Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [NH2:1][C:2]1[N:7]=[C:6]([C:8]2[CH:16]=[CH:15][C:11]3[O:12][CH2:13][O:14][C:10]=3[CH:9]=2)[C:5]([C:17]#[N:18])=[C:4]([S:19]([CH3:22])(=O)=O)[N:3]=1.[C:23]1(S)[CH:28]=[CH:27]C=[CH:25][CH:24]=1.C1CCN2C(=NCCC2)CC1>COCCOC>[NH2:1][C:2]1[N:7]=[C:6]([C:8]2[CH:16]=[CH:15][C:11]3[O:12][CH2:13][O:14][C:10]=3[CH:9]=2)[C:5]([C:17]#[N:18])=[C:4]([S:19][C:22]2[CH:27]=[CH:28][CH:23]=[CH:24][CH:25]=2)[N:3]=1
Reactant: CS(=O)(=O)c1nc(N)nc(-c2ccc3c(c2)OCO3)c1C#N
Reactant: Sc1ccccc1
Solvent: COCCOC
Solvent: C1CCC2=NCCCN2CC1
Product: N#Cc1c(Sc2ccccc2)nc(N)nc1-c1ccc2c(c1)OCO2

Procedure:
From 2-amino-4-benzo[1,3]dioxol-5-yl-6-methanesulfonyl-pyrimidine-5-carbonitrile, thiophenol and DBU in DME. EI-MS m/e (%): 348 (M+, 96), 347 ([M—H]+, 100).
Reaction SMILES: [F:1][C:2]([F:7])([F:6])[C:3]([NH2:5])=[NH:4].F[P-](F)(F)(F)(F)F.[Cl:15]/[C:16](=[CH:21]\N(C)C)/[CH:17]=[N+](C)C.C(N(CC)CC)C>C(#N)C>[Cl:15][C:16]1[CH:17]=[N:4][C:3]([C:2]([F:7])([F:6])[F:1])=[N:5][CH:21]=1
Reactant: N=C(N)C(F)(F)F
Reactant: CN(C)/C=C(\Cl)C=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CCN(CC)CC
Solvent: CC#N
Product: FC(F)(F)c1ncc(Cl)cn1
Temperature: 25 °C
Reaction time: 5 h

Procedure:
To a solution of 38 mmol trifluoroacetamidine in 70 ml acetonitrile was added 37.92 mmol ((Z)-2-Chloro-3-dimethylamino-allylidene)-dimethyl-ammonium hexafluoro phosphate (CAS: 291756-76-8) followed by 45.5 mmol triethylamine. The yellow solution was stirred at room temperature for 5 hours, then poured onto water and extracted 3 times with ether. The combined extracts were dried over sodium sulfate, filtered and distilled at 760 mm Hg to provide the title compound. MS (m/e): 182.2 (M+, 100%)
Reaction SMILES: COC1C=CC(C[S:8][C@@H:9]2[CH2:13][N:12]([C:14]([O:16][CH2:17][C:18]3[CH:23]=[CH:22][C:21]([N+:24]([O-:26])=[O:25])=[CH:20][CH:19]=3)=[O:15])[C@H:11]([C:27]([OH:29])=O)[CH2:10]2)=CC=1.[C:32]([CH:35]1[CH2:40][NH:39][CH2:38][CH2:37][N:36]1[C:41]([O:43][CH2:44][C:45]1[CH:50]=[CH:49][C:48]([N+:51]([O-:53])=[O:52])=[CH:47][CH:46]=1)=[O:42])(=[O:34])[NH2:33]>>[C:32]([CH:35]1[N:36]([C:41]([O:43][CH2:44][C:45]2[CH:50]=[CH:49][C:48]([N+:51]([O-:53])=[O:52])=[CH:47][CH:46]=2)=[O:42])[CH2:37][CH2:38][N:39]([C:27]([C@@H:11]2[CH2:10][C@H:9]([SH:8])[CH2:13][N:12]2[C:14]([O:16][CH2:17][C:18]2[CH:19]=[CH:20][C:21]([N+:24]([O-:26])=[O:25])=[CH:22][CH:23]=2)=[O:15])=[O:29])[CH2:40]1)(=[O:34])[NH2:33]
Reactant: NC(=O)C1CNCCN1C(=O)OCc1ccc([N+](=O)[O-])cc1
Reactant: COc1ccc(CS[C@H]2C[C@@H](C(=O)O)N(C(=O)OCc3ccc([N+](=O)[O-])cc3)C2)cc1
Product: NC(=O)C1CN(C(=O)[C@@H]2C[C@H](S)CN2C(=O)OCc2ccc([N+](=O)[O-])cc2)CCN1C(=O)OCc1ccc([N+](=O)[O-])cc1
Yield: 70.7 %

