-d]pyrimidin-1-yl)ethyl]-7-chloro-2,3,4,5-tetrahydro-1,4-benzoxazepine-6-carbonitrile as a white amorphous solid (0.004 g, 33%). LCMS calculated for C23H26ClN8O2 (M+H)+: m/z=481.2; found: 481.2.
Reaction SMILES: [CH3:1][O:2][C:3](=[O:16])[CH2:4][C:5]1[CH:10]=[CH:9][CH:8]=[C:7]([O:11][CH2:12][CH2:13][CH2:14]Br)[CH:6]=1.[Cl:17][C:18]1[C:34]([C:35]([F:38])([F:37])[F:36])=[CH:33][CH:32]=[CH:31][C:19]=1[CH2:20][NH:21][CH2:22][C@H:23]([C:25]1[CH:30]=[CH:29][CH:28]=[CH:27][CH:26]=1)[CH3:24].C(=O)([O-])[O-].[K+].[K+]>C(#N)C>[CH3:1][O:2][C:3](=[O:16])[CH2:4][C:5]1[CH:10]=[CH:9][CH:8]=[C:7]([O:11][CH2:12][CH2:13][CH2:14][N:21]([CH2:20][C:19]2[CH:31]=[CH:32][CH:33]=[C:34]([C:35]([F:36])([F:37])[F:38])[C:18]=2[Cl:17])[CH2:22][C@H:23]([C:25]2[CH:26]=[CH:27][CH:28]=[CH:29][CH:30]=2)[CH3:24])[CH:6]=1
Reactant: COC(=O)Cc1cccc(OCCCBr)c1
Reactant: C[C@H](CNCc1cccc(C(F)(F)F)c1Cl)c1ccccc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC#N
Product: COC(=O)Cc1cccc(OCCCN(Cc2cccc(C(F)(F)F)c2Cl)C[C@@H](C)c2ccccc2)c1
Temperature: 25 °C
Reaction time: 48 h
Yield: 74.9 %

Procedure:
A solution of (3-{3-bromo-propoxy}-phenyl)acetic acid methyl ester (0.55 g, 1.5 mmol) and (S)-(2-Chloro-3-trifluoromethyl-benzyl)-(2-phenyl-propyl)-amine (0.55 g, 1.6 mmol) in acetonitrile (10 ml) was treated with solid potassium carbonate(0.4 g, 2.4 mmol). The reaction was heated to reflux and stirred for 48 h. Upon cooling to RT, the reaction was filtered through a pad of celite, washed with ethyl acetate, and the filtrate was concentrated in vacuo. The crude product was purified by column chromatograph (Ethyl acetate:Hexane/20:80) to give the title compound as an oil (0.6 g, 67%). MS (ESI) 534.6 (M+H)+.
Reaction SMILES: [CH3:1][C:2]1[C:7]2[O:8][CH2:9][C:10]3([CH2:12][CH2:11]3)[C:6]=2[C:5]([O:13][C:14]2[N:19]=[CH:18][C:17]([N+:20]([O-])=O)=[CH:16][N:15]=2)=[CH:4][CH:3]=1.O.[Cl-].[NH4+]>O1CCCC1>[CH3:1][C:2]1[C:7]2[O:8][CH2:9][C:10]3([CH2:12][CH2:11]3)[C:6]=2[C:5]([O:13][C:14]2[N:15]=[CH:16][C:17]([NH2:20])=[CH:18][N:19]=2)=[CH:4][CH:3]=1
Reactant: Cc1ccc(Oc2ncc([N+](=O)[O-])cn2)c2c1OCC21CC1
Agent: [Cl-]
Agent: [NH4+]
Solvent: C1CCOC1
Solvent: O
Product: Cc1ccc(Oc2ncc(N)cn2)c2c1OCC21CC1
Temperature: 25 °C
Reaction time: 48 h
Yield: 22.7 %

