Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: Br[C:2]1[C:7](=[O:8])[N:6]([CH3:9])[C:5]2[N:10]([C:13]3[C:18]([F:19])=[CH:17][CH:16]=[CH:15][C:14]=3[F:20])[N:11]=[CH:12][C:4]=2[CH:3]=1.[CH:21]1([NH:24][C:25](=[O:43])[C:26]2[CH:31]=[C:30](B3OC(C)(C)C(C)(C)O3)[C:29]([CH3:41])=[C:28]([F:42])[CH:27]=2)[CH2:23][CH2:22]1>O1CCOCC1.C([O-])([O-])=O.[Na+].[Na+].CCOC(C)=O.C1C=CC([P]([Pd]([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)[P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1>[CH:21]1([NH:24][C:25](=[O:43])[C:26]2[CH:27]=[C:28]([F:42])[C:29]([CH3:41])=[C:30]([C:2]3[C:7](=[O:8])[N:6]([CH3:9])[C:5]4[N:10]([C:13]5[C:18]([F:19])=[CH:17][CH:16]=[CH:15][C:14]=5[F:20])[N:11]=[CH:12][C:4]=4[CH:3]=3)[CH:31]=2)[CH2:22][CH2:23]1
Reactant: Cn1c(=O)c(Br)cc2cnn(-c3c(F)cccc3F)c21
Reactant: Cc1c(F)cc(C(=O)NC2CC2)cc1B1OC(C)(C)C(C)(C)O1
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: CCOC(C)=O
Solvent: C1COCCO1
Product: Cc1c(F)cc(C(=O)NC2CC2)cc1-c1cc2cnn(-c3c(F)cccc3F)c2n(C)c1=O
Temperature: 130 °C
Yield: 66.3 %

Procedure:
A mixture of 5-bromo-1-(2,6-difluorophenyl)-7-methyl-1H-pyrazolo[3,4-b]pyridin-6(7H)-one (110 mg, 0.32 mmol), N-cyclopropyl-3-fluoro-4-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzamide (122 mg, 0.38 mmol) and 15 mg of Pd(PPh3)4 in 2.0 mL dioxane and 0.8 mL of 1 M Na2CO3 in a sealed glass tube was heated at 130° C. for 30 min. The reaction mixture was diluted in EtOAc, washed with 1 N NaOH solution. The organic phase was dried over MgSO4, filtered and concentrated. Purification of the brown residue on an ISCO 12 g column (40-80% EtOAc in Hexanes) afforded the title compound (96 mg) as an off white amorphous solid. MS (ESI, pos.ion) m/z: 453.1 (M+1).
Reaction SMILES: Cl[C:2]1[N:7]=[CH:6][C:5]([S:8]([N:11]2[CH2:20][CH2:19][C:18]3[C@:13]([CH2:31][O:32][CH2:33][CH2:34][OH:35])([CH2:14][C:15]4[CH:23]=[N:22][N:21]([C:24]5[CH:29]=[CH:28][C:27]([F:30])=[CH:26][CH:25]=5)[C:16]=4[CH:17]=3)[CH2:12]2)(=[O:10])=[O:9])=[CH:4][CH:3]=1.[F:36][C@@H:37]1[CH2:41][CH2:40][NH:39][CH2:38]1>>[F:30][C:27]1[CH:28]=[CH:29][C:24]([N:21]2[C:16]3[CH:17]=[C:18]4[C@:13]([CH2:31][O:32][CH2:33][CH2:34][OH:35])([CH2:14][C:15]=3[CH:23]=[N:22]2)[CH2:12][N:11]([S:8]([C:5]2[CH:6]=[N:7][C:2]([N:39]3[CH2:40][CH2:41][C@@H:37]([F:36])[CH2:38]3)=[CH:3][CH:4]=2)(=[O:9])=[O:10])[CH2:20][CH2:19]4)=[CH:25][CH:26]=1
Reactant: O=S(=O)(c1ccc(Cl)nc1)N1CCC2=Cc3c(cnn3-c3ccc(F)cc3)C[C@]2(COCCO)C1
Reactant: F[C@@H]1CCNC1
Product: O=S(=O)(c1ccc(N2CC[C@@H](F)C2)nc1)N1CCC2=Cc3c(cnn3-c3ccc(F)cc3)C[C@]2(COCCO)C1