Procedure:
Following a procedure similar to that described in Preparation 8, but using 2.18 g of (2S,4S)-4-(4-methoxybenzylthio)-1-(4-nitrobenzyloxycarbonyl)-2-pyrrolidinecarboxylic acid, 0.79 g of N,N'-carbonyldiimidazole and 1.81 g of 2-carbamoyl-1-(4-nitrobenzyloxycarbonyl)piperazine, 2.13 g of the title compound were obtained as an amorphous solid.
Reaction SMILES: F[C:2]1[CH:7]=[CH:6][C:5]([N+:8]([O-:10])=[O:9])=[C:4]([O:11][CH3:12])[CH:3]=1.[CH3:13][S-:14].[Na+]>CN(C=O)C.O>[CH3:12][O:11][C:4]1[CH:3]=[C:2]([S:14][CH3:13])[CH:7]=[CH:6][C:5]=1[N+:8]([O-:10])=[O:9]
Reactant: C[S-]
Reactant: COc1cc(F)ccc1[N+](=O)[O-]
Agent: [Na+]
Solvent: O
Solvent: CN(C)C=O
Product: COc1cc(SC)ccc1[N+](=O)[O-]
Temperature: 25 °C
Reaction time: 18 h
Yield: 59.2 %

Procedure:
A mixture of 4-fluoro-2-methoxy-1-nitrobenzene (1.38 g, 8.06 mmol) and sodium methyl mercaptide (0.622 g, 8.87 mmol) in DMF (25 mL) was stirred at room temperature for 18 hours. The reaction was the diluted with water and extracted with EtOAc. The combined extracts were washed with brine, dried over sodium sulfate, filtered and concentrated to give (3-methoxy-4-nitrophenyl)(methyl)sulfane (0.95 g, 59%).
Reaction SMILES: [CH3:1][C:2]1[C:6]([CH2:7][O:8][C:9]2[CH:14]=[CH:13][C:12]([CH2:15][OH:16])=[CH:11][CH:10]=2)=[CH:5][N:4]([C:17]2[CH:22]=[CH:21][CH:20]=[CH:19][N:18]=2)[N:3]=1.Cl[C:24]1[C:29]([C:30]#[N:31])=[CH:28][CH:27]=[CH:26][N:25]=1.CN(C)C=O.[H-].[Na+]>O>[CH3:1][C:2]1[C:6]([CH2:7][O:8][C:9]2[CH:10]=[CH:11][C:12]([CH2:15][O:16][C:24]3[N:25]=[CH:26][CH:27]=[CH:28][C:29]=3[C:30]#[N:31])=[CH:13][CH:14]=2)=[CH:5][N:4]([C:17]2[CH:22]=[CH:21][CH:20]=[CH:19][N:18]=2)[N:3]=1
Reactant: N#Cc1cccnc1Cl
Reactant: Cc1nn(-c2ccccn2)cc1COc1ccc(CO)cc1
Agent: [H-]
Agent: [Na+]
Solvent: O
Solvent: CN(C)C=O
Product: Cc1nn(-c2ccccn2)cc1COc1ccc(COc2ncccc2C#N)cc1
Temperature: 25 °C
Reaction time: 3 h
Yield: 92.1 %

Procedure:
To a mixture of [4-[[3-methyl-1-(2-pyridyl)-1H-pyrazol-4-yl]methoxy]phenyl]methanol (2.00 g), 2-chloro-3-cyanopyridine (1.00 g) and N,N-dimethylformamide (20 mL) was added sodium hydride (60%, oil, 0.30 g) under ice-cooling. The reaction mixture was stirred at room temperature for 3 hrs. Water was added to the reaction mixture and the mixture was extracted with ethyl acetate. The organic layer was washed successively with water and saturated brine dried over anhydrous magnesium sulfate and concentrated to give crystals (2.48 g, 92%) of 2-[4-[[3-methyl-1-(2-pyridyl)-1H-pyrazol-4-yl]methoxy]benzyloxy]nicotinonitrile. Recrystallization from acetone-hexane gave colorless prism crystals. melting point: 108-109° C.
Reaction SMILES: [NH:1]([CH2:5][CH2:6][CH2:7][CH2:8][CH2:9][CH2:10][C:11]([O:13][CH2:14][CH3:15])=[O:12])[C:2]([NH2:4])=O.C1(C)C=CC(S(Cl)(=O)=O)=CC=1.O>N1C=CC=CC=1>[NH:1]([CH2:5][CH2:6][CH2:7][CH2:8][CH2:9][CH2:10][C:11]([O:13][CH2:14][CH3:15])=[O:12])[C:2]#[N:4]
Reactant: CCOC(=O)CCCCCCNC(N)=O
Agent: Cc1ccc(S(=O)(=O)Cl)cc1
Solvent: O
Solvent: c1ccncc1
Product: CCOC(=O)CCCCCCNC#N
Temperature: 25 °C
Reaction time: 2 h