Procedure:
To a solution of 2-(7-methylspiro[2H-benzofuran-3,1′-cyclopropane]-4-yl)oxy-5-nitro-pyrimidine (Intermediate 18, 255 mg) in tetrahydrofuran (5 ml)/water (2.5 ml) iron (234 mg, 4.25 mmol) and then ammonium chloride (227 mg, 4.25 mmol) were added and the reaction mixture was stirred for 48 hours at room temperature. The catalyst was filtered off and the residue was diluted with an aqueous saturated solution of NaHCO3 (5 ml) and extracted with ethyl acetate (3×10 ml). The organic layer was dried over sodium sulphate, filtered and evaporated and the residue was purified by flash chromatography (Biotage system) on silica gel using a 10 g SNAP column and cyclohexane/ethyl acetate 8:2 to cyclohexane/ethyl acetate 4:6 as eluents affording the title compound (52 mg) as a light orange solid.
Reaction SMILES: Cl.[Cl:2][C:3]1[CH:4]=[C:5]2[C:9](=[CH:10][CH:11]=1)[NH:8][CH:7]=[C:6]2[CH2:12][CH2:13][NH2:14].[CH2:15]([C:22]1[S:26][N:25]=[C:24]([C:27](O)=[O:28])[CH:23]=1)[C:16]1[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=1.CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.C(N(CC)C(C)C)(C)C>CN(C=O)C>[CH2:15]([C:22]1[S:26][N:25]=[C:24]([C:27]([NH:14][CH2:13][CH2:12][C:6]2[C:5]3[C:9](=[CH:10][CH:11]=[C:3]([Cl:2])[CH:4]=3)[NH:8][CH:7]=2)=[O:28])[CH:23]=1)[C:16]1[CH:17]=[CH:18][CH:19]=[CH:20][CH:21]=1
Reactant: NCCc1c[nH]c2ccc(Cl)cc12
Reactant: O=C(O)c1cc(Cc2ccccc2)sn1
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: Cl
Agent: F[P-](F)(F)(F)(F)F
Solvent: CN(C)C=O
Solvent: CCN(C(C)C)C(C)C
Product: O=C(NCCc1c[nH]c2ccc(Cl)cc12)c1cc(Cc2ccccc2)sn1

Procedure:
The 5-Benzyl-N-(2-(5-chloro-1H-indol-3-yl)ethyl)isothiazole-3-carboxamide is prepared following method A starting from 2-(5-chloro-1H-indol-3-yl)ethanamine hydrochloride, 5-benzylisothiazole-3-carboxylic acid (which can be prepared by procedures known to the skilled in the art), HATU and N,N-diisopropylethylamine in DMF.
Reaction SMILES: [OH:1][C:2]1[CH:3]=[C:4]([CH:7]=[CH:8][C:9]=1[OH:10])[CH:5]=[O:6].[Br:11]Br.O>CC(O)=O>[Br:11][C:8]1[CH:7]=[C:4]([CH:3]=[C:2]([OH:1])[C:9]=1[OH:10])[CH:5]=[O:6]
Reactant: BrBr
Reactant: O=Cc1ccc(O)c(O)c1
Solvent: CC(=O)O
Solvent: O
Product: O=Cc1cc(O)c(O)c(Br)c1
Yield: 447 %

Procedure:
To a solution of 3,4-dihydroxy benzaldehyde (115.48 g, 12 mmol) in 500 ml AcOH was added bromine (6.1 ml, 118 mmol) drop-wise in 50 ml AcOH over 10 min. After 4 h the mixture was poured into cold H2O. The precipitate was filtered, washed with cold H2O and dried in vacuum to give 3-bromo-4,5-dihydroxy-benzaldehyde (11.64 g, 48%) as a grey solid.
Reaction SMILES: [Br:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[CH2:12][CH:11]([CH2:13][OH:14])[O:10][N:9]=2)=[CH:4][C:3]=1[F:15].C(N(CC)CC)C.[Si:23](Cl)([C:26]([CH3:29])([CH3:28])[CH3:27])([CH3:25])[CH3:24]>ClCCl.CN(C)C1C=CN=CC=1>[Br:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[CH2:12][CH:11]([CH2:13][O:14][Si:23]([C:26]([CH3:29])([CH3:28])[CH3:27])([CH3:25])[CH3:24])[O:10][N:9]=2)=[CH:4][C:3]=1[F:15]
Reactant: OCC1CC(c2ccc(Br)c(F)c2)=NO1
Reactant: CC(C)(C)[Si](C)(C)Cl
Agent: CN(C)c1ccncc1
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: CC(C)(C)[Si](C)(C)OCC1CC(c2ccc(Br)c(F)c2)=NO1
Temperature: 0 °C
Reaction time: 8 h
Yield: 87 %