Procedure:
The title compound was prepared by the method of Example 20 using 2-[(R)-6-(6-chloropyridine-3-sulfonyl)-1-(4-fluorophenyl)-1,4,5,6,7,8-hexahydro-1,2,6-triaza-cyclopenta[b]naphthalene-4a-ylmethoxy]-ethanol and (R)-3-fluoropyrrolidine. 1H NMR (400 MHz, CHCl3-d): δ 8.55 (d, 1H), 7.78 (dd, 1H), 7.51-7.40 (m, 3H), 7.15 (t, 2H), 6.41 (d, 1H), 6.28 (s, 1H), 5.40 (d, 1H), 4.26 (d, 1H), 3.91 (s, 2H), 3.74-3.61 (m, 6H), 3.55 (d, 1H), 3.48 (d, 1H), 3.21 (d, 1H), 3.13 (d, 1H), 2.49-2.38 (m, 2H), 2.21 (d, 1H), 2.07 (d, 1H).
Reaction SMILES: [F:1][C:2]1[C:7]([F:8])=[CH:6][CH:5]=[CH:4][C:3]=1[CH2:9][S:10][C:11]1[N:16]=[C:15]([NH:17][S:18]([N:21]2[CH2:24][CH2:23][CH2:22]2)(=[O:20])=[O:19])[CH:14]=[C:13]([O:25][C@@H:26]([C@@H:28]2[CH2:32][O:31]C(C)(C)[O:29]2)[CH3:27])[N:12]=1.C(=O)(O)[O-].[Na+]>C(Cl)Cl.O.O.O.O.O.O.[Fe](Cl)(Cl)Cl>[F:1][C:2]1[C:7]([F:8])=[CH:6][CH:5]=[CH:4][C:3]=1[CH2:9][S:10][C:11]1[N:16]=[C:15]([NH:17][S:18]([N:21]2[CH2:24][CH2:23][CH2:22]2)(=[O:20])=[O:19])[CH:14]=[C:13]([O:25][C@H:26]([CH3:27])[C@@H:28]([OH:29])[CH2:32][OH:31])[N:12]=1
Reactant: C[C@@H](Oc1cc(NS(=O)(=O)N2CCC2)nc(SCc2cccc(F)c2F)n1)[C@@H]1COC(C)(C)O1
Agent: Cl[Fe](Cl)Cl
Agent: O=C([O-])O
Agent: [Na+]
Solvent: ClCCl
Solvent: O
Product: C[C@@H](Oc1cc(NS(=O)(=O)N2CCC2)nc(SCc2cccc(F)c2F)n1)[C@@H](O)CO
Temperature: 25 °C
Reaction time: 1 h

Procedure:
To a solution of N-[2-[[(2,3-difluorophenyl)methyl]thio]-6-[(1R)-1-[(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]ethoxy]-4-pyrimidinyl]-1-azetidinesulfonamide (the product of step (0.13 g) in DCM (5 mL) was added iron (III) chloride hexahydrate (0.24 g). The reaction mixture was stirred at ambient temperature for 1 h, then saturated aqueous sodium bicarbonate (10 mL) was added. The layers were separated and the aqueous material extracted with DCM (3×10 mL) and EtOAc (3×10 mL). The combined organic extracts were washed with saturated sodium chloride, dried (MgSO4), filtered and evaporated. The residual pale yellow solid was slowly precipitated from DCM, filtered and the resulting material washed with minimal cold DCM (2×1 mL) to afford the title compound as a white powder. Yield: 45 mg.
Reaction SMILES: [Cl:1][C:2]1[C:3](Cl)=[C:4]2[N:10]=[C:9]([C:11]3[CH:16]=[CH:15][C:14]([O:17][CH2:18][CH2:19][N:20]4[CH2:25][CH2:24][O:23][CH2:22][CH2:21]4)=[CH:13][CH:12]=3)[NH:8][C:5]2=[N:6][CH:7]=1.[CH:27]1([NH2:32])[CH2:31][CH2:30][CH2:29][CH2:28]1>>[Cl:1][C:2]1[C:3]([NH:32][CH:27]2[CH2:31][CH2:30][CH2:29][CH2:28]2)=[C:4]2[NH:10][C:9]([C:11]3[CH:12]=[CH:13][C:14]([O:17][CH2:18][CH2:19][N:20]4[CH2:21][CH2:22][O:23][CH2:24][CH2:25]4)=[CH:15][CH:16]=3)=[N:8][C:5]2=[N:6][CH:7]=1
Reactant: NC1CCCC1
Reactant: Clc1cnc2[nH]c(-c3ccc(OCCN4CCOCC4)cc3)nc2c1Cl
Product: Clc1cnc2nc(-c3ccc(OCCN4CCOCC4)cc3)[nH]c2c1NC1CCCC1
Yield: 47 %

