Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [C:1]1([CH2:7][CH:8]=O)[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.Cl.[CH2:11]([O:18][NH2:19])[C:12]1[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1.C(=O)([O-])[O-].[K+].[K+]>CO>[CH2:11]([O:18][N:19]=[CH:8][CH2:7][C:1]1[CH:2]=[CH:3][CH:4]=[CH:5][CH:6]=1)[C:12]1[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1
Reactant: NOCc1ccccc1
Reactant: O=CCc1ccccc1
Agent: Cl
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CO
Product: C(Cc1ccccc1)=NOCc1ccccc1
Yield: 85.3 %

Procedure:
A mixture of 5 g of phenylacetaldehyde, 6.7 g of O-benzylhydroxylamine hydrochloride, and 3 g of potassium carbonate in 30 ml of aqueous methanol (1:1) was refluxed for 2 hours. The aqueous solution was extracted with ethyl acetate and the organic solution was dried and evaporated to give 8 g of crude product which was used without purification.
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]([NH2:17])[C:14]([NH2:18])=[C:13]([NH2:19])[N:12]=1.[C:20](OCC)(=O)[CH:21]=[O:22].O.Cl>[Na].CO>[NH2:17][C:15]1[C:14]2[N:18]=[CH:20][C:21](=[O:22])[NH:19][C:13]=2[N:12]=[C:11]([S:10][CH2:9][C:3]2[CH:4]=[CH:5][CH:6]=[C:7]([F:8])[C:2]=2[F:1])[N:16]=1
Reactant: Nc1nc(SCc2cccc(F)c2F)nc(N)c1N
Reactant: CCOC(=O)C=O
Agent: Cl
Agent: [Na]
Solvent: O
Solvent: CO
Product: Nc1nc(SCc2cccc(F)c2F)nc2[nH]c(=O)cnc12
Temperature: 25 °C
Reaction time: 0.25 h

Procedure:
The product of example 2, step (c) (100 mg) was dissolved in a solution of sodium (0.05 g) in methanol (5 ml). This was left to stir for 15 min at room temperature, then ethyl glyoxalate (134 μl) was added to the mixture which was left to stir for 12 hr at room temperature. Water (5 ml) was added, then concentrated hydrochloric acid was slowly .5 added to acidify the solution to ˜pH5 whereupon a solid precipitated which was isolated by filtration and dried over P2O5 at 50° C. to yield a pale yellow solid (44.5 mg).
Reaction SMILES: C(N(C(C)C)CC)(C)C.O=[C:11]1[CH2:17][C@H:16]2[N:13]([C:14](=[O:35])[C@H:15]2[C:18]([CH3:34])([O:20][C:21]([O:23][CH2:24][C:25]2[CH:30]=[CH:29][C:28]([N+:31]([O-:33])=[O:32])=[CH:27][CH:26]=2)=[O:22])[CH3:19])[C@H:12]1[C:36]([O:38][CH2:39][C:40]1[CH:45]=[CH:44][C:43]([N+:46]([O-:48])=[O:47])=[CH:42][CH:41]=1)=[O:37].P(Cl)(OC1C=CC=CC=1)(OC1C=CC=CC=1)=O.[NH2:66][C:67]1[CH:72]=[CH:71][CH:70]=[CH:69][C:68]=1[SH:73]>C(#N)C.CN(C1C=CN=CC=1)C>[NH2:66][C:67]1[CH:72]=[CH:71][CH:70]=[CH:69][C:68]=1[S:73][C:11]1[CH2:17][C@H:16]2[N:13]([C:14](=[O:35])[C@H:15]2[C:18]([CH3:19])([O:20][C:21]([O:23][CH2:24][C:25]2[CH:30]=[CH:29][C:28]([N+:31]([O-:33])=[O:32])=[CH:27][CH:26]=2)=[O:22])[CH3:34])[C:12]=1[C:36]([O:38][CH2:39][C:40]1[CH:45]=[CH:44][C:43]([N+:46]([O-:48])=[O:47])=[CH:42][CH:41]=1)=[O:37]
Reactant: CC(C)(OC(=O)OCc1ccc([N+](=O)[O-])cc1)[C@@H]1C(=O)N2[C@@H](C(=O)OCc3ccc([N+](=O)[O-])cc3)C(=O)C[C@H]12
Reactant: Nc1ccccc1S
Agent: CN(C)c1ccncc1
Agent: O=P(Cl)(Oc1ccccc1)Oc1ccccc1
Solvent: CC#N
Solvent: CCN(C(C)C)C(C)C
Product: CC(C)(OC(=O)OCc1ccc([N+](=O)[O-])cc1)[C@@H]1C(=O)N2C(C(=O)OCc3ccc([N+](=O)[O-])cc3)=C(Sc3ccccc3N)C[C@H]12
Temperature: 0 °C
Reaction time: 0.5 h
Yield: 78.7 %