Procedure:
[3-(4-Bromo-3-fluorophenyl)-4,5-dihydroisoxazol-5-yl]methanol (7.518 g, 27.4 mmol) was dissolved in a mixture of triethylamine (4.59 ml, 33.0 mmol) and dichloromethane (100 ml). The resulting solution was cooled to 0° C., then a 1M solution of tert-butyldimethylsilylchloride (30.2 ml) in dichloromethane was added dropwise over 30 minutes. 4-Dimethylamino pyridine (0.67 g, 5.48 mmol) was added and the reaction mixture left to stir overnight at room temperature. The reaction mixture was washed with water (200 ml). The dichloromethane layer was separated, dried over magnesium sulfate, filtered and concentrated in vacuo to yield 9.263 g (87%) of the desired compound as a colourless oil.
Reaction SMILES: [CH2:1]([N:8]1[C:16]2[C:11](=[CH:12][C:13]([C:17]3[CH:22]=[CH:21][C:20]([F:23])=[C:19]([Cl:24])[CH:18]=3)=[CH:14][CH:15]=2)[CH:10]=[CH:9]1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.C([Li])CCC.[C:30](=[O:32])=[O:31]>C1COCC1>[CH2:1]([N:8]1[C:16]2[C:11](=[CH:12][C:13]([C:17]3[CH:22]=[CH:21][C:20]([F:23])=[C:19]([Cl:24])[CH:18]=3)=[CH:14][CH:15]=2)[C:10]([C:30]([OH:32])=[O:31])=[CH:9]1)[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: O=C=O
Reactant: Fc1ccc(-c2ccc3c(ccn3Cc3ccccc3)c2)cc1Cl
Agent: [Li]CCCC
Solvent: C1CCOC1
Product: O=C(O)c1cn(Cc2ccccc2)c2ccc(-c3ccc(F)c(Cl)c3)cc12
Yield: 32 %