Procedure:
6,7-Dichloro-2-[4-(2-morpholin-4-ylethoxy)phenyl]-3H-imidazo[4,5-b]pyridine (Example 206) (30 mg, 7.6 μmol) and cyclopentylamine (1 ml) were heated in a microwave oven (170-° C.: 30 min). The excess amine was removed in vacuo and the residue dissolved in acetonitrile (1 ml) with a drop of TFA. This mixture was subjected to semi-preparative HPLC-C18. The appropriate fractions were pooled and evaporated in vacuo. The residue was dissolved in EtOAc (5 ml). This solution was washed with saturated aqueous NaHCO3 (5 ml) and brine (2 ml). The organic phase was dried (MgSO4) and evaporated in vacuo and the residue recrystallized from methanol to afford the pure product (16 mg, 47%).
Reaction SMILES: [CH:1]1([C@H:4]([N:8]2[C:13](=[O:14])[C:12]([NH:15][C:16]3[C:17]([CH3:25])=[N:18][C:19]([O:23]C)=[C:20]([CH3:22])[CH:21]=3)=[N:11][C:10]([C:26]#[N:27])=[CH:9]2)[CH2:5][O:6][CH3:7])[CH2:3][CH2:2]1>C(O)(=O)C>[CH:1]1([C@H:4]([N:8]2[C:13](=[O:14])[C:12]([NH:15][C:16]3[C:17]([CH3:25])=[N:18][C:19]([OH:23])=[C:20]([CH3:22])[CH:21]=3)=[N:11][C:10]([C:26]#[N:27])=[CH:9]2)[CH2:5][O:6][CH3:7])[CH2:3][CH2:2]1
Reactant: COC[C@H](C1CC1)n1cc(C#N)nc(Nc2cc(C)c(OC)nc2C)c1=O
Solvent: CC(=O)O
Product: COC[C@H](C1CC1)n1cc(C#N)nc(Nc2cc(C)c(O)nc2C)c1=O
Reaction time: 1 h

Procedure:
(S)-4-(1-Cyclopropyl-2-methoxyethyl)-6-(6-methoxy-2,5-dimethylpyridin-3-ylamino)-5-oxo-4,5-dihydropyrazine-2-carbonitrile (3.00 g, 8.12 mmol) and KI (6.2 g, 37.3 mmol) in glacial acetic acid (80 mL) was heated at 100° C. with stirring for 1 h. LC-MS analysis indicated >98% conversion to the required product. The reaction mixture was cooled to ambient temperature and acetic acid was evaporated in vacuo. The residue was partitioned between ethyl acetate (3×150 mL) and H2O (˜100 mL). The organic layer was washed with brine (100 mL) and then dried over Na2SO4. The organic layer was evaporated in vacuo and the dark brown residue was purified by Biotage SiO2 column chromatography (5% MeOH/CH2Cl2, Rf=0.16) to give pure (S)-4-(1-cyclopropyl-2-methoxyethyl)-6-(6-hydroxy-2,5-dimethylpyridin-3-ylamino)-5-oxo-4,5-dihydropyrazine-2-carbonitrile (2.33 g, 81%) as pale yellow solid: 1H NMR (CDCl3) δ 7.85-7.55 (br. s, 1H), 7.48 (s, 1H), 4.16-4.12 (m, 1H), 3.73 (dd, 1H, JAB=10.3 Hz, JAX=4.9 Hz), 3.66 (dd, JBX=2.2 Hz), 3.35 (s, 3H), 2.40-2.20 (br s, 6H), 1.39-1.32 (m, 1H), 0.85-0.79 (m, 1H), 0.67-0.61 (m, 1H), 0.55-0.51 (m, 1H), 0.34-0.29 (m, 1H); LRMS (ESI) m/e 356 [(M+H)+, calcd for C18H21N5O3 356]; tR=1.8 min (Solvent A: MeOH:H2O:TFA=10:90:0.1; Solvent B: MeOH:H2O:TFA=90:10:0.1; 0% B in A to 100% B in A linear gradient in a 3 min run with 1 min hold time at the end, λ=280 nm).
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:4]=[C:5]2[C:10](=[CH:11][C:12]=1[O:13][CH2:14][CH2:15][CH2:16]Cl)[N:9]=[CH:8][NH:7][C:6]2=[O:18].[NH:19]1[CH2:24][CH2:23][O:22][CH2:21][CH2:20]1>>[CH3:1][O:2][C:3]1[CH:4]=[C:5]2[C:10](=[CH:11][C:12]=1[O:13][CH2:14][CH2:15][CH2:16][N:19]1[CH2:24][CH2:23][O:22][CH2:21][CH2:20]1)[N:9]=[CH:8][NH:7][C:6]2=[O:18]
Reactant: COc1cc2c(=O)[nH]cnc2cc1OCCCCl
Reactant: C1COCCN1
Product: COc1cc2c(=O)[nH]cnc2cc1OCCCN1CCOCC1
Temperature: 105 °C
Reaction time: 4 h
Yield: 91.8 %