Procedure:
A solution of N,N-diisopropyl-N-ethylamine (0.247 ml) in acetonitrile (2.2 ml) was added to a solution of 4-nitrobenzyl (2R,5R,6R)-3,7-dioxo-6-[1-methyl-1-(4-nitrobenzyloxycarbonyloxy)ethyl]-1-azabicyclo[3.2.0]heptane-2-carboxylate (640 mg) and 4-(N,N-dimethylamino)pyridine (14.4 mg) in acetonitrile (32 ml) at 0° C. A solution of diphenyl chlorophosphate (0.257 ml) in acetonitrile (2.3 ml) was then added thereto at 0° C. After the mixture was stirred at 0° C. for 30 minutes, N,N-diisopropyl-N-ethylamine (0.824 ml) and a solution of 2-aminobenzenethiol (155 mg) in acetonitrile (1.4 ml) were added at 0° C. After stirring at 0° C. for an hour, the mixture was evaporated in vacuo and the residue was dissolved in ethyl acetate (50 ml). This solution was washed twice with water (X2) and an aqueous sodium chloride, dried over magnesium sulfate, and then evaporated in vacuo. The residue was chromatographed on silica gel (20 g) eluting with a mixture of benzene and acetone (50:1 to 10:1) to give 4-nitrobenzyl (5R,6R)-3-(2-aminophenylthio)-6-[1-methyl-1-(4-nitrobenzyloxycarbonyloxy)ethyl]-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylate (603 mg) as an oil.
Reaction SMILES: [H-].[Na+].[I-].[CH3:4][S+](C)C.[I-].[OH:9][C:10]1[C:11]([CH2:16][N+](C)(C)C)=[N:12][CH:13]=[CH:14][CH:15]=1>CS(C)=O.O>[O:9]1[C:10]2[C:11](=[N:12][CH:13]=[CH:14][CH:15]=2)[CH2:16][CH2:4]1
Reactant: C[N+](C)(C)Cc1ncccc1O
Reactant: C[S+](C)C
Agent: [H-]
Agent: [I-]
Agent: [Na+]
Solvent: O
Solvent: CS(C)=O
Product: c1cnc2c(c1)OCC2
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 47.2 %

Procedure:
To a suspension of 60% sodium hydride (11.4 g, 286 mmol) in DMSO (170 mL) was added trimethylsulfonium iodide (29.9 g, 136 mmol), and the mixture was stirred at room temperature for 30 min. A solution of (3-hydroxypyridin-2-yl)-N,N,N-trimethylmethanaminium iodide (40.0 g, 136 mmol) in DMSO (130 mL) was added dropwise thereto, and the mixture was further stirred at room temperature for 2 hr. The reaction mixture was diluted with water, and the mixture was extracted with ethyl acetate. 1M Hydrochloric acid was added to the extract, and the mixture was extracted with water. The extract was basified with 1M aqueous sodium hydroxide solution and extracted again with ethyl acetate. The extract was washed with saturated brine and dried over anhydrous sodium sulfate. The solvent was evaporated under reduced pressure and the residue was purified by silica gel column chromatography (ethyl acetate/hexane=20/80→50/50) to give the title compound (7.77 g, yield 47%).
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[CH2:14][CH2:13][C:12]2[C:15]([S:20][CH2:21][C:22]3[CH:27]=[CH:26][C:25]([C:28]#[C:29][C:30]4[CH:35]=[CH:34][C:33]([F:36])=[CH:32][CH:31]=4)=[CH:24][N:23]=3)=[C:16]([Cl:19])[CH:17]=[CH:18][C:11]=2[CH2:10][CH2:9]1)=[O:7])([CH3:4])([CH3:3])[CH3:2].N1C2C(=CC=CC=2)C=CC=1>[Pd].CC([O-])=O.CC([O-])=O.[Pb+2].CO>[C:1]([O:5][C:6]([N:8]1[CH2:14][CH2:13][C:12]2[C:15]([S:20][CH2:21][C:22]3[CH:27]=[CH:26][C:25](/[CH:28]=[CH:29]\[C:30]4[CH:31]=[CH:32][C:33]([F:36])=[CH:34][CH:35]=4)=[CH:24][N:23]=3)=[C:16]([Cl:19])[CH:17]=[CH:18][C:11]=2[CH2:10][CH2:9]1)=[O:7])([CH3:4])([CH3:2])[CH3:3]
Reactant: CC(C)(C)OC(=O)N1CCc2ccc(Cl)c(SCc3ccc(C#Cc4ccc(F)cc4)cn3)c2CC1
Agent: [Pd]
Agent: CC(=O)[O-]
Agent: [Pb+2]
Solvent: CO
Solvent: c1ccc2ncccc2c1
Product: CC(C)(C)OC(=O)N1CCc2ccc(Cl)c(SCc3ccc(/C=C\c4ccc(F)cc4)cn3)c2CC1
Reaction time: 36 h
Yield: 63.1 %

