Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [NH2:1][CH2:2][CH:3]([OH:12])[C:4]1[CH:9]=[CH:8][C:7]([Cl:10])=[C:6]([Cl:11])[CH:5]=1.C1(C)C(C)=CC=CC=1.N([C:25]1[NH:26][CH2:27][CH2:28][N:29]=1)[N+]([O-])=O>CC(C)=O>[Cl:11][C:6]1[CH:5]=[C:4]([CH:9]=[CH:8][C:7]=1[Cl:10])[CH:3]([OH:12])[CH2:2][NH:1][C:25]1[NH:29][CH2:28][CH2:27][N:26]=1
Reactant: NCC(O)c1ccc(Cl)c(Cl)c1
Reactant: O=[N+]([O-])NC1=NCCN1
Solvent: Cc1ccccc1C
Solvent: CC(C)=O
Product: OC(CNC1=NCCN1)c1ccc(Cl)c(Cl)c1
Temperature: 160 °C

Procedure:
To a stirred solution of 8 parts of α-(aminomethyl)-3,4-dichlorobenzyl alcohol in 4.5 parts of xylene are added 5.2 parts of 2-(nitramino)-2-imidazoline. The whole is heated in an oil-bath at a temperature of about 160°C. till a clear melt is obtained (about 15 minutes). After cooling to about 60°C., the melt is dissolved in acetone and allowed to crystallize. The precipitated product is filtered off and recrystallized from 20 parts of 4-methyl-2-pentanone, yielding 3,4-dichloro-α-(2-imidazolin-2-ylaminomethyl)benzyl alcohol; m.p. 148°C.
Reaction SMILES: [F:1][C:2]1[C:3]([C:9](N(OC)C)=[O:10])=[N:4][CH:5]=[C:6]([F:8])[CH:7]=1.[CH2:15]([O:22][C:23]1[CH:28]=[CH:27][C:26]([Mg]Br)=[CH:25][CH:24]=1)[C:16]1[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=1.[NH4+].[Cl-]>C1COCC1>[CH2:15]([O:22][C:23]1[CH:28]=[CH:27][C:26]([C:9]([C:3]2[C:2]([F:1])=[CH:7][C:6]([F:8])=[CH:5][N:4]=2)=[O:10])=[CH:25][CH:24]=1)[C:16]1[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=1
Reactant: CON(C)C(=O)c1ncc(F)cc1F
Reactant: Br[Mg]c1ccc(OCc2ccccc2)cc1
Agent: [Cl-]
Agent: [NH4+]
Solvent: C1CCOC1
Product: O=C(c1ccc(OCc2ccccc2)cc1)c1ncc(F)cc1F
Temperature: -78 °C
Reaction time: 3 h

Procedure:
To a stirred solution of 3,5-difluoro-N-methoxy-N-methylpyridine-2-carboxamide (2.5 g) in THF (50 mL) was added [4-(benzyloxy)phenyl](bromo)magnesium (1 M solution in THF, 12.3 mL) at −78° C. The mixture was stirred at −78° C. for 3 h, treated with saturated NH4Cl aqueous solution and extracted with AcOEt. The organic layer was dried over MgSO4 and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (AcOEt/hexane). The product was crystallized from AcOEt/hexane to give the title compound (2.3 g).
Reaction SMILES: [NH:1]1[CH:8]=[CH:7][C:5]([NH2:6])=[N:4][C:2]1=[O:3].[C:9]1([CH:15]([C:19]2[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=2)[C:16](Cl)=[O:17])[CH:14]=[CH:13][CH:12]=[CH:11][CH:10]=1.O>N1C=CC=CC=1>[C:19]1([CH:15]([C:9]2[CH:10]=[CH:11][CH:12]=[CH:13][CH:14]=2)[C:16]([NH:6][C:5]2[CH:7]=[CH:8][NH:1][C:2](=[O:3])[N:4]=2)=[O:17])[CH:20]=[CH:21][CH:22]=[CH:23][CH:24]=1
Reactant: Nc1cc[nH]c(=O)n1
Reactant: O=C(Cl)C(c1ccccc1)c1ccccc1
Solvent: O
Solvent: c1ccncc1
Product: O=C(Nc1cc[nH]c(=O)n1)C(c1ccccc1)c1ccccc1