Procedure:
To a solution of ethyl 7-ureidoheptanoate (2.1 g., 0.01 mole) in pyridine (10 ml.) is added p-toluenesulfonylchloride (2.0 g., excess). The reaction is stirred at room temperature for two hours, poured into water (100 ml.), then extracted with ether (2 × 100 ml.). The ether is washed with 5% hydrochloric acid (2 × 25 ml.), brine, then dried over sodium sulfate. The solvent is removed in vacuo to give ethyl 7-cyanamidoheptanoate as a light yellow oil, yield 1.7 g. (86%).
Reaction SMILES: [CH3:1][N:2]1[C:14]2[C:13]3[CH:12]=[C:11]4[CH:15]=[CH:16][CH:17]=[CH:18][C:10]4=[CH:9][C:8]=3[N:7]=[C:6](Cl)[C:5]=2[N:4]=[CH:3]1.[CH3:20][NH2:21]>CCOC(C)=O>[CH3:1][N:2]1[C:14]2[C:13]3[CH:12]=[C:11]4[CH:15]=[CH:16][CH:17]=[CH:18][C:10]4=[CH:9][C:8]=3[N:7]=[C:6]([NH:21][CH3:20])[C:5]=2[N:4]=[CH:3]1
Reactant: CN
Reactant: Cn1cnc2c(Cl)nc3cc4ccccc4cc3c21
Solvent: CCOC(C)=O
Product: CNc1nc2cc3ccccc3cc2c2c1ncn2C
Temperature: 80 °C
Yield: 4 %

Procedure:
A mixture of 1-methyl-4-chlorobenzo(g)imidazo(4,5-c)quinoline (Preparation 19) (130 mg, 0.49 mmol) and MeNH2 (2.0M/THF, 1.5 mL, 2.92 mmol) was heated in a pressure tube at 80° C. for 18 hours. After the reaction mixture was cooled to RT, it was diluted with EtOAc (100 mL), washed with sat'd NaCO3 (50 mL), and brine. The organic layer was dried over MgSO4, filtered and evaporated in vacuo. The crude material was submitted to flash chromatography (5% MeOH/EtOAc) affording the title compound as a pale white solid (5.2 mg, 4%). 1H NMR(CDCl3): 8.44(s, 1H), 8.35(s, 1H), 7.94(d, J=8.3, 1H), 7.90(d, J=8.3, 1H), 7.72(s, 1H), 7.46(m, 1H), 7.40(m, 1H), 5.95(b, 1H), 4.28(s, 3H), 3.31(s, 3H). (ESI) m/z (M+H)+=263.14.
Reaction SMILES: [CH3:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[CH:9]=[CH:10][C:11]3S[CH2:16][CH2:15][C:14]([C:18]([O:20][CH3:21])=[O:19])=[CH:13][C:12]=3[CH:22]=2)=[CH:4][CH:3]=1.C1C=C(Cl)C=C(C(OO)=O)C=1.[S:34]([O-:38])([O-])(=[O:36])=S.[Na+].[Na+]>ClCCl>[CH3:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[CH:9]=[CH:10][C:11]3[S:34](=[O:38])(=[O:36])[CH2:16][CH2:15][C:14]([C:18]([O:20][CH3:21])=[O:19])=[CH:13][C:12]=3[CH:22]=2)=[CH:4][CH:3]=1
Reactant: O=S([O-])([O-])=S
Reactant: COC(=O)C1=Cc2cc(-c3ccc(C)cc3)ccc2SCC1
Agent: O=C(OO)c1cccc(Cl)c1
Agent: [Na+]
Solvent: ClCCl
Product: COC(=O)C1=Cc2cc(-c3ccc(C)cc3)ccc2S(=O)(=O)CC1