Procedure:
Dissolve 3-tert-butoxycarbonyl-7-chloro-6-[5-(4-fluorophenylethynyl)-pyridin-2-ylmethylthio]-2,3,4,5-tetrahydro-1H-benzo[d]azepine (1.0 g, 1.9 mmol), Lindlar catalyst (240 mg), and quinoline (0.8 mL) in methanol (30 mL). Degas, purge with nitrogen, and stir under a balloon of hydrogen for 36 h. Filter the mixture and wash the catalyst with additional methanol. Concentrate the filtrate in vacuo. Purify by chromatography on silica gel eluting with hexane/EtOAc (8:1) to give (Z)-3-tert-butoxycarbonyl-7-chloro-6-{5-[2-(4-fluoro-phenyl)-vinyl]-pyridin-2-ylmethylthio}-2,3,4,5-tetrahydro-1H-benzo[d]azepine as a clear oil (630 mg, 63%). MS (APCI+) m/z: 525 (M+H), 425 (M+H−Boc)+. Use a method similar to the General Procedure 1-4 to give the title compound as a pale yellow solid. MS (APCI+) m/z: 425 (M+H)+.
Reaction SMILES: C(=O)(O)[O-].[Na+].[C:6]([O:10][C:11](=[O:31])[NH:12][CH2:13][CH2:14][N:15]1[CH2:22][CH:21]2[O:23][CH:17]([CH2:18][N:19](CC3C=CC=CC=3)[CH2:20]2)[CH2:16]1)([CH3:9])([CH3:8])[CH3:7]>C(O)C.ClCCl.[Pd]>[C:6]([O:10][C:11](=[O:31])[NH:12][CH2:13][CH2:14][N:15]1[CH2:16][CH:17]2[O:23][CH:21]([CH2:20][NH:19][CH2:18]2)[CH2:22]1)([CH3:9])([CH3:7])[CH3:8]
Reactant: CC(C)(C)OC(=O)NCCN1CC2CN(Cc3ccccc3)CC(C1)O2
Agent: [Pd]
Agent: O=C([O-])O
Agent: [Na+]
Solvent: ClCCl
Solvent: CCO
Product: CC(C)(C)OC(=O)NCCN1CC2CNCC(C1)O2
Reaction time: 18 h
Yield: 89.1 %