Procedure:
To stirred suspension of (3 gr, 27 mmol) of cytosine (C) in 30 ml of dry pyridine at room temperature (6.85 g, 29.7 mmol) of diphenylacetyl chloride were added in portions. The reaction mixture was stirred at room temperature overnight. TLC indicated the end of the reaction. 2 ml of water was added and the solvent was evaporated under reduced pressure. 100 ml of water were added to the residue and the mixture was stirred vigorously for 30 minutes. The desired product (11) was precipitate and filtered. The white precipitate was washed with 100 ml of ether and dried.
Reaction SMILES: [NH2:1][CH2:2][CH2:3][S:4][CH2:5][C:6]1[O:7][C:8]2[CH:14]=[C:13]([CH2:15][N:16]([CH3:18])[CH3:17])[CH:12]=[CH:11][C:9]=2[CH:10]=1.[CH3:19][S:20][C:21](SC)=[CH:22][N+:23]([O-:25])=[O:24]>C(#N)C>[CH3:17][N:16]([CH2:15][C:13]1[CH:12]=[CH:11][C:9]2[CH:10]=[C:6]([CH2:5][S:4][CH2:3][CH2:2][NH:1][C:21]([S:20][CH3:19])=[CH:22][N+:23]([O-:25])=[O:24])[O:7][C:8]=2[CH:14]=1)[CH3:18]
Reactant: CN(C)Cc1ccc2cc(CSCCN)oc2c1
Reactant: CSC(=C[N+](=O)[O-])SC
Solvent: CC#N
Product: CSC(=C[N+](=O)[O-])NCCSCc1cc2ccc(CN(C)C)cc2o1

Procedure:
A solution of 2-(2-aminoethylthiomethyl)-6-(dimethylaminomethyl)benzofuran (Example 1, Step E) (8.0 g., 0.0303 mole) and 1,1-bismethylthio-2-nitroethene (5.25 g., 0.0318 mole) in acetonitrile (80 ml.) is heated at 55° C. for 16 hours. The solvent is evaporated at reduced pressure. The residue is chromatographed on a column containing 175 g. of silica gel made up in chloroform. The product is eluted with 5% methanol in chloroform and is obtained as a light orange viscous oil weighing 6.1 g. (53%).
Reaction SMILES: Cl[CH2:2][CH2:3][CH2:4][S:5]([NH:8][C:9]1[CH:14]=[CH:13][C:12]([F:15])=[C:11]([F:16])[C:10]=1[NH:17][C:18]1[CH:23]=[CH:22][C:21]([I:24])=[CH:20][C:19]=1[F:25])(=[O:7])=[O:6].[OH-:26].[K+]>O1CCOCC1.O>[F:16][C:11]1[C:10]([NH:17][C:18]2[CH:23]=[CH:22][C:21]([I:24])=[CH:20][C:19]=2[F:25])=[C:9]([NH:8][S:5]([CH2:4][CH2:3][CH2:2][OH:26])(=[O:7])=[O:6])[CH:14]=[CH:13][C:12]=1[F:15]
Reactant: O=S(=O)(CCCCl)Nc1ccc(F)c(F)c1Nc1ccc(I)cc1F
Reactant: [OH-]
Agent: [K+]
Solvent: C1COCCO1
Solvent: O
Product: O=S(=O)(CCCO)Nc1ccc(F)c(F)c1Nc1ccc(I)cc1F

Procedure:
To a solution of 3-chloro-N-(3,4-difluoro-2-(2-fluoro-4-iodophenylamino)phenyl)-propane-1-sulfonamide (69.4 mg, 0.138 mmol) in a mixture of 8 ml 1,4-dioxane and 2 ml H2O was added KOH powder (0.674 g, 12.0 mmol) and the mixture was heated to the reflux temperature for 3 days. It was extracted using EtOAc/brine, the organic fraction was dried with Na2SO4 and the volatiles were removed. The residue was purified using flash-column chromatography (Si, DCM/MeOH 5:1, 0.3). Yield: 41 mg (62%). 1H-NMR (500 MHz, MeOH [d4]): δ=7.38-7.21 (d, 1H), 7.23-7.21 (d, 1H), 7.06-7.00 (q, 1H), 6.52-6.50 (m, 1H), 6.17-6.13 (t, 1H), 3.30-3.27 (t, 2H), 2.86-2.83 (t, 2H), 2.05-2.00 (m, 2H); m/z=485 [M−1]−.
Reaction SMILES: [C:1]([N:4]1[CH2:9][CH2:8][C:7](=O)[CH2:6][CH2:5]1)(=[O:3])[CH3:2].[NH2:11][C@H:12]([C:20]([NH2:22])=[O:21])[CH2:13][C:14]1[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=1>CCO>[C:1]([N:4]1[CH2:9][CH2:8][C:7]2([NH:22][C:20](=[O:21])[C@H:12]([CH2:13][C:14]3[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=3)[NH:11]2)[CH2:6][CH2:5]1)(=[O:3])[CH3:2]
Reactant: CC(=O)N1CCC(=O)CC1
Reactant: NC(=O)[C@@H](N)Cc1ccccc1
Solvent: CCO
Product: CC(=O)N1CCC2(CC1)NC(=O)[C@H](Cc1ccccc1)N2
Temperature: 25 °C
Reaction time: 16 h