Procedure:
To a solution of methyl 7-(4-methylphenyl)-2,3-dihydro-1-benzothiepine-4-carboxylate (1.5 g) in dichloromethane (25 ml) was added, under ice-cooling, 70% mCPBA (2.4 g), and the mixture was stirred at room temperature for 1 hour. To the solution was added an aqueous solution of sodium thiosulfate, and the mixture was concentrated and extracted with ethyl acetate. The organic layer was washed with sodium hydrogen carbonate solution, water and saturated brine, and dried with anhydrous magnesium sulfate. Under reduced pressure, the solvent was evaporated to give methyl 7-(4-methylphenyl)-1,1-dioxo-2,3-dihydro-1-benzothiepine-4-carboxylate (1.6 g) as colorless crystals.
Reaction SMILES: [NH2:1][C:2]1[N:7]=[CH:6][N:5]=[C:4]2[N:8]([CH2:27][C@H:28]3[CH2:32][CH2:31][CH2:30][N:29]3[C:33](=[O:37])[CH2:34][C:35]#[N:36])[N:9]=[C:10]([C:11]3[CH:16]=[CH:15][C:14]([O:17][C:18]4[CH:23]=[CH:22][CH:21]=[C:20]([F:24])[C:19]=4[F:25])=[CH:13][C:12]=3[F:26])[C:3]=12.[CH:38]1([CH:41]=O)[CH2:40][CH2:39]1.N1CCCCC1>C(O)C>[NH2:1][C:2]1[N:7]=[CH:6][N:5]=[C:4]2[N:8]([CH2:27][C@H:28]3[CH2:32][CH2:31][CH2:30][N:29]3[C:33]([C:34](=[CH:41][CH:38]3[CH2:40][CH2:39]3)[C:35]#[N:36])=[O:37])[N:9]=[C:10]([C:11]3[CH:16]=[CH:15][C:14]([O:17][C:18]4[CH:23]=[CH:22][CH:21]=[C:20]([F:24])[C:19]=4[F:25])=[CH:13][C:12]=3[F:26])[C:3]=12
Reactant: O=CC1CC1
Reactant: N#CCC(=O)N1CCC[C@@H]1Cn1nc(-c2ccc(Oc3cccc(F)c3F)cc2F)c2c(N)ncnc21
Solvent: C1CCNCC1
Solvent: CCO
Product: N#CC(=CC1CC1)C(=O)N1CCC[C@@H]1Cn1nc(-c2ccc(Oc3cccc(F)c3F)cc2F)c2c(N)ncnc21
Reaction time: 0.33 h
Yield: 38 %

Procedure:
A solution of 3-((R)-2-((4-amino-3-(4-(2,3-difluorophenoxy)-2-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)methyl)pyrrolidin-1-yl)-3-oxopropanenitrile (240 mg, 0.47 mmol, 1.00 equiv), cyclopropanecarbaldehyde (98.7 mg, 1.41 mmol, 3.00 equiv) and piperidine (42 mg, 0.47 mmol, 1.00 equiv) in ethanol (15 mL) was stirred for 3 h at 65° C. The resulting mixture was concentrated under vacuum. The residue was purified on Prep-HPLC. Conditions: (1#-Pre-HPLC-001(SHIMADZU)): Column, SunFire Prep C18, 19*150 mm 5 um; mobile phase, water with 0.05% TFA and CH3CN (40% CH3CN up to 100% in 20 min); Detector, 254 nm. This resulted in 100 mg (36%) of the title compound as a white solid. MS (ESI, pos. ion) m/z: 560 (M+1) H-NMR (400 MHz, CD3OD, ppm): 8.36 (s, 1H), 7.68-7.65 (t, J=7.6 Hz, 1H), 7.30-7.20 (m, 2H), 7.14-7.11 (t, 1H), 7.03-7.00 (d, J=9.2 Hz, 2H), 6.58 (d, J=10.8 Hz, 1H), 4.92-4.87 (m, 1H) 3.65-3.60 (m, 1H), 3.50-3.46 (m, 1H), 2.14 (m, 1H), 1.99-1.81 (m, 4H), 1.24-1.23 (m, 2H), 0.93-0.77 (m, 2H).
Reaction SMILES: [F:1][C:2]1[CH:9]=[CH:8][C:5]([CH:6]=O)=[CH:4][CH:3]=1.[CH3:10][O:11][CH:12]([O:15][CH3:16])[CH2:13][NH2:14].O.C1(C)C=CC(S(O)(=O)=O)=CC=1>C1(C)C=CC=CC=1>[CH3:10][O:11][CH:12]([O:15][CH3:16])[CH2:13][NH:14][CH2:6][C:5]1[CH:8]=[CH:9][C:2]([F:1])=[CH:3][CH:4]=1
Reactant: O=Cc1ccc(F)cc1
Reactant: COC(CN)OC
Agent: Cc1ccc(S(=O)(=O)O)cc1
Solvent: Cc1ccccc1
Solvent: O
Product: COC(CNCc1ccc(F)cc1)OC
Reaction time: 8 h
Yield: 93.9 %