Procedure:
Sodium bicarbonate (0.058 g, 0.069 mmol) and 5% Pd/C (0.250 g, Johnson Matthey Type 440 paste) were added to a solution of [2-(7-benzyl-9-oxa-3,7-diazabicyclo[3.3.1]non-3-yl)ethyl]carbamic acid tert-butyl ester (see Example I (Alternative I) above; 1 g, 2.77 mmol) in ethanol (10 mL). The mixture was then hydrogenated at 500 kPa (5 bar) for 18 hours. The reaction mixture was filtered through Celite® and then washed with ethanol (20 mL). The solution was concentrated under reduced pressure to give an oil. This was dissolved in dichloromethane (20 mL) and washed with sodium hydroxide (1 M, 10 mL). The organic phase was separated, dried over magnesium sulfate and then filtered. The filtrate was concentrated under reduced pressure to give the title compound as a yellow solid (0.67 g, 87%).
Reaction SMILES: Cl[C:2]1[N:7]=[CH:6][N:5]=[C:4]([C:8]([NH:10][C:11]2[CH:16]=[CH:15][C:14]([S:17](=[O:21])(=[O:20])[NH:18][CH3:19])=[CH:13][C:12]=2[CH3:22])=[O:9])[CH:3]=1.C(NC(C)C)(C)C.[CH:30]1([CH2:33][NH:34][CH:35]2[CH2:40][CH2:39][CH2:38][CH2:37][CH2:36]2)[CH2:32][CH2:31]1>C(O)C>[CH:35]1([N:34]([CH2:33][CH:30]2[CH2:31][CH2:32]2)[C:2]2[N:7]=[CH:6][N:5]=[C:4]([C:8]([NH:10][C:11]3[CH:16]=[CH:15][C:14]([S:17]([NH:18][CH3:19])(=[O:21])=[O:20])=[CH:13][C:12]=3[CH3:22])=[O:9])[CH:3]=2)[CH2:36][CH2:37][CH2:38][CH2:39][CH2:40]1
Reactant: CNS(=O)(=O)c1ccc(NC(=O)c2cc(Cl)ncn2)c(C)c1
Reactant: C1CCC(NCC2CC2)CC1
Solvent: CCO
Solvent: CC(C)NC(C)C
Product: CNS(=O)(=O)c1ccc(NC(=O)c2cc(N(CC3CC3)C3CCCCC3)ncn2)c(C)c1
Temperature: 160 °C
Yield: 69.7 %

Procedure:
A solution of 6-chloro-N-(2-methyl-4-(N-methylsulfamoyl)phenyl)pyrimidine-4-carboxamide (Intermediate 37, 80 mg; 0.235 mmol) and diisopropylamine (82 mL; 0.47 mmol) in ethanol (2.5 ml) was treated with N-(cyclopropylmethyl)cyclohexanamine (49.1 mg; 0.29 mmol). The mixture was heated to 160° C. in a microwave for 1 hour and then filtered. The solid was washed with a 1:1 mixture of water:ethanol and allowed to dry to give the title compound as a white solid (75 mg, 70%).
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:10]=[CH:9][C:6]([CH:7]=O)=[CH:5][CH:4]=1.[NH2:11][NH2:12]>C(O)(C)C>[CH3:1][O:2][C:3]1[CH:10]=[CH:9][C:6]([CH2:7][NH:11][NH:12][CH2:7][C:6]2[CH:9]=[CH:10][C:3]([O:2][CH3:1])=[CH:4][CH:5]=2)=[CH:5][CH:4]=1
Reactant: COc1ccc(C=O)cc1
Reactant: NN
Solvent: CC(C)O
Product: COc1ccc(CNNCc2ccc(OC)cc2)cc1

Procedure:
Di-(4-methoxybenzyl) azine was first prepared by reacting 2 moles of p-methoxybenzaldehyde with 1 mole hydrazine in isopropyl alcohol at 10° C. Di-(4-methoxybenzyl) hydrazine was obtained by reacting the azine with diborane in tetrahydrofurane under nitrogen atmosphere at or below 10° C. and isolated as an oil. The dihydrochloride salt of bis-(4-methoxybenzyl) hydrazine was obtained as white solid by mixing with hydrogen chloride gas in isopropanol followed by addition of methylene chloride and toluene (81% yield based on azine). 1,2-Di-(4-methoxybenzyl)hydrazine (3.5 g., 0.01 mole) and 1,3-dimorpholine-1,2-nitropropane (2.6 g., 0.01 mole) were suspended in a mixture of 30 ml of methanol and 20 ml of toluene and heated to reflux for 3 hr. The reaction mixture was evaporated to dryness and the residue extracted with toluene and filtered. The toluene filtrate was evaporated to give 3.5 g. brown oil which was purified by column chromatography using 10% diethyl ether - 90% methylene chloride on silica gel. Nuclear Magnetic Resonance and mass spectra confirmed the structure of title compound. The oil solidified after one day standing at room temperature.
Reaction SMILES: O1B([C@@H](NC(=O)[C@@H](NC(C2C=NC=CN=2)=O)CC2C=CC=CC=2)CC(C)C)[O:5][B:4]([C@@H:32]([NH:37][C:38](=[O:56])[C@@H:39]([NH:47][C:48]([C:50]2[CH:55]=[N:54][CH:53]=[CH:52][N:51]=2)=[O:49])[CH2:40][C:41]2[CH:46]=[CH:45][CH:44]=[CH:43][CH:42]=2)[CH2:33][CH:34]([CH3:36])[CH3:35])[O:3]B1[C@@H](NC(=O)[C@@H](NC(C1C=NC=CN=1)=O)CC1C=CC=CC=1)CC(C)C.[C:82](O)(=[O:90])[C@@H:83]([C@H:85]([C:87]([OH:89])=[O:88])[OH:86])O.CCCCCCC>CC(C)=O>[OH:86][C@H:85]([C@@H:83]1[C:82](=[O:90])[O:3][B:4]([C@@H:32]([NH:37][C:38](=[O:56])[C@@H:39]([NH:47][C:48]([C:50]2[CH:55]=[N:54][CH:53]=[CH:52][N:51]=2)=[O:49])[CH2:40][C:41]2[CH:46]=[CH:45][CH:44]=[CH:43][CH:42]=2)[CH2:33][CH:34]([CH3:35])[CH3:36])[O:5]1)[C:87]([OH:89])=[O:88]
Reactant: CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cnccn1)B1OB([C@H](CC(C)C)NC(=O)[C@H](Cc2ccccc2)NC(=O)c2cnccn2)OB([C@H](CC(C)C)NC(=O)[C@H](Cc2ccccc2)NC(=O)c2cnccn2)O1
Reactant: O=C(O)[C@H](O)[C@@H](O)C(=O)O
Solvent: CCCCCCC
Solvent: CC(C)=O
Product: CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cnccn1)B1OC(=O)[C@@H]([C@@H](O)C(=O)O)O1
Temperature: 25 °C
Reaction time: 1.5 h