Procedure:
In a 25 mL volume glass vessel equipped with a stirrer, a thermometer and a reflux condenser were placed 2.0 g (7.4 mmol) of 6-methoxy-7-(3-chloropropoxy)quinazolin-4-one prepared by procedures similar to those of Reference Example V-1, and 6.45 g (74 mmol) of morpholine. The resulting mixture was stirred at 105° C. for 4 hours. After the reaction was complete, the reaction mixture was analyzed by high performance liquid chromatography (absolute quantitative analysis). There was produced 2.17 g (reaction yield: 92%) of 6-methoxy-7-(3-morpholinopropoxy)quinazolin-4-one.
Reaction SMILES: [NH2:1][C:2]1[C:3]([Cl:17])=[C:4]([C:12]([O:14][CH2:15][CH3:16])=[O:13])[C:5]([CH3:11])=[N:6][C:7]=1[NH:8][CH2:9][CH3:10].[CH2:18](OC(OCC)OCC)C>>[Cl:17][C:3]1[C:4]([C:12]([O:14][CH2:15][CH3:16])=[O:13])=[C:5]([CH3:11])[N:6]=[C:7]2[N:8]([CH2:9][CH3:10])[CH:18]=[N:1][C:2]=12
Reactant: CCNc1nc(C)c(C(=O)OCC)c(Cl)c1N
Reactant: CCOC(OCC)OCC
Product: CCOC(=O)c1c(C)nc2c(ncn2CC)c1Cl

Procedure:
25.7 g. of 5-amino-6-ethylamino-4-chloro-2-methylpyridine-3-carboxylic acid, ethyl ester (0.1 mol.) is refluxed for 12 hours with 100 ml. of orthoformic acid triethyl ester with stirring. The excess ester is removed in vacuo and the oily residue distilled to obtain 7-chloro-3-ethyl-5-methyl-3H-imidazo[4,5-b]pyridine-6-carboxylic acid, ethyl ester, b.p. 195°/0.01. Yield 23 g. (86%).
Reaction SMILES: [Br:1][C:2]1[CH:3]=[C:4]([NH:10][C:11]2[CH:15]=[C:14]([CH3:16])[NH:13][N:12]=2)[C:5](=[O:9])[N:6]([CH3:8])[CH:7]=1.[H-].[Na+].Br[CH2:20][CH2:21][O:22][Si:23]([C:26]([CH3:29])([CH3:28])[CH3:27])([CH3:25])[CH3:24].O>CN(C=O)C>[Br:1][C:2]1[CH:3]=[C:4]([NH:10][C:11]2[CH:15]=[C:14]([CH3:16])[N:13]([CH2:20][CH2:21][O:22][Si:23]([C:26]([CH3:29])([CH3:28])[CH3:27])([CH3:25])[CH3:24])[N:12]=2)[C:5](=[O:9])[N:6]([CH3:8])[CH:7]=1
Reactant: Cc1cc(Nc2cc(Br)cn(C)c2=O)n[nH]1
Reactant: CC(C)(C)[Si](C)(C)OCCBr
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: O
Product: Cc1cc(Nc2cc(Br)cn(C)c2=O)nn1CCO[Si](C)(C)C(C)(C)C
Yield: 59.6 %

Procedure:
A solution of 5-bromo-1-methyl-3-(5-methyl-1H-pyrazol-3-ylamino)pyridin-2(1H)-one 112a (1.08 g, 3.8 mmol) in anhydrous DMF (10 mL) was treated with 60% dispersion of NaH in mineral oil (0.17 g, 4.3 mmol) while stirring under nitrogen. After effervescence the reaction was stirred for an additional 30 min. At this time the reaction was treated with (2-bromoethoxy)(tert-butyl)dimethylsilane (15-1) (0.908 g, 3.8 mmol) and continued to stir under nitrogen for 10 hours. After reaction water (50 mL) was added slowly and the mixture was filtered. The filtrate was concentrated under reduced pressure and the residue was purified by flash column chromatography eluting with petroleum ether/ethyl acetate to afford 161a (1 g, 35%), which was used directly without further purification. LCMS: (M+H)+ 443.
Reaction SMILES: C1N=CN(C(N2C=NC=C2)=O)C=1.[C:13]1([S:19]([CH2:22][CH2:23][S:24][C:25]2[N:33]=[CH:32][CH:31]=[CH:30][C:26]=2[C:27]([OH:29])=O)(=[O:21])=[O:20])[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1.[CH2:34]([NH2:41])[C:35]1[CH:40]=[CH:39][CH:38]=[CH:37][CH:36]=1>C(Cl)Cl>[CH2:34]([NH:41][C:27](=[O:29])[C:26]1[CH:30]=[CH:31][CH:32]=[N:33][C:25]=1[S:24][CH2:23][CH2:22][S:19]([C:13]1[CH:14]=[CH:15][CH:16]=[CH:17][CH:18]=1)(=[O:20])=[O:21])[C:35]1[CH:40]=[CH:39][CH:38]=[CH:37][CH:36]=1
Reactant: O=C(O)c1cccnc1SCCS(=O)(=O)c1ccccc1
Reactant: NCc1ccccc1
Agent: O=C(n1ccnc1)n1ccnc1
Solvent: ClCCl
Product: O=C(NCc1ccccc1)c1cccnc1SCCS(=O)(=O)c1ccccc1
Temperature: 25 °C
Reaction time: 1 h
Yield: 83.1 %