Procedure:
12.4 g of 4-Fluorobenzaldehyde were dissolved in 100 ml of toluene and reacted with 10.5 g 2-aminoacetaldehyde dimethylacetal and 1.90 g (10 mmol) p-toluenesulfonic acid monohydrate for two hours at a Dean Stark apparatus. The solution was allowed to cool down, extracted with saturated sodium bicarbonate, water and brine, dried over magnesium sulfate and evaporated to dryness. The crude product was dissolved in 100 ml of ethanol. 1.89 g of sodium borohydride were added portionwise. Stirring was continued overnight. For workup, acetic acid was added until no gas evolution could be observed. Then the solution was evaporated to dryness, taken up in dichloromethane and washed twice with water. The organic layer was extracted with brine, dried over magnesium sulfate and evaporated to dryness. The obtained crude product (20 g) was used without purification. Rt=0.86 min (Method #1). Detected mass: 182.1 (M−OMe−), 214.2 (M+H+).
Reaction SMILES: [OH:1][C@:2]1([CH2:9][NH:10][C:11]([C:13]2[C:14]3[CH:15]=[CH:16][C:17](Cl)=[N:18][C:19]=3[CH:20]=[CH:21][C:22]=2[Cl:23])=[O:12])[CH2:7][CH2:6][CH2:5][C@@H:4]([CH3:8])[CH2:3]1.CCN(C(C)C)C(C)C.[F:34][C:35]1([F:40])[CH2:39][CH2:38][NH:37][CH2:36]1>>[OH:1][C@:2]1([CH2:9][NH:10][C:11]([C:13]2[C:14]3[CH:15]=[CH:16][C:17]([N:37]4[CH2:38][CH2:39][C:35]([F:40])([F:34])[CH2:36]4)=[N:18][C:19]=3[CH:20]=[CH:21][C:22]=2[Cl:23])=[O:12])[CH2:7][CH2:6][CH2:5][C@@H:4]([CH3:8])[CH2:3]1
Reactant: C[C@@H]1CCC[C@](O)(CNC(=O)c2c(Cl)ccc3nc(Cl)ccc23)C1
Reactant: FC1(F)CCNC1
Solvent: CCN(C(C)C)C(C)C
Product: C[C@@H]1CCC[C@](O)(CNC(=O)c2c(Cl)ccc3nc(N4CCC(F)(F)C4)ccc23)C1

Procedure:
The title compound was synthesized according to the procedure described in example 1 using 2,6-dichloro-quinoline-5-carboxylic acid ((1R,3R)-1-hydroxy-3methyl-cyclohexylmethyl)-amide, DIPEA and 3,3-difluoropyrrolidine. 1H NMR (400 MHz, DMSO-d6) δ ppm 8.75 (1H), 7.85 (m, 1H), 7.58 (2H), 7.05 (1H), 4.16 (s, 1H), 4.00 (t, 2H), 3.80 (t, 1H), 3.55 (m, 1H), 3.26 (m, 2H), 2.44 (m, 2H), 2.06 (m, 2H), 1.85 (m, 2H), 1.74-1.76 (m, 5H), 1.27-1.32 (m, 1H), 0.83 (d, 3H). m/z: 438 [M+H]
Reaction SMILES: [CH3:1][C:2]1[CH2:7][CH2:6][CH:5]([OH:8])[CH2:4][CH:3]=1.[C:9]1([CH3:19])[CH:14]=[CH:13][C:12]([S:15](Cl)(=[O:17])=[O:16])=[CH:11][CH:10]=1.Cl>N1C=CC=CC=1>[S:15]([O:8][CH:5]1[CH2:6][CH2:7][C:2]([CH3:1])=[CH:3][CH2:4]1)([C:12]1[CH:13]=[CH:14][C:9]([CH3:19])=[CH:10][CH:11]=1)(=[O:17])=[O:16]
Reactant: Cc1ccc(S(=O)(=O)Cl)cc1
Reactant: CC1=CCC(O)CC1
Agent: Cl
Solvent: c1ccncc1
Product: CC1=CCC(OS(=O)(=O)c2ccc(C)cc2)CC1
Reaction time: 2 h

Procedure:
To a solution of alcohol 4C (R=methyl) (10 g) and p-toluenesulfonyl chloride (20.8 g) in anhydrous tetrahydrofaran (21 mL) at 0° C. is added anhydrous pyridine (21 mL). The reaction is allowed to stir in an ice bath for 2 hours, and is then allowed to stand at −20° C. for a further 16 hours. The reaction mixture is then poured into 2M HCl (75 mL) and extracted with ethyl acetate. The combined organic layers are extracted with brine and dried over sodium sulfate. The solvent is removed in vacuo.
Reaction SMILES: Cl[C:2]1[CH:11]=[CH:10][C:5]([C:6]([O:8][CH3:9])=[O:7])=[C:4]([NH:12][C@H:13]([C:15]2[CH:20]=[CH:19][C:18]([F:21])=[CH:17][CH:16]=2)[CH3:14])[N:3]=1.[NH2:22][C:23]1[CH:28]=[N:27][CH:26]=[CH:25][N:24]=1.C1(P(C2CCCCC2)C2C=CC=CC=2C2C(C(C)C)=CC(C(C)C)=CC=2C(C)C)CCCCC1.P([O-])([O-])([O-])=O.[K+].[K+].[K+]>C(OCC)(=O)C.O1CCOCC1>[F:21][C:18]1[CH:19]=[CH:20][C:15]([C@@H:13]([NH:12][C:4]2[N:3]=[C:2]([NH:22][C:23]3[CH:28]=[N:27][CH:26]=[CH:25][N:24]=3)[CH:11]=[CH:10][C:5]=2[C:6]([O:8][CH3:9])=[O:7])[CH3:14])=[CH:16][CH:17]=1
Reactant: Nc1cnccn1
Reactant: COC(=O)c1ccc(Cl)nc1N[C@@H](C)c1ccc(F)cc1
Agent: CC(C)c1cc(C(C)C)c(-c2ccccc2P(C2CCCCC2)C2CCCCC2)c(C(C)C)c1
Agent: O=P([O-])([O-])[O-]
Agent: [K+]
Solvent: CCOC(C)=O
Solvent: C1COCCO1
Product: COC(=O)c1ccc(Nc2cnccn2)nc1N[C@@H](C)c1ccc(F)cc1
Temperature: 100 °C
Reaction time: 1 h
Yield: 93.4 %