Procedure:
A mixture of N,N′,N″-(boroxin-2,4,6-triyltris{[(1R)-3-methylbutane-1,1-diyl]imino[(2S)-1-oxo-3-phenylpropane-1,2-diyl]})tripyrazine-2-carboxamide (0.270 g, 0.246 mmol) and L-tartaric acid (149.5 mg, 0.33 mmol) were mixed in acetone (3 mL). The mixture was heated to form a solution. The solution was cooled uncontrolled until the internal temperature was about 25° C. Heptane (2.5 mL) was added. White solid precipitated out and the resultant slurry was agitated at ambient temperature for 1.5 h. The slurry was filtered to collect solid (R)-2-hydroxy-2-((R)-2-((R)-3-methyl-1-((S)-3-phenyl-2-(pyrazine-2-carboxamido)propanamido)butyl)-5-oxo-1,3,2-dioxaborolan-4-yl)acetic acid (0.388 g) which also contained a dimeric species. MS (m/z) in CH3CN: [M+H] calculated for C23H28BN4O8, 499.2000. found, 499.2.
Reaction SMILES: [CH3:1][O:2][C:3](=[O:22])[CH2:4][NH:5][C:6](=[O:21])[C@H:7]([CH2:16][O:17][CH2:18][CH:19]=[CH2:20])[NH:8]C(OC(C)(C)C)=O.[C:23]([OH:29])([C:25]([F:28])([F:27])[F:26])=[O:24]>C(Cl)Cl>[F:26][C:25]([F:28])([F:27])[C:23]([OH:29])=[O:24].[CH3:1][O:2][C:3](=[O:22])[CH2:4][NH:5][C:6](=[O:21])[C@H:7]([CH2:16][O:17][CH2:18][CH:19]=[CH2:20])[NH2:8]
Reactant: C=CCOC[C@H](NC(=O)OC(C)(C)C)C(=O)NCC(=O)OC
Solvent: O=C(O)C(F)(F)F
Solvent: ClCCl
Product: C=CCOC[C@H](N)C(=O)NCC(=O)OC