Procedure:
A solution of 1-acetylpiperidin-4-one (1.5 g, 10.8 mmol) and (S)-phenylalaninamide (1.8 g, 10.8 mmol) in EtOH (30 ml) was heated under reflux for 2.5 h and stirred at RT for a further 16 h. After removal of the solvent and drying in vacuo, the product 8-acetyl-3-(S)-benzyl-1,4,8-triazaspiro[4,5]decan-2-one was obtained in a yield of 3.0 g (99%).
Reaction SMILES: [NH2:1][C:2]1[CH:3]=[C:4]([CH:9]([CH3:15])[C:10]([O:12][CH2:13][CH3:14])=[O:11])[CH:5]=[CH:6][C:7]=1[OH:8].[Cl:16][CH2:17][C:18](Cl)=[O:19].O>CC(C)CC(=O)C>[Cl:16][CH2:17][C:18]([NH:1][C:2]1[CH:3]=[C:4]([CH:9]([CH3:15])[C:10]([O:12][CH2:13][CH3:14])=[O:11])[CH:5]=[CH:6][C:7]=1[OH:8])=[O:19]
Reactant: O=C(Cl)CCl
Reactant: CCOC(=O)C(C)c1ccc(O)c(N)c1
Solvent: CC(=O)CC(C)C
Solvent: O
Product: CCOC(=O)C(C)c1ccc(O)c(NC(=O)CCl)c1
Temperature: 80 °C
Reaction time: 20 h

Procedure:
Ethyl 2-(3-amino-4-hydroxyphenyl)propanoate (104 mg, 0.497 mmol) in 4-methyl-2-pentanone (4 mL) was added chloroacetylchloride (56 mg, 0.496 mmol) at room temperature and stirred for 20 hours at 80° C. The reaction mixture was cooled to room temperature and added water (30 mL). The mixture was extracted with EtOAc. The organic layer was dried with MgSO4 and filtered. EtOAc was removed by evaporation. The residue was purified by column chromatography eluting with n-Hexane/EtOAc=2/1.
Reaction SMILES: [CH2:1]([O:5][C:6]1[CH:11]=[CH:10][C:9]([CH2:12][C@H:13]([NH:18][C:19]([C@@H:21](/[CH:34]=[CH:35]/[CH2:36][CH2:37][CH2:38][CH2:39][CH2:40][CH2:41][C:42]2([CH2:47][CH2:48][CH2:49][CH2:50][CH2:51][CH2:52][CH3:53])[O:46][CH2:45][CH2:44][O:43]2)[C@@:22]([OH:33])([CH2:30][CH2:31]O)[C:23]([O:25][C:26]([CH3:29])([CH3:28])[CH3:27])=[O:24])=[O:20])[C:14]([O:16][CH3:17])=[O:15])=[CH:8][CH:7]=1)[C:2]#[C:3][CH3:4].C(N(S(F)(F)[F:60])CC)C>O1CCCC1>[CH2:1]([O:5][C:6]1[CH:11]=[CH:10][C:9]([CH2:12][C@H:13]([NH:18][C:19]([C@@H:21](/[CH:34]=[CH:35]/[CH2:36][CH2:37][CH2:38][CH2:39][CH2:40][CH2:41][C:42]2([CH2:47][CH2:48][CH2:49][CH2:50][CH2:51][CH2:52][CH3:53])[O:46][CH2:45][CH2:44][O:43]2)[C@:22]([CH2:30][CH2:31][F:60])([OH:33])[C:23]([O:25][C:26]([CH3:29])([CH3:28])[CH3:27])=[O:24])=[O:20])[C:14]([O:16][CH3:17])=[O:15])=[CH:8][CH:7]=1)[C:2]#[C:3][CH3:4]
Reactant: CCN(CC)S(F)(F)F
Reactant: CC#CCOc1ccc(C[C@H](NC(=O)[C@@H](/C=C/CCCCCCC2(CCCCCCC)OCCO2)[C@@](O)(CCO)C(=O)OC(C)(C)C)C(=O)OC)cc1
Solvent: C1CCOC1
Product: CC#CCOc1ccc(C[C@H](NC(=O)[C@@H](/C=C/CCCCCCC2(CCCCCCC)OCCO2)[C@@](O)(CCF)C(=O)OC(C)(C)C)C(=O)OC)cc1
Reaction time: 4 h
Yield: 45.2 %