Procedure:
1-Benzyl-5-(3-chloro-4-fluoro-phenyl)-1H-indole-3-carboxylic acid was prepared from 1-benzyl-5-(3-chloro-4-fluorophenyl)-1H-indole (17.99 g, 53.6 mmol), n-butyllithium (26 mL, 65 mmol), crushed dry ice (20 g, 450 mmol) in dry THF (180 mL) according to the procedure described in Example 60. Purification by HPLC using 85% acetonitrile in water as the mobile phase afforded the title compound as a light pink solid (6.51 g, 32%), mp: 189-194° C. Mass spectrum (+APCI, [M+H]+) m/z 380. 1HNMR (400 MHz, DMSO-d6): δ 13.5-13.8 (br s, 1H), 8.05 (dd, 1H, J=6.5 Hz and 2.6 Hz), 8.0 (dd, 1H, J=6.1 Hz and 2.4 Hz ), 7.9 (d, 1H, J=1.5 Hz), 7.5-7.55 (m, 2H), 7.4 (dd, 1H, J=8.5 Hz and 2.0 Hz), 7.3-7.35 (m, 2H), 7.2-7.25 (m, 3H), 6.55 (dd, 1H, J=3.2 Hz and 0.75 Hz) and 5.45 ppm (s, 2H).
Reaction SMILES: Cl.[NH2:2][CH:3]1[CH2:7][CH2:6][N:5]([CH2:8][C:9]2[CH:10]=[C:11]([C:14]#[N:15])[S:12][CH:13]=2)[C:4]1=[O:16].[N+:17]([C:20]1[C:25]([O:26][C:27]2[CH:32]=[CH:31][C:30]([S:33](Cl)(=[O:35])=[O:34])=[CH:29][CH:28]=2)=[C:24]([Cl:37])[CH:23]=[CH:22][CH:21]=1)([O-:19])=[O:18].C(N(CC)CC)C>C(Cl)Cl.Cl>[N+:17]([C:20]1[C:25]([O:26][C:27]2[CH:32]=[CH:31][C:30]([S:33]([NH:2][C@H:3]3[CH2:7][CH2:6][N:5]([CH2:8][C:9]4[CH:10]=[C:11]([C:14]#[N:15])[S:12][CH:13]=4)[C:4]3=[O:16])(=[O:34])=[O:35])=[CH:29][CH:28]=2)=[C:24]([Cl:37])[CH:23]=[CH:22][CH:21]=1)([O-:19])=[O:18]
Reactant: N#Cc1cc(CN2CCC(N)C2=O)cs1
Reactant: O=[N+]([O-])c1cccc(Cl)c1Oc1ccc(S(=O)(=O)Cl)cc1
Agent: Cl
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: N#Cc1cc(CN2CC[C@H](NS(=O)(=O)c3ccc(Oc4c(Cl)cccc4[N+](=O)[O-])cc3)C2=O)cs1
Reaction time: 18 h
Yield: 96.4 %

Procedure:
4-{3-(S)-[(4-(6-Nitro-2-chlorophenoxy)benzenesulfonyl)amino]-2-oxopyrrolidin-1-ylmethyl}thiophene-2-carbononitrile is prepared as described in EXAMPLE 125, Part C from of 4-(3-Amino-2-oxopyrrolidine-1-ylmethyl)thiophene-2-carbonitrile hydrochloride (0.36 g, 1.4 mmol), and 4-(6-Nitro-2-chlorophenoxy)-benzenesulfonyl chloride (0.63 g, 1.8 mmol) and triethyl amine (0.57 g, 5.7 mmol). After 18 hours, the solution is diluted with CH2Cl2 and 0.5 N HCl. The layers are separated; the organic layer is dried over NA2SO4, filtered and concentrated. The crude product is triturated with ether to afford the title compound (0.72 g, 1.35 mmol) as a white foam.
Reaction SMILES: C(OC([N:8]1[CH2:13][CH2:12][CH:11]([C:14](=[O:23])[C:15]2[CH:20]=[CH:19][C:18]([Cl:21])=[C:17]([Cl:22])[CH:16]=2)[CH2:10][CH2:9]1)=O)(C)(C)C.FC(F)(F)C(O)=O>C(Cl)Cl>[Cl:22][C:17]1[CH:16]=[C:15]([CH:20]=[CH:19][C:18]=1[Cl:21])[C:14]([CH:11]1[CH2:10][CH2:9][NH:8][CH2:13][CH2:12]1)=[O:23]
Reactant: CC(C)(C)OC(=O)N1CCC(C(=O)c2ccc(Cl)c(Cl)c2)CC1
Solvent: O=C(O)C(F)(F)F
Solvent: ClCCl
Product: O=C(c1ccc(Cl)c(Cl)c1)C1CCNCC1
Reaction time: 1 h
Yield: 99.8 %