Procedure:
2.83 g of methyl (S)-6-chloro-2-[1-(4-fluorophenyl)ethylamino]nicotinate, 870 mg of 2-aminopyrazine, 1.06 g of 2-dicyclohexylphosphino-2′,4′,6′-triisopropylbiphenyl, 4.09 g of tripotassium phosphate and 475 mg of tris(dibenzylideneacetone)(chloroform)dipalladium were added in turn to 15 ml of degassed 1,4-dioxane, and the mixture was stirred at 100° C. for 1 hour under argon atmosphere. The reaction solution was diluted with ethyl acetate. The solution was washed in turn with water and brine and then dried over magnesium sulfate. The solvent was distilled off under reduced pressure, and then the obtained residue was purified by silica gel column chromatography to obtain 3.14 g of the objective compound as orange powder.
Reaction SMILES: [OH-].[K+].[C:3]([O:7][C:8]([N:10]1[CH2:16][CH2:15][C:14]2[C:17]([S:22]C(=O)N(C)C)=[C:18]([Cl:21])[CH:19]=[CH:20][C:13]=2[CH2:12][CH2:11]1)=[O:9])([CH3:6])([CH3:5])[CH3:4].Cl[CH2:29][CH2:30][CH2:31][C:32]1[CH:33]=[C:34]2[C:38](=[CH:39][CH:40]=1)[NH:37][C:36](=[O:41])[C:35]2([CH3:43])[CH3:42].[I-].[K+]>CO.ClCCl>[C:3]([O:7][C:8]([N:10]1[CH2:16][CH2:15][C:14]2[C:17]([S:22][CH2:29][CH2:30][CH2:31][C:32]3[CH:33]=[C:34]4[C:38](=[CH:39][CH:40]=3)[NH:37][C:36](=[O:41])[C:35]4([CH3:42])[CH3:43])=[C:18]([Cl:21])[CH:19]=[CH:20][C:13]=2[CH2:12][CH2:11]1)=[O:9])([CH3:6])([CH3:5])[CH3:4]
Reactant: CC1(C)C(=O)Nc2ccc(CCCCl)cc21
Reactant: CN(C)C(=O)Sc1c(Cl)ccc2c1CCN(C(=O)OC(C)(C)C)CC2
Agent: [I-]
Agent: [K+]
Agent: [OH-]
Solvent: CO
Solvent: ClCCl
Product: CC(C)(C)OC(=O)N1CCc2ccc(Cl)c(SCCCc3ccc4c(c3)C(C)(C)C(=O)N4)c2CC1
Temperature: 25 °C
Reaction time: 8 h
Yield: 96.3 %