Procedure:
132 mg (0.81 mmol) of CDI were added to a solution of 250 mg (0.77 mmol) of 2-(2-(phenylsulfonyl)ethylthio)nicotinic acid in DCM (6 ml), and the mixture was stirred for 1 h at RT. A solution of 82 mg (0.77 mmol) of benzylamine in DCM (6 ml) was then added, and stirring was continued for a further 16 hours at RT. The reaction solution was then washed in each case three times with a sat. aq. ammonium chloride solution and saturated aqueous NaHCO3 solution. The organic phase was dried over MgSO4, filtered and concentrated in vacuo. 266 mg (0.64 mmol, 83%) of N-benzyl-2-(2-(phenylsulfonyl)ethylthio)nicotinamide were obtained as residue.
Reaction SMILES: [N+:1]([C:4]1[CH:5]=[C:6]([CH:10]=[CH:11][C:12]=1[N+:13]([O-:15])=[O:14])[C:7](Cl)=[O:8])([O-:3])=[O:2].[C:16]([NH:19][C:20]1[CH:25]=[CH:24][CH:23]=[CH:22][CH:21]=1)(=[O:18])[CH3:17].[Al+3].[Cl-].[Cl-].[Cl-]>C(Cl)Cl>[C:16]([NH:19][C:20]1[CH:25]=[CH:24][C:23]([C:7]([C:6]2[CH:10]=[CH:11][C:12]([N+:13]([O-:15])=[O:14])=[C:4]([N+:1]([O-:3])=[O:2])[CH:5]=2)=[O:8])=[CH:22][CH:21]=1)(=[O:18])[CH3:17]
Reactant: O=C(Cl)c1ccc([N+](=O)[O-])c([N+](=O)[O-])c1
Reactant: CC(=O)Nc1ccccc1
Agent: [Al+3]
Agent: [Cl-]
Solvent: ClCCl
Product: CC(=O)Nc1ccc(C(=O)c2ccc([N+](=O)[O-])c([N+](=O)[O-])c2)cc1
Temperature: 40 °C
Yield: 6.6 %

Procedure:
A mixture of 3,4-dinitrobenzoyl chloride (4 mmol), acetoanilide (540 mg, 4 mmol), and AlCl3 (1.6 g) in CH2Cl2 was heated at 40° C. for 24 h. The slurry was washed with HCl (aq) and the product was extracted with ether. It was washed with K2CO3 (aq), dried, and evaporated. Purification by column-chromatography on silica-gel (hexane:AcOEt=1:3) provided 87 mg of the title compound; MS m/e 328 (M−1).
Reaction SMILES: C(=O)([O-])[O-].[K+].[K+].[Br:7][C:8]1[CH:9]=[CH:10][C:11](F)=[C:12]([CH:15]=1)[C:13]#[N:14].[CH3:17][C:18]1[N:19]=[CH:20][NH:21][CH:22]=1>CN(C=O)C>[Br:7][C:8]1[CH:9]=[CH:10][C:11]([N:19]2[C:18]([CH3:17])=[CH:22][N:21]=[CH:20]2)=[C:12]([CH:15]=1)[C:13]#[N:14]
Reactant: N#Cc1cc(Br)ccc1F
Reactant: Cc1c[nH]cn1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Product: Cc1cncn1-c1ccc(Br)cc1C#N
Temperature: 100 °C
Reaction time: 4.5 h
Yield: 2.3 %