Procedure:
tert-Butyl (E)-(2S,3S)-3-[(S)-2-(4-but-2-ynyloxy-phenyl)-1-methoxycarbonyl-ethylcarbamoyl]-11-(2-heptyl-[1,3]dioxolan-2-yl)-2-hydroxy-2-(2-hydroxy-ethyl)-undec-4-enoate (157 mg, 0.211 mmol) was dissolved in tetrahydrofuran (5.0 mL), and (diethylamino)sulfur trifluoride (0.0360 mL, 0.273 mmol) was then added at room temperature. The mixture was stirred for 4 hours, then quenched with a saturated aqueous solution (15 mL) of sodium bicarbonate, and extracted with dichloromethane (15 mL). The organic layer was then dried over anhydrous sodium sulfate and filtered. The solvent was distilled off under reduced pressure. The residue was purified on Biotage (silica gel, n-hexane/ethyl acetate) to obtain 71.1 mg (0.0953 mmol, 45% yield) of tert-butyl (E)-(2S,3S)-3-[(S)-2-(4-but-2-ynyloxy-phenyl)-1-methoxycarbonyl-ethylcarbamoyl]-2-(2-fluoro-ethyl)-11-(2-heptyl-[1,3]dioxolan-2-yl)-2-hydroxy-undec-4-enoate.
Reaction SMILES: [CH3:1][CH:2]([CH3:9])[CH2:3][C:4](=[CH2:8])[C:5]([OH:7])=[O:6].[C:10]([OH:13])(=[S:12])[CH3:11]>>[CH3:1][CH:2]([CH3:9])[CH2:3][CH:4]([CH2:8][S:12][C:10](=[O:13])[CH3:11])[C:5]([OH:7])=[O:6]
Reactant: C=C(CC(C)C)C(=O)O
Reactant: CC(O)=S
Product: CC(=O)SCC(CC(C)C)C(=O)O
Temperature: 95 °C

Procedure:
A mixture of 4-methyl-2-methylenepentanoic acid (5.0 g) and thioacetic acid (25 mL) was heated at 95° C. under argon for 3 days. The excess thioacetic acid was evaporated and the residual oil was dissolved in ethyl acetate (40 mL) and extracted with saturated NaHCO3 (3×40 mL). The combined NaHCO3 extracts were combined and acidified at 0° C. to pH 2 with 1M HCl. The aqueous layer was extracted with CHCl2 (3×40 mL), the combined organic phases were dried (MgSO4) and evaporated to give 3.0 g of 4-methyl-2-acetylthiomethyl-pentanoic acid; 1H NMR (80 MHz, CDCl3) δ 0.95 (d, J=8.0, 6H), 1.20-1.90 (m, 4H), 2.35 (s, 3H), 2.50-3.20 (m, 3H), 6.7 (br s, 1H).
Reaction SMILES: [C:1]([C:6]1[CH:7]=[N:8][C:9]2[C:14]([C:15]=1[NH:16][C:17]1[CH:22]=[CH:21][CH:20]=[CH:19][C:18]=1[CH3:23])=[CH:13][CH:12]=[CH:11][C:10]=2[O:24][CH2:25][CH2:26][CH2:27][S:28][CH3:29])(=O)[CH2:2][CH2:3][CH3:4].[OH2:30].[O-]Cl.[Na+]>C(Cl)Cl>[CH2:1]([C:6]1[CH:7]=[N:8][C:9]2[C:14]([C:15]=1[NH:16][C:17]1[CH:22]=[CH:21][CH:20]=[CH:19][C:18]=1[CH3:23])=[CH:13][CH:12]=[CH:11][C:10]=2[O:24][CH2:25][CH2:26][CH2:27][S:28]([CH3:29])=[O:30])[CH2:2][CH2:3][CH3:4]
Reactant: O
Reactant: CCCC(=O)c1cnc2c(OCCCSC)cccc2c1Nc1ccccc1C
Agent: [Na+]
Agent: [O-]Cl
Solvent: ClCCl
Product: CCCCc1cnc2c(OCCCS(C)=O)cccc2c1Nc1ccccc1C
Temperature: 25 °C
Reaction time: 4 h
Yield: 53 %