Procedure:
N-tert-butoxycarbonyl O-allyl L-seryl glycine methyl ester 18 (5.86 g, 18.3 mmol) was dissolved in CH2Cl2 (30 mL) and TFA (30 mL) added at room temperature. The reaction mixture was stirred for 2 hours before the solvent and bulk of excess TFA were evaporated affording a brownish liquid (7.50 g). The residue was washed with Et2O (2×25 mL), redissolved in CH2Cl2 (25 mL), the solvents evaporated and the residue dried under reduced pressure affording a brownish, viscous liquid (6.01 g, 98%); δH (300 MHz; d6-DMSO) 9.02 (1H, t, J 6, NH), 8.33 (3H, br s, NH3+), 5.87 (1H, ddt, J 5, 10 and 17, CH═CH2), 5.29 (1H, ddt, J 1, 2 and 17, CH═CHH), 5.21-5.14 (1H, m, CH═CHH), 4.10 (1H, m, CαH(Ser(All))), 4.00 (2H, ddd, J 1, 1 and 5, CH2CH═CH2), 3.95 (2H, d, J 6, CαH2(Gly)), 3.78-3.67 (2H, m, CH2), 3.64 (3H, s, OCH3); δC (75 MHz; d6-DMSO) 169.7, 167.0, 158.4 (q, JCF 32), 134.4, 116.7 (q, JCF 296), 71.4, 68.0, 54.9, 52.3, 51.8, 40.7; m/z (ESI) 217.1194 (M+; C9H17N2O4 requires 217.1188)
Reaction SMILES: [Br:1][C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[CH:8]([NH:12][C:13](=[O:22])[C:14]1[C:19]([F:20])=[CH:18][CH:17]=[CH:16][C:15]=1[F:21])[CH2:9][CH2:10]O.S(Cl)([Cl:25])=O>C1C=CC=CC=1>[Br:1][C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[CH:8]([NH:12][C:13](=[O:22])[C:14]1[C:19]([F:20])=[CH:18][CH:17]=[CH:16][C:15]=1[F:21])[CH2:9][CH2:10][Cl:25]
Reactant: O=C(NC(CCO)c1ccccc1Br)c1c(F)cccc1F
Reactant: O=S(Cl)Cl
Solvent: c1ccccc1
Product: O=C(NC(CCCl)c1ccccc1Br)c1c(F)cccc1F
Reaction time: 0.5 h
Yield: 96 %

Procedure:
To a solution of 12.9 g of N-[1-(2-bromophenyl)-3-hydroxypropyl]-2,6-difluorobenzamide in 80 ml of benzene under refluxing, was added dropwise 5.0 g of thionyl chloride for 10 minutes and stirring continued for an additional 30 minutes. Aftercooling, the precipitated solid was filtered, washed several times with n-hexane and dried to afford 13.0 g of N-[1-(2-bromophenyl)-3-chloropropyl]-2,6-difluorobenzamide. m.p. 183°-185° C.
Reaction SMILES: [C:1]([N:5]1[CH2:27][CH2:26][CH2:25][CH2:24][C:8]2[C:9]([Cl:23])=[C:10]3[C:19]4[CH:18]=[C:17](Br)[C:16]([O:21][CH3:22])=[CH:15][C:14]=4[CH2:13][CH2:12][N:11]3[C:7]=2[C:6]1=[O:28])([CH3:4])([CH3:3])[CH3:2].[N:29]1[CH:34]=[CH:33][CH:32]=[C:31](B(O)O)[CH:30]=1.C([O-])([O-])=O.[K+].[K+].C(COC)OC>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>[C:1]([N:5]1[CH2:27][CH2:26][CH2:25][CH2:24][C:8]2[C:9]([Cl:23])=[C:10]3[C:19]4[CH:18]=[C:17]([C:31]5[CH:30]=[N:29][CH:34]=[CH:33][CH:32]=5)[C:16]([O:21][CH3:22])=[CH:15][C:14]=4[CH2:13][CH2:12][N:11]3[C:7]=2[C:6]1=[O:28])([CH3:4])([CH3:3])[CH3:2]
Reactant: COc1cc2c(cc1Br)-c1c(Cl)c3c(n1CC2)C(=O)N(C(C)(C)C)CCCC3
Reactant: OB(O)c1cccnc1
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: [K+]
Solvent: O
Solvent: COCCOC
Product: COc1cc2c(cc1-c1cccnc1)-c1c(Cl)c3c(n1CC2)C(=O)N(C(C)(C)C)CCCC3
Temperature: 90 °C