Procedure:
Under nitrogen atmosphere, add potassium hydroxide (138 mg, 2.46 mmol) to a stirred solution of 3-tert-butoxycarbonyl-7-chloro-6-dimethylcarbamoylthio-2,3,4,5-tetrahydro-1H-benzo[d]azepine (375 mg, 0.97 mmol) in methanol (10 mL). Heat under reflux for 2 h then add further potassium hydroxide (159 mg, 2.83 mmol) and continue heating under reflux for another 6 h. Cool the reaction mixture and add dropwise via cannula a solution of 5-(3-chloropropyl)-3,3-dimethyl-1,3-dihydro-indol-2-one (245 mg, 1.03 mmol) in methanol (10 mL). Stir at ambient temperature overnight then heat at 50° C. for 5 h. Add potassium iodide (186 mg, 1.12 mmol) to the reaction mixture and then heat under reflux for 5 h. Concentrate in vacuo and partition the residue between water (100 mL) and EtOAc (50 mL). Extract the aqueous phase with EtOAc (2×50 mL). Wash the combined extracts with brine (50 mL), dry over MgSO4, filter and concentrate in vacuo to obtain the crude mixture as a yellow oil. Dilute this oil with dichloromethane then re-concentrate in vacuo and repeat until a solid remains. Dry the solid in a vacuum oven to give 3-tert-butoxycarbonyl-7-chloro-6-[3-(3,3-dimethyl-2-oxo-2,3-dihydro-1H-indol-5-yl)-propylthio]-2,3,4,5-tetrahydro-1H-benzo[d]azepine as a yellow solid (481 mg) that was used without further purification. MS (ES+) m/z: 537 (M+Na)÷.
Reaction SMILES: [CH3:1][C@@H:2]1[N:6]([C:7]([O:9][C:10]([CH3:13])([CH3:12])[CH3:11])=[O:8])[C@H:5]([C:14]([O:16][CH2:17][C:18](=[O:38])[C:19]2[CH:20]=[CH:21][C:22]3[C:31]4[CH:30]=[C:29]5[CH2:32][CH2:33][CH2:34][C:35](=[O:36])[C:28]5=[CH:27][C:26]=4[O:25][CH2:24][C:23]=3[CH:37]=2)=[O:15])[CH2:4][CH2:3]1.[Br-:39].[Br-].[Br-].[NH+]1C=CC=CC=1.[NH+]1C=CC=CC=1.[NH+]1C=CC=CC=1>C(Cl)Cl.CO.Cl>[CH3:1][C@@H:2]1[N:6]([C:7]([O:9][C:10]([CH3:11])([CH3:13])[CH3:12])=[O:8])[C@H:5]([C:14]([O:16][CH2:17][C:18]([C:19]2[CH:20]=[CH:21][C:22]3[C:31]4[CH:30]=[C:29]5[CH2:32][CH2:33][CH:34]([Br:39])[C:35](=[O:36])[C:28]5=[CH:27][C:26]=4[O:25][CH2:24][C:23]=3[CH:37]=2)=[O:38])=[O:15])[CH2:4][CH2:3]1
Reactant: C[C@H]1CC[C@@H](C(=O)OCC(=O)c2ccc3c(c2)COc2cc4c(cc2-3)CCCC4=O)N1C(=O)OC(C)(C)C
Reactant: [Br-]
Agent: Cl
Agent: c1cc[nH+]cc1
Solvent: CO
Solvent: ClCCl
Product: C[C@H]1CC[C@@H](C(=O)OCC(=O)c2ccc3c(c2)COc2cc4c(cc2-3)CCC(Br)C4=O)N1C(=O)OC(C)(C)C
Temperature: 25 °C
Reaction time: 1 h

Procedure:
(2S,5S)-1-tert-butyl 2-(2-oxo-2-(8-oxo-8,9,10,11-tetrahydro-5H-dibenzo[c,g]chromen-3-yl)ethyl) 5-methylpyrrolidine-1,2-dicarboxylate (1.29 g, 2.48 mmol) was dissolved in a solution of DCM (17.5 mL) and MeOH (7 mL), then treated with pyridinium tribromide (873 mg, 2.73 mmol). After stirring at RT for 1 h, the reaction mixture was diluted with DCM and 10% HCl, and extracted with DCM. The organic phase was dried over MgSO4, filtered and concentrated under reduced pressure and the crude material was carried on without further purification.
Reaction SMILES: Cl.[C:2]1([CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][N:13]([CH2:15][CH2:16][C:17]([OH:19])=O)[CH3:14])[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[P:20](=[O:24])([OH:23])([OH:22])O.P(Cl)(Cl)Cl>ClC1C=CC=CC=1>[C:2]1([CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][N:13]([CH2:15][CH2:16][C:17]([OH:19])([P:20]([OH:24])(=[O:22])[OH:23])[P:20]([OH:23])(=[O:24])[OH:22])[CH3:14])[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: O=P(O)(O)O
Reactant: CN(CCCCCc1ccccc1)CCC(=O)O
Agent: Cl
Solvent: Clc1ccccc1
Solvent: ClP(Cl)Cl
Product: CN(CCCCCc1ccccc1)CCC(O)(P(=O)(O)O)P(=O)(O)O