Procedure:
Potassium carbonate (2.07 g) was added to a DMF (20 mL) solution of 5-bromo-2-fluorobenzonitrile (2.00 g) and 4-methylimidazole (1.23 g) and the reaction solution was agitated at 100° C. for 4.5 hours. The reaction mixture was concentrated under reduced pressure, water and ethyl acetate were added to the residue, and the organic layer was partitioned. The organic layer was washed with a saturated saline solution, dried over anhydrous magnesium sulfate, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (elution solvent: hexane-ethyl acetate system), and 5-bromo-2-(4-methyl-1H-imidazol-1-yl)benzonitrile (962 mg) and 5-bromo-2-(5-methyl-1H-imidazol-1-yl)benzonitrile (60 mg) were obtained.
Reaction SMILES: Br[C:2]1[N:7]=[C:6]([CH:8]=[O:9])[CH:5]=[CH:4][CH:3]=1.[CH:10]#[C:11][CH2:12][CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][CH2:21][CH2:22][CH2:23][CH2:24][CH3:25].C(N(CC)CC)C>O1CCCC1.C1C=CC(P(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1.C1C=CC(P(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1.Cl[Pd]Cl.[Cu]I>[C:10]([C:2]1[N:7]=[C:6]([CH:8]=[O:9])[CH:5]=[CH:4][CH:3]=1)#[C:11][CH2:12][CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][CH2:21][CH2:22][CH2:23][CH2:24][CH3:25]
Reactant: C#CCCCCCCCCCCCCCC
Reactant: O=Cc1cccc(Br)n1
Agent: Cl[Pd]Cl
Agent: [Cu]I
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: C1CCOC1
Solvent: CCN(CC)CC
Product: CCCCCCCCCCCCCCC#Cc1cccc(C=O)n1
Temperature: 25 °C
Yield: 53.1 %

Procedure:
A solution of 6-bromo-2-pyridinecarboxaldehyde (12.3 g), 1-hexadecyne (16.1 g), triethylamine (20.0 g), bis(triphenylphosphine)palladium(II)chloride (0.92 g), and copper(I)iodide (0.13 g) in dry tetrahydrofuran (55 ml) was heated at 50° C. for 29 hrs, under nitrogen. The reaction mixture was cooled to room temperature, filtered, and the filter cake was washed with ethyl acetate. The filtrate was evaporated and the residue was taken up in ethyl acetate (100 ml). The mixture was washed with 1:1-water:saturated sodium chloride solution, dried over anhydrous magnesium sulfate, filtered, and the filtrate was evaporated. The residue was flash chromatographed on silica gel, eluting with 1% ethyl acetate:hexanes. The appropriate fractions were collected and evaporated. The residue was dissolved in ethyl acetate and the solution was washed with half-saturated sodium chloride solution, dried over anhydrous magnesium sulfate, filtered, and the filtrate was evaporated to give 11.5 g (53.5%) of product, mp 38.5°-40° C.
Reaction SMILES: CO[C:3]([O:6][CH3:7])([CH3:5])[CH3:4].O.C1(C)C=CC(S(O)(=O)=O)=CC=1.[C:20]([O:24][C:25]([NH:27][C@@H:28]([CH2:31][CH2:32][OH:33])CO)=[O:26])([CH3:23])([CH3:22])[CH3:21]>ClCCl>[C:20]([O:24][C:25]([N:27]1[C@@H:28]([CH2:31][CH2:32][OH:33])[CH2:7][O:6][C:3]1([CH3:4])[CH3:5])=[O:26])([CH3:23])([CH3:22])[CH3:21]
Reactant: COC(C)(C)OC
Reactant: CC(C)(C)OC(=O)N[C@H](CO)CCO
Agent: Cc1ccc(S(=O)(=O)O)cc1
Solvent: O
Solvent: ClCCl
Product: CC(C)(C)OC(=O)N1[C@@H](CCO)COC1(C)C
Yield: 47.8 %