Procedure:
3-butyryl-4-(2-methylphenylamino)-8-(3-methylthiopropoxy)quinoline (0.33 g, 0.8 mmol) was dissolved in methylene chloride (15 ml), 5 ml water was added and then a solution of 1.5 ml (1.09 mmol) of 5% NaOCl in 10 ml methylene chloride was added. The mixture was stirred for 4 h at room temperature. The organic phase was separated and evaporated. Chromatography with methylene chloride: methanol 95:5 as the eluent gave 0.18 g (53%) of the title compound.
Reaction SMILES: [Cl:1][C:2]1[C:3](F)=[C:4]([F:19])[CH:5]=[C:6]2[C:11]=1[N:10]([CH:12]1[CH2:14][CH2:13]1)[CH:9]=[C:8]([C:15]([OH:17])=[O:16])[C:7]2=[O:18].[CH3:21][NH:22][CH2:23][CH:24]1[CH:28]([CH3:29])[CH2:27][NH:26][CH2:25]1.C1CCN2C(=NCCC2)CC1>C(#N)C>[Cl:1][C:2]1[C:3]([N:26]2[CH2:27][CH:28]([CH3:29])[CH:24]([CH2:23][NH:22][CH3:21])[CH2:25]2)=[C:4]([F:19])[CH:5]=[C:6]2[C:11]=1[N:10]([CH:12]1[CH2:14][CH2:13]1)[CH:9]=[C:8]([C:15]([OH:17])=[O:16])[C:7]2=[O:18]
Reactant: CNCC1CNCC1C
Reactant: O=C(O)c1cn(C2CC2)c2c(Cl)c(F)c(F)cc2c1=O
Solvent: C1CCC2=NCCCN2CC1
Solvent: CC#N
Product: CNCC1CN(c2c(F)cc3c(=O)c(C(=O)O)cn(C4CC4)c3c2Cl)CC1C
Reaction time: 8 h
Yield: 45.6 %

Procedure:
A mixture of 8-chloro-1-cyclopropyl-6,7-difluoro-1,4-dihydro-4-oxo-3-quinolinecarboxylic acid (0.5 g), anhydrous acetonitrile (5 ml), 3-methylaminomethyl-4-methylpyrrolidine (0.32 g) and DBU (0.25 g) was refluxed for an hour and allowed to stand overnight at room temperature. The resulting precipitate was collected by filtration, washed with acetonitrile and ether successively and recrystallized from chloroform-methanol-concentrated aqueous ammonia to give the title compound (0.31 g) as pale yellow powder, mp 253°-255° C.
Reaction SMILES: [CH3:1][C:2]1[C:8]([CH3:9])=[C:7]([OH:10])[CH:6]=[CH:5][C:3]=1[OH:4].[C:11](O)(=[O:13])[CH3:12]>>[CH3:1][C:2]1[C:8]([CH3:9])=[C:7]([OH:10])[CH:6]=[C:5]([C:11](=[O:13])[CH3:12])[C:3]=1[OH:4]
Reactant: CC(=O)O
Reactant: Cc1c(O)ccc(O)c1C
Product: CC(=O)c1cc(O)c(C)c(C)c1O
Temperature: 80 °C