Procedure:
A mixture of 65 mg of 19e, 25 mg of 3-pyridine-boronic acid, 45 mg of K2CO3 and 12 mg of Pd(PPh3)4 in 3 ml of degassed 90% aq. dimethoxyethane was heated under a nitrogen atmosphere for 16 h at 90° C. The mixture was diluted with water, extracted with ethyl acetate, dried and concentrated. The residues were purified by chromatography over silica gel, using a gradient of heptane/ethyl acetate as eluent. The material thus obtained was triturated with pentane, to provide 45 mg of white crystalline 19f; Mp: 190-192° C. MS-ESI: [M+1] 464.17, 465.17 and 466.17. NMR (CDCl3) δ 1.58 (s, 3, tertC4H9), 1.62-1.77 (bm, 2, CH2), 1.80-2.05 (bm, 2, CH2), 2.60-2.77 (bm, 2, CH2), 2.970-3.18 (bm, 2, CH2), 3.50 bm, 1, CH), 3.76-3.92 (bm, 2, CH2), 3.86 (s, 3, OCH3), 4.50 (bm, 1, CH), 6.87 (s, 1, ArH), 8.20 (s, 1, ArH), 7.36, 7.89, 8.57, 8.83 (4×m, 4, pyridine-H).
Reaction SMILES: [C:1]([C:3]1[CH:4]=[C:5]([CH:10]=[CH:11][C:12]=1[OH:13])[C:6]([O:8][CH3:9])=[O:7])#[N:2].[C:14](=O)([O-])[O-].[K+].[K+].COS(=O)(=O)OC>CN(C)C=O>[C:1]([C:3]1[CH:4]=[C:5]([CH:10]=[CH:11][C:12]=1[O:13][CH3:14])[C:6]([O:8][CH3:9])=[O:7])#[N:2]
Reactant: COC(=O)c1ccc(O)c(C#N)c1
Reactant: O=C([O-])[O-]
Agent: [K+]
Solvent: COS(=O)(=O)OC
Solvent: CN(C)C=O
Product: COC(=O)c1ccc(OC)c(C#N)c1
Temperature: 25 °C
Reaction time: 1 h
Yield: 85.5 %

Procedure:
Methyl 3-cyano-4-hydroxybenzoate (1.00 g) was dissolved in N,N-dimethylformamide (5 mL), and potassium carbonate (1.56 g) and dimethylsulfuric acid (0.70 mL) were added to the solution, and then the mixture was stirred at room temperature for 1 hour. After the reaction solution was filtered, water was added and the reaction mixture was extracted with ethyl acetate. The organic layer was washed with saturated brine, and then dried over anhydrous sodium sulfate. The solvent was distilled off under reduced pressure to obtain the title compound (923 mg) as a yellow solid.
Reaction SMILES: C(OC([N:8]1[CH2:13][CH2:12][CH:11]([N:14]2[CH2:18][CH2:17][CH2:16][C@H:15]2[CH2:19][O:20][C:21](=[O:28])[C:22]2[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=2)[CH2:10][CH2:9]1)=O)(C)(C)C.C(O)(C(F)(F)F)=O.C(=O)([O-])[O-].[Na+].[Na+]>C(Cl)Cl>[NH:8]1[CH2:13][CH2:12][CH:11]([N:14]2[CH2:18][CH2:17][CH2:16][C@H:15]2[CH2:19][O:20][C:21](=[O:28])[C:22]2[CH:23]=[CH:24][CH:25]=[CH:26][CH:27]=2)[CH2:10][CH2:9]1
Reactant: CC(C)(C)OC(=O)N1CCC(N2CCC[C@H]2COC(=O)c2ccccc2)CC1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: O=C(O)C(F)(F)F
Solvent: ClCCl
Product: O=C(OC[C@@H]1CCCN1C1CCNCC1)c1ccccc1
Reaction time: 16 h
Yield: 94.4 %

Procedure:
To a solution of 2.78 g (7.2 mmol) of 4-((S)-2-benzoyloxymethyl-pyrrolidin-1-yl)-piperidine-1-carboxylic acid tert-butyl ester in 80 ml of CH2Cl2 was added 5.83 ml of TFA (90% in water) drop by drop. After 16 hours, the reaction mixture was poured into crashed ice; then, the pH was adjusted to 9-10 with sodium carbonate solution and the mixture was extracted three times with CH2Cl2; the organic phases were washed with water, dried over magnesium sulfate, filtered and evaporated. The residue was purified by flash column chromatography [CH2Cl2 (sat. with NH3) and MeOH 1:0 to 9:1] to give 1.96 g (95%) of the title compound as yellow oil. MS: 289.1 (MH+).
Reaction SMILES: [Cl:1][C:2]1[NH:3][CH:4]=[CH:5][N:6]=1.[Cl:7][C:8]1[CH:13]=[C:12](Cl)[N:11]=[CH:10][N:9]=1.CCN(C(C)C)C(C)C>C(O)CCC>[Cl:7][C:8]1[CH:13]=[C:12]([N:3]2[CH:4]=[CH:5][N:6]=[C:2]2[Cl:1])[N:11]=[CH:10][N:9]=1
Reactant: Clc1ncc[nH]1
Reactant: Clc1cc(Cl)ncn1
Solvent: CCCCO
Solvent: CCN(C(C)C)C(C)C
Product: Clc1cc(-n2ccnc2Cl)ncn1
Temperature: 120 °C
Yield: 60.5 %