Procedure:
2,2-Dimethoxypropane (87 ml, 0.707 mol) and p-toluenesulphonic acid monohydrate (1.33 g, 7 mmol) were added to a stirred solution of the diol 4 (14.39 g, 70 mmol) in dichloromethane (319 ml) at 25° C. The reaction was monitored by TLC (ethyl acetate-hexanes 2:1) until complete (36 h). The reaction mixture was then washed with aqueous NaHCO3 (5%, 2×50 ml), brine (50 ml), dried (MgSO4) and concentrated to form a colourless oil, which crystallised upon standing. The ratio of the desired five-membered ring product 5 to the undesired six-membered ring product 6 was 6.4:3.6. Recrystallisation from heptane gave 5 as colourless needles (8.2 g, 48%). Spectral data for this sample were consistent with those given in the literature3. 1 H NMR (200 MHz, CDCl3) 4.17 (m, 1H), 3.97 (m, 1H), 3.86-3.42 (m, 3H), 3.33 (br, 1H), 1.76 (m, 2H), 1.5 (s, 3H), 1.46 (s, 9H); 13C NMR (50 MHz, CDCl3) 153.9, 93.6, 80.9, 68.2, 58.6, 53.9, 37.7, 27.7, 26.3, 243.
Reaction SMILES: [C:1](Cl)(=[O:4])[CH:2]=[CH2:3].[F:6][C:7]1[CH:28]=[C:27]([N+:29]([O-:31])=[O:30])[CH:26]=[CH:25][C:8]=1[O:9][C:10]1[CH:15]=[CH:14][N:13]=[C:12]2[CH:16]=[C:17]([C:19]3[CH2:20][CH2:21][NH:22][CH2:23][CH:24]=3)[S:18][C:11]=12.C([O-])([O-])=O.[K+].[K+]>>[F:6][C:7]1[CH:28]=[C:27]([N+:29]([O-:31])=[O:30])[CH:26]=[CH:25][C:8]=1[O:9][C:10]1[CH:15]=[CH:14][N:13]=[C:12]2[CH:16]=[C:17]([C:19]3[CH2:20][CH2:21][N:22]([C:1](=[O:4])[CH:2]=[CH2:3])[CH2:23][CH:24]=3)[S:18][C:11]=12
Reactant: O=[N+]([O-])c1ccc(Oc2ccnc3cc(C4=CCNCC4)sc23)c(F)c1
Reactant: C=CC(=O)Cl
Agent: O=C([O-])[O-]
Agent: [K+]
Product: C=CC(=O)N1CC=C(c2cc3nccc(Oc4ccc([N+](=O)[O-])cc4F)c3s2)CC1
Temperature: 25 °C
Reaction time: 8 h
Yield: 101.1 %

Procedure:
Acryloyl chloride (131.3 mL, 1.62 mmol) was added to a suspension of 7-(2-fluoro-4-nitrophenoxy)-2-(1,2,3,6-tetrahydropyridin-4-yl)thieno[3,2-b]pyridine (85) [US 2007/0004675 A1](150 mg, 0.40 mmol) and K2CO3 (223.4 1.62 mmol) and the mixture was stirred overnight at room temperature. It was then filtered and concentrated under reduced pressure affording title compound 98 (172 mg, 100% yield) that was used in the next step without further purification. MS (m/z): 426.1 (M+1)
Reaction SMILES: [Br:1][C:2]1[C:3]([CH3:11])=[C:4]([CH:8]=[CH:9][CH:10]=1)[C:5]([OH:7])=[O:6].S(=O)(=O)(O)O.[OH-].[Na+].[CH3:19]O>>[Br:1][C:2]1[C:3]([CH3:11])=[C:4]([CH:8]=[CH:9][CH:10]=1)[C:5]([O:7][CH3:19])=[O:6]
Reactant: CO
Reactant: Cc1c(Br)cccc1C(=O)O
Agent: O=S(=O)(O)O
Agent: [Na+]
Agent: [OH-]
Product: COC(=O)c1cccc(Br)c1C

Procedure:
A solution of 3-bromo-2-methylbenzoic acid (9.95 g) and conc. sulfuric acid (0.2 ml) in methanol (50 ml) was stirred at room temperature for 69 h and heated under reflux for 96 h. The reaction mixture was neutralized with 1N aqueous sodium hydroxide solution and concentrated. The residue was diluted with ethyl acetate, washed 3 times with 1N aqueous sodium hydroxide solution and with saturated brine and dried over anhydrous magnesium sulfate. The solvent was evaporated under reduced pressure to give the title compound (10.2 g) as a colorless oil.
Reaction SMILES: [CH2:1]([N:7]1[C:18](=[O:19])[C:17]2[N:15]([CH3:16])[CH:14]=[N:13][C:12]=2[N:10](C)[C:8]1=O)[CH2:2][CH2:3][CH2:4][CH2:5][CH3:6].[OH-].[Na+]>C(Cl)(Cl)Cl.C(O)C>[CH2:1]([NH:7][C:18]([C:17]1[N:15]([CH3:16])[CH:14]=[N:13][C:12]=1[NH:10][CH3:8])=[O:19])[CH2:2][CH2:3][CH2:4][CH2:5][CH3:6]
Reactant: CCCCCCn1c(=O)c2c(ncn2C)n(C)c1=O
Agent: [Na+]
Agent: [OH-]
Solvent: ClC(Cl)Cl
Solvent: CCO
Product: CCCCCCNC(=O)c1c(NC)ncn1C
Temperature: 25 °C
Yield: 38.4 %