Procedure:
276 g (2 mole) of 2,3-dimethyl-hydroquinone were suspended in 300 ml of acetic acid and heated to 80° C. with stirring. Through the obtained solution boron trifluoride was bubbled whereby care was taken that the temperature did not exceed 100° C. The reaction mixture was stirred at 120° C. for 3.5 h and then poured into 4 l of ice-water containing 500 g of dissolved sodium acetate. This mixture was stirred for 12 h till the precipitate could be separated by suction. This precipitate was then treated with 3 l of water whereto enough sodium hydrogen carbonate was added to reach a final pH of 7.5. The precipitate was suction filtered again, washed with water till neutral and recrystallized from toluene. Yield: 230 g. Melting point: 151° C. (structure confirmed by NMR).
Reaction SMILES: [CH3:1][N:2]1[C:10]2[C:5](=[CH:6][CH:7]=[CH:8][CH:9]=2)[CH:4]=[C:3]1[C:11](Cl)=[O:12].[NH2:14][C:15]1[C:20]2[C:21]([C:24]3[CH:29]=[CH:28][C:27]([NH2:30])=[C:26]([O:31][CH3:32])[CH:25]=3)=[CH:22][S:23][C:19]=2[C:18]([NH:33][C:34](=[O:42])[CH2:35][CH2:36][N:37]2[CH2:41][CH2:40][CH2:39][CH2:38]2)=[CH:17][N:16]=1>ClCCl.N1C=CC=CC=1>[NH2:14][C:15]1[C:20]2[C:21]([C:24]3[CH:29]=[CH:28][C:27]([NH:30][C:11]([C:3]4[N:2]([CH3:1])[C:10]5[C:5]([CH:4]=4)=[CH:6][CH:7]=[CH:8][CH:9]=5)=[O:12])=[C:26]([O:31][CH3:32])[CH:25]=3)=[CH:22][S:23][C:19]=2[C:18]([NH:33][C:34](=[O:42])[CH2:35][CH2:36][N:37]2[CH2:41][CH2:40][CH2:39][CH2:38]2)=[CH:17][N:16]=1
Reactant: COc1cc(-c2csc3c(NC(=O)CCN4CCCC4)cnc(N)c23)ccc1N
Reactant: Cn1c(C(=O)Cl)cc2ccccc21
Solvent: c1ccncc1
Solvent: ClCCl
Product: COc1cc(-c2csc3c(NC(=O)CCN4CCCC4)cnc(N)c23)ccc1NC(=O)c1cc2ccccc2n1C
Temperature: 25 °C
Reaction time: 8 h

Procedure:
1-Methyl-1H-indole-2-carbonyl chloride (109 mg, 0.6 mmol) in dichloromethane (2 mL) was added to N-[4-amino-3-(4-amino-3-methoxyphenyl)thieno[3,2-c]pyridin-7-yl]-3-pyrrolidin-1-ylpropanamide (0.5 mmol) in pyridine (3 mL) at about 0° C. The ice-water bath was removed and the reaction mixture was stirred at room temperature overnight. The solvent was removed and residue was purified by reverse phase preparative HPLC to give the title compound as the acetate salt (116 mg, 37%). 1H NMR (DMSO, d6) δ 1.75 (m, 4H), 1.90 (s, 3H), 2.55 (m, 6H), 2.77 (t, 2H), 3.91 (s, 3H), 4.04 (s, 3H), 5.44 (s, 2H), 7.08 (d, 1H), 7.15 (t, 1H), 7.20 (s, 1H), 7.33(t, 1H), 7.35 (s, 1H), 7.55 (s, 1H), 7.59 (d, 1H), 7.71 (d, 1H), 7.91 (s, 1H), 7.99 (d, 1H), 9.51 (s, 1H), 10.14 (s, 1H). LCMS: MH+=567.3, Rt =2.579 min. (a).
Reaction SMILES: [CH:1]([N:4]1[CH2:9][CH2:8][N:7]([C:10]([C:12]2[CH:13]=[C:14]3[C:18](=[CH:19][CH:20]=2)[NH:17][C:16]([C:21]([N:23]2[CH2:28][CH2:27][N:26]([S:29]([N:32]4[CH2:37][CH2:36][CH2:35][CH2:34][CH2:33]4)(=[O:31])=[O:30])[CH2:25][CH2:24]2)=[O:22])=[CH:15]3)=[O:11])[CH2:6][CH2:5]1)([CH3:3])[CH3:2].[Cl:38][C:39]1[CH:44]=[C:43](B(O)O)[CH:42]=[CH:41][N:40]=1>>[Cl:38][C:39]1[CH:44]=[C:43]([N:17]2[C:18]3[C:14](=[CH:13][C:12]([C:10]([N:7]4[CH2:8][CH2:9][N:4]([CH:1]([CH3:3])[CH3:2])[CH2:5][CH2:6]4)=[O:11])=[CH:20][CH:19]=3)[CH:15]=[C:16]2[C:21]([N:23]2[CH2:28][CH2:27][N:26]([S:29]([N:32]3[CH2:37][CH2:36][CH2:35][CH2:34][CH2:33]3)(=[O:31])=[O:30])[CH2:25][CH2:24]2)=[O:22])[CH:42]=[CH:41][N:40]=1
Reactant: CC(C)N1CCN(C(=O)c2ccc3[nH]c(C(=O)N4CCN(S(=O)(=O)N5CCCCC5)CC4)cc3c2)CC1
Reactant: OB(O)c1ccnc(Cl)c1
Product: CC(C)N1CCN(C(=O)c2ccc3c(c2)cc(C(=O)N2CCN(S(=O)(=O)N4CCCCC4)CC2)n3-c2ccnc(Cl)c2)CC1
Yield: 31 %