Procedure:
2-Chloro-1H-imidazole (2.0 g, 20 mmol), 4,6-dichloropyrimidine (6 g, 40 mmol) and DIEA (10.4 ml, 60 mmol) were mixed in 40 mL butanol and refluxed at 120° C. for 24 hours. The solvent was removed by rotary evaporation. The crude product was purified by flash chromatography on silica gel (0% EtOAc/hexanes to 20% EtOAc/hexanes gradient), afforded the title compound (2.6 g, 62% yield) as yellow solid. Rf=0.25 (20% EtOAc/hexanes); 1H NMR 400 MHz (DMSO-d6) δ 9.13 (s, 1H), 8.17 (s, 1H), 7.94 (d, 1H), 7.17 (d, 1 H); MS m/z 215.4 (M+1).
Reaction SMILES: COC([C:5]1[S:13][C:8]2=[N:9][CH:10]=[CH:11][CH:12]=[C:7]2[C:6]=1[NH2:14])=O.N1CCNCC1.CN1CCCC1=O>O>[S:13]1[C:8]2=[N:9][CH:10]=[CH:11][CH:12]=[C:7]2[C:6]([NH2:14])=[CH:5]1
Reactant: COC(=O)c1sc2ncccc2c1N
Agent: C1CNCCN1
Solvent: CN1CCCC1=O
Solvent: O
Product: Nc1csc2ncccc12
Temperature: 145 °C
Yield: 85.6 %

Procedure:
A mixture of 3-aminothieno[2,3-b]pyridine-2-carboxylic acid methyl ester (8.00 g), piperazine (6.70 g), and N-methyl-2-pyrrolidinone (80 ml) was heated to 145° C. for 3 hr, under a nitrogen atmosphere. The solution was allowed to cool, diluted with water (400 ml), and extracted with ethyl acetate. The combined extracts were washed with water and brine dried over anhydrous sodium sulfate, filtered, and the filtrate was concentrated to give 4.94 g (86.0%) of residual thieno[2,3-b]pyridine-3-amine.
Reaction SMILES: [F:1][C:2]1[CH:10]=[CH:9][C:5]([CH2:6][C:7]#[N:8])=[CH:4][CH:3]=1.Br[C:12]1[CH:17]=[C:16]([CH3:18])[CH:15]=[CH:14][N:13]=1.C1(C)C=CC(S([O-])=O)=CC=1.[Na+].[H-].[Na+]>C1COCC1>[C:7]([CH:6]([C:12]1[CH:17]=[C:16]([CH3:18])[CH:15]=[CH:14][N:13]=1)[C:5]1[CH:9]=[CH:10][C:2]([F:1])=[CH:3][CH:4]=1)#[N:8]
Reactant: N#CCc1ccc(F)cc1
Reactant: Cc1ccnc(Br)c1
Agent: Cc1ccc(S(=O)[O-])cc1
Agent: [H-]
Agent: [Na+]
Solvent: C1CCOC1
Product: Cc1ccnc(C(C#N)c2ccc(F)cc2)c1
Yield: 45.3 %

Procedure:
p-Fluorobenzyl cyanide (4.1 g), 2-bromo-4-methylpyridine (5.2 g) and sodium p-toluene sulfinate (5.4 g) were suspended in THF (50 ml), and to the solution was added a suspension of 40% sodium hydride (1.2 g) in THF (5 ml) under ice-cooling. The mixture was refluxed for 3 hours, the solvent was distilled off, water was added to the mixture and the mixture was extracted with ethyl acetate. The organic layer was washed with water and saturated brine, dried over anhydrous magnesium sulfate, and then, the solvent was distilled off. The residue was purified by silica gel column chromatography (elution solvent: ethyl acetate/hexane), to give 2-(α-cyano-4-fluorobenzyl)-4-methylpyridine (3.1 g) as brown oil.