Procedure:
12.75 g (0.0446 mol) of 3-[N-(5-phenylpentyl)-N-methylamino]-propionic acid hydrochloride are heated under reflux at 100° with 6.1 ml of 85% phosphoric acid and 30 ml of chlorobenzene, while stirring. 11.7 ml of phosphorus trichloride are then added dropwise at 100°, evolution of the gas taking place. The reaction mixture precipitates a thick mass in the course of 30 minutes. The mixture is heated at 100° for a further 3 hours and the supernatant chlorobenzene is then decanted off. The viscous mass which remains is heated at the boil under reflux with 45 ml of 9N hydrochloric acid for 3 hours, while stirring. It is filtered hot, with addition of charcoal, and the filtrate is concentrated under reduced pressure. Addition of acetone gives the crude 3-[N-(5-phenylpentyl)-N-methyl-amino]-1-hydroxypropane-1,1-diphosphonic acid, which is recrystallized from water: melting point 124°-127° (decomposition).
Reaction SMILES: [NH2:1][C:2]1[CH:3]=[C:4]([C@:8]23[CH2:16][N:15]([C:17]4[N:22]=[CH:21][C:20]([F:23])=[CH:19][N:18]=4)[CH2:14][C@H:13]2[CH2:12][S:11][C:10]([NH:24][C:25](=[O:32])[C:26]2[CH:31]=[CH:30][CH:29]=[CH:28][CH:27]=2)=[N:9]3)[CH:5]=[CH:6][CH:7]=1.[C:33]([C:35]1[CH:36]=[CH:37][C:38]([C:41](O)=[O:42])=[N:39][CH:40]=1)#[N:34].ON1C2C=CC=CC=2N=N1.Cl.CN(C)CCCN=C=NCC.C(N(C(C)C)CC)(C)C>ClCCl>[C:25]([NH:24][C:10]1[S:11][CH2:12][C@@H:13]2[CH2:14][N:15]([C:17]3[N:22]=[CH:21][C:20]([F:23])=[CH:19][N:18]=3)[CH2:16][C@:8]2([C:4]2[CH:3]=[C:2]([NH:1][C:41]([C:38]3[CH:37]=[CH:36][C:35]([C:33]#[N:34])=[CH:40][N:39]=3)=[O:42])[CH:7]=[CH:6][CH:5]=2)[N:9]=1)(=[O:32])[C:26]1[CH:27]=[CH:28][CH:29]=[CH:30][CH:31]=1
Reactant: N#Cc1ccc(C(=O)O)nc1
Reactant: Nc1cccc([C@]23CN(c4ncc(F)cn4)C[C@H]2CSC(NC(=O)c2ccccc2)=N3)c1
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: CCN(C(C)C)C(C)C
Solvent: ClCCl
Product: N#Cc1ccc(C(=O)Nc2cccc([C@]34CN(c5ncc(F)cn5)C[C@H]3CSC(NC(=O)c3ccccc3)=N4)c2)nc1
Temperature: 25 °C
Reaction time: 8 h
Yield: 92.9 %

Procedure:
N-[(4aR,7aS)-7a-(3-Aminophenyl)-6-(5-fluoropyrimidin-2-yl)-4,4a,5,7-tetrahydropyrrolo[3,4-d][1,3]thiazin-2-yl]benzamide (0.30 g, 0.67 mmol) is dissolved in dichloromethane (10 mL) and 5-cyanopyridine-2-carboxylic acid (129 mg, 0.87 mmol), 1-hydroxybenzotriazole (185 mg, 1.34 mmol) and 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (169 mg, 0.87 mmol) are added. Diisopropylethyamine (0.35 mL, 2 mmol) is added and the reaction is stirred at room temperature overnight. The material is purified directly with silica gel chromatography eluting with a 0-100% ethyl acetate/hexanes gradient to give the title compound (360 mg, 88%). ES/MS (m/e): 579 (M+H).
Reaction SMILES: [CH2:1]([N:3]1[C:12]2[C:7](=[CH:8][C:9]([F:16])=[C:10](F)[C:11]=2[O:13][CH3:14])[C:6](=[O:17])[C:5]([C:18]([OH:20])=[O:19])=[CH:4]1)[CH3:2].[NH:21]1[CH2:26][CH2:25][CH2:24][CH2:23][CH2:22]1.COB(OC)OC.C(#N)C>O>[CH2:1]([N:3]1[C:12]2[C:7](=[CH:8][C:9]([F:16])=[C:10]([N:21]3[CH2:26][CH2:25][CH2:24][CH2:23][CH2:22]3)[C:11]=2[O:13][CH3:14])[C:6](=[O:17])[C:5]([C:18]([OH:20])=[O:19])=[CH:4]1)[CH3:2]
Reactant: CCn1cc(C(=O)O)c(=O)c2cc(F)c(F)c(OC)c21
Reactant: C1CCNCC1
Agent: COB(OC)OC
Solvent: CC#N
Solvent: O
Product: CCn1cc(C(=O)O)c(=O)c2cc(F)c(N3CCCCC3)c(OC)c21
Temperature: 25 °C
Yield: 63.2 %

Procedure:
A mixture of 2.83 g of 1-ethyl-6,7-difluoro-1,4-dihydro-8-methoxy-4-oxo-3-quinolinecarboxylic acid (10 mmol), 1.70 g of piperidine (20 mmol), 1.04 g of trimethoxyborane (10 mmol) and 15 ml of acetonitrile was refluxed with heating for 4.5 hours. The reaction solution was cooled to room temperature, 30 ml of water was added therein, a pH was adjusted to 8 with 6N--HCl, and separated crystals were filtered and dried to obtain 2.20 g of the objective compound.