Procedure:
To a room temperature solution of 4-(3,4-dichlorobenzoyl)piperidine-1-carboxylic acid tert-butyl ester (3.8 g, 10.6 mmol) in methylene chloride (100 mL) was added trifluoroacetic acid (25 mL) and the solution was stirred for 1 h. After removing the organics, ethyl acetate (200 mL) was added and the resulting solution was basified with 1N aqueous sodium hydroxide solution. The ethyl acetate layer was separated, dried with magnesium sulfate and concentrated to give 4-(3,4-dichlorobenzoyl)piperidine (2.73 g) as a white solid.
Reaction SMILES: [CH:1]1([N:6]2[C:10]3=[N:11][C:12]([C:16]4[CH:21]=[CH:20][CH:19]=[C:18]([O:22][CH2:23][C:24]([O:26]CC)=[O:25])[CH:17]=4)=[N:13][C:14](=[O:15])[C:9]3=[C:8]([CH2:29][CH3:30])[NH:7]2)[CH2:5][CH2:4][CH2:3][CH2:2]1.O.[OH-].[K+]>C(O)C>[CH:1]1([N:6]2[C:10]3=[N:11][C:12]([C:16]4[CH:21]=[CH:20][CH:19]=[C:18]([O:22][CH2:23][C:24]([OH:26])=[O:25])[CH:17]=4)=[N:13][C:14](=[O:15])[C:9]3=[C:8]([CH2:29][CH3:30])[NH:7]2)[CH2:2][CH2:3][CH2:4][CH2:5]1
Reactant: CCOC(=O)COc1cccc(-c2nc3n(C4CCCC4)[nH]c(CC)c-3c(=O)n2)c1
Agent: [K+]
Agent: [OH-]
Solvent: O
Solvent: CCO
Product: CCc1[nH]n(C2CCCC2)c2nc(-c3cccc(OCC(=O)O)c3)nc(=O)c1-2
Temperature: 25 °C
Yield: 85.4 %

Procedure:
To a slurry of 1-cyclopentyl-3-ethyl-6-[3-(ethoxycarbonylmethoxy)phenyl]pyrazolo[3,4-d]pyrimidin-4-one (1.23 g, 3.0 mmol) in ethanol (10 ml) was added water (100 ml), followed by 85% KOH (0.4 g). The reaction mixture was heated on a steam bath for 3 hours, cooled to room temperature and filtered. The filtrate was chilled and acidified with acetic acid to afford a white precipitate, which was collected by filtration and washed with water, then ethanol, and finally ether. The product was combined with the product from another experimental run and then was recrystallized from DMF/CH3CN to afford 0.98 g of 1-cyclopentyl-3-ethyl-6-[3-(carboxymethoxy)phenyl]pyrazolo[3,4-d]pyrimidin-4-one, m.p. 299°-300° C.
Reaction SMILES: [CH:1]1([Si:6](OC)([O:9][CH3:10])[O:7][CH3:8])[CH2:5][CH2:4][CH2:3][CH2:2]1.[CH:13]([OH:17])([CH2:15][CH3:16])[CH3:14].C[Si](C)(C)Cl>C[O-].[Na+]>[CH:13]([O:17][Si:6]([CH:1]1[CH2:5][CH2:4][CH2:3][CH2:2]1)([O:9][CH3:10])[O:7][CH3:8])([CH2:15][CH3:16])[CH3:14]
Reactant: CCC(C)O
Reactant: CO[Si](OC)(OC)C1CCCC1
Agent: C[O-]
Agent: C[Si](C)(C)Cl
Agent: [Na+]
Product: CCC(C)O[Si](OC)(OC)C1CCCC1
Yield: 84.3 %

Procedure:
In a 100 ml three-neck flask provided with a magnetic stirrer were charged 10.3 g (0.0542 mole) of cyclopentyl trimethoxysilane, 40.3 g (0.543 mole) of sec-butyl alcohol and 33.7 mg (0.625 m mole) of sodium methoxide, which were then reacted with each other at room temperature for 2 hours under stirring. Then, trimethylchlorosilane was added to neutralize the alkali. Then, 10.6 g (0.0457 mole) of sec-butoxy cyclopentyl dimethoxysilane were obtained by vacuum distillation. Its structure was confirmed as in Example 1. FIGS. 1 and 2 are charts of 1H-NMR and IR, respectively. The yield was 84%.