Procedure:
The title compound was synthesized in analogy to example 5, from [5-(4-isopropyl-piperazine-1-carbonyl)-1H-indol-2-yl]-[4-(piperidine-1-sulfonyl)-piperazin-1-yl]-methanone (example 2) and 2-chloropyridine-4-boronic acid to afford the desired product as a colorless foam (31%). MS (ISP): 642.5 (M+H)+.
Reaction SMILES: [F:1][C:2]([F:11])([F:10])[C:3]1[CH:9]=[CH:8][CH:7]=[CH:6][C:4]=1[NH2:5].N1C=CC=CC=1.[N+:18]([C:21]1[CH:26]=[CH:25][C:24]([S:27](Cl)(=[O:29])=[O:28])=[CH:23][CH:22]=1)([O-:20])=[O:19]>C(Cl)Cl>[N+:18]([C:21]1[CH:22]=[CH:23][C:24]([S:27]([NH:5][C:4]2[CH:6]=[CH:7][CH:8]=[CH:9][C:3]=2[C:2]([F:10])([F:11])[F:1])(=[O:29])=[O:28])=[CH:25][CH:26]=1)([O-:20])=[O:19]
Reactant: Nc1ccccc1C(F)(F)F
Reactant: O=[N+]([O-])c1ccc(S(=O)(=O)Cl)cc1
Solvent: c1ccncc1
Solvent: ClCCl
Product: O=[N+]([O-])c1ccc(S(=O)(=O)Nc2ccccc2C(F)(F)F)cc1
Temperature: 25 °C
Reaction time: 18 h
Yield: 82.4 %

Procedure:
A solution of 2-(trifluoromethyl)aniline (1.51 g, 9.37 mmol) and pyridine (1.08 mL, 13.38 mmol) in DCM (30 mL) was treated with 4-nitrobenzenesulfonyl chloride (1.48 g, 6.69 mmol) and stirred at room temperature for 18 hours. The mixture was diluted with DCM, washed with 1 M aqueous HCl, saturated aqueous NaHCO3, water and brine, dried over Na2SO4 and concentrated under vacuum. Trituration with pentane gave 4-nitro-N-(2-trifluoromethyl-phenyl)-benzenesulfonamide (1.91 g, 82%). 1H NMR (300 MHz, CDCl3) δ 8.31-8.23 (m, 2H), 7.95-7.85 (m, 3H), 7.64-7.50 (m, 2H), 7.31 (t, J=7.7 Hz, 1H), 6.89 (br s, 1H). LCMS (m/z, Method A) ES+ 347.1 [M+1]+.
Reaction SMILES: [CH3:1][O:2][CH2:3][C@@H:4]1[CH2:8][N:7]([C:9]([O:11][C:12]([CH3:15])([CH3:14])[CH3:13])=[O:10])[C@H:6]([C:16]([O:18]C)=[O:17])[CH2:5]1.[Li+].[OH-].Cl>C1COCC1.CO>[C:12]([O:11][C:9]([N:7]1[CH2:8][C@@H:4]([CH2:3][O:2][CH3:1])[CH2:5][C@H:6]1[C:16]([OH:18])=[O:17])=[O:10])([CH3:15])([CH3:13])[CH3:14]
Reactant: COC[C@H]1C[C@@H](C(=O)OC)N(C(=O)OC(C)(C)C)C1
Agent: Cl
Agent: [Li+]
Agent: [OH-]
Solvent: C1CCOC1
Solvent: CO
Product: COC[C@H]1C[C@@H](C(=O)O)N(C(=O)OC(C)(C)C)C1
Temperature: 25 °C
Reaction time: 2 h
Yield: 100.2 %