Procedure:
Hexyltheobromine (7.5 g) was added to 60 ml of 3N sodium hydroxide, and the mixture was refluxed at elevated temperatures for 6 hours. After the reaction mixture was cooled to ambient temperature, it was extracted with chloroform and the extract was dried and concentrated under reduced pressure to give the residue which in turn was subjected to silica gel column chromatography using a chloroform/ethanol (25:2(v/v)) eluent, thereby yielding 2.6 g (38%) of 5-hexylaminocarbonyl-1-methyl-4-methylaminoimidazole as an oil. A portion of this product was then treated with an ethanolic solution of picric acid to give its picrate.
Reaction SMILES: [CH3:1][N:2]([CH3:32])[C:3]([C:5]1[N:26]([CH:27]2[CH2:31][CH2:30][CH2:29][CH2:28]2)[C:8]2[N:9]=[C:10]([NH:13][C:14]3[CH:19]=[CH:18][C:17]([N:20]4[CH2:25][CH2:24][NH:23][CH2:22][CH2:21]4)=[CH:16][N:15]=3)[N:11]=[CH:12][C:7]=2[CH:6]=1)=[O:4].[N:33]1([C:39](Br)=[O:40])[CH2:38][CH2:37][CH2:36][CH2:35][CH2:34]1>>[CH3:1][N:2]([CH3:32])[C:3]([C:5]1[N:26]([CH:27]2[CH2:31][CH2:30][CH2:29][CH2:28]2)[C:8]2[N:9]=[C:10]([NH:13][C:14]3[CH:19]=[CH:18][C:17]([N:20]4[CH2:21][CH2:22][N:23]([C:39]([N:33]5[CH2:38][CH2:37][CH2:36][CH2:35][CH2:34]5)=[O:40])[CH2:24][CH2:25]4)=[CH:16][N:15]=3)[N:11]=[CH:12][C:7]=2[CH:6]=1)=[O:4]
Reactant: CN(C)C(=O)c1cc2cnc(Nc3ccc(N4CCNCC4)cn3)nc2n1C1CCCC1
Reactant: O=C(Br)N1CCCCC1
Product: CN(C)C(=O)c1cc2cnc(Nc3ccc(N4CCN(C(=O)N5CCCCC5)CC4)cn3)nc2n1C1CCCC1
Yield: 66.1 %

Procedure:
Following General Procedure G, 7-cyclopentyl-2-(5-piperazin-1-yl-pyridin-2-ylamino)-7H-pyrrolo[2,3-d]pyrimidine-6-carboxylic acid dimethylamide (100 mg, 0.230 mmol) and piperidine-1-carbonyl bromide (32 mL, 0.690 mmol) gave 7-cyclopentyl-2-{5-[4-(piperidine-1-carbonyl)-piperazin-1-yl]-pyridin-2-ylamino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxylic acid dimethylamide (83 mg, 64%). MS (ESI) m/z 546.3 (M+H)+
Reaction SMILES: [CH3:1][C:2]([C:5]1[CH:10]=[C:9]([SH:11])[CH:8]=[C:7]([C:12]([CH3:15])([CH3:14])[CH3:13])[C:6]=1[OH:16])([CH3:4])[CH3:3].C(N(CC)CC)C.[CH3:24][C:25]([CH:27]=[CH2:28])=[O:26].Cl>CO>[CH3:4][C:2]([C:5]1[CH:10]=[C:9]([S:11][CH2:28][CH2:27][C:25](=[O:26])[CH3:24])[CH:8]=[C:7]([C:12]([CH3:15])([CH3:14])[CH3:13])[C:6]=1[OH:16])([CH3:1])[CH3:3]
Reactant: CC(C)(C)c1cc(S)cc(C(C)(C)C)c1O
Reactant: C=CC(C)=O
Agent: Cl
Solvent: CCN(CC)CC
Solvent: CO
Product: CC(=O)CCSc1cc(C(C)(C)C)c(O)c(C(C)(C)C)c1
Reaction time: 20 h

Procedure:
The title compound of Example 2 (2.0 g) was dissolved in methanol (20 ml) and triethylamine (0.5 ml) added followed by methylvinylketone (0.0084 mole). The reaction was stirred under nitrogen for about 20 hours. 0.1 N Hydrochloric acid (80 ml) was added and the aqueous phase extracted with ethyl ether. The organic extracts were dried over sodium sulfate, filtered, the solvent removed in vacuo and the residue chromatographed on silica to give the title compound, m.p. ca. 79-81° C.