Procedure:
To a solution of (2S,4S)-1-tert-butyl 2-methyl 4-(methoxymethyl)pyrrolidine-1,2-dicarboxylate (2.11 g, 7.7 mmol) in a mixture of THF (38 mL) and MeOH (15 mL) was added LiOH (2.5 M aqueous, 15 mL, 38.6 mmol). The resulting solution was stirred at room temperature for 2 h, and acidified with aqueous HCl (1N). The desired product was extracted with CH2Cl2 (4×). The combined organic layers were dried over Na2SO4 and concentrated to provide (2S,4S)-1-(tert-butoxycarbonyl)-4-(methoxymethyl)pyrrolidine-2-carboxylic acid (2.0 g, 99%). 1H-NMR: 400 MHz, (CDCl3) δ: (mixture of rotamers, major reported) 4.33 (t, 1H), 3.65 (m, 1H), 3.35 (m, 2H), 3.32 (s, 3H), 3.16 (t, 1H), 2.45 (m, 2H), 2.12 (m, 1H), 1.46 (s, 9H).
Reaction SMILES: [Cl:1][C:2]1[CH:17]=[C:16]([C:18]2[C:19]3[C:20]4[CH:33]=[CH:32][S:31][C:21]=4[C:22](=[O:30])[NH:23][C:24]=3[CH:25]=[CH:26][C:27]=2[O:28][CH3:29])[CH:15]=[CH:14][C:3]=1[CH2:4][CH2:5][NH:6][C:7](=[O:13])[O:8][C:9]([CH3:12])([CH3:11])[CH3:10].C1C(=O)N([Cl:41])C(=O)C1>>[Cl:1][C:2]1[CH:17]=[C:16]([C:18]2[C:19]3[C:20]4[CH:33]=[CH:32][S:31][C:21]=4[C:22](=[O:30])[NH:23][C:24]=3[C:25]([Cl:41])=[CH:26][C:27]=2[O:28][CH3:29])[CH:15]=[CH:14][C:3]=1[CH2:4][CH2:5][NH:6][C:7](=[O:13])[O:8][C:9]([CH3:12])([CH3:11])[CH3:10]
Reactant: O=C1CCC(=O)N1Cl
Reactant: COc1ccc2[nH]c(=O)c3sccc3c2c1-c1ccc(CCNC(=O)OC(C)(C)C)c(Cl)c1
Product: COc1cc(Cl)c2[nH]c(=O)c3sccc3c2c1-c1ccc(CCNC(=O)OC(C)(C)C)c(Cl)c1
Yield: 51.8 %

Procedure:
Following General Procedure H, tert-butyl 2-chloro-4-(8-methoxy-4-oxo-4,5-dihydrothieno[2,3-c]quinolin-9-yl)phenethylcarbamate (127 mg, 0.26 mmol) was reacted with NCS (43 mg, 0.312 mmol) to afford the desired product (70 mg, 52%) as a yellow solid: ESI MS m/z 519 [C25H24Cl2N2O4S+H]+.
Reaction SMILES: [CH2:1]([C:3]1[CH:8]=[C:7]([C:9]2[N:13]=[C:12]([C:14]3[CH:19]=[C:18]([CH3:20])[C:17]([CH2:21][CH:22]([CH3:24])[CH3:23])=[CH:16][N:15]=3)[O:11][N:10]=2)[CH:6]=[C:5]([CH3:25])[C:4]=1[OH:26])[CH3:2].Br[CH2:28][CH2:29][OH:30]>C(O)(C)C.[OH-].[Na+].CC(=O)OCC>[CH2:1]([C:3]1[CH:8]=[C:7]([C:9]2[N:13]=[C:12]([C:14]3[CH:19]=[C:18]([CH3:20])[C:17]([CH2:21][CH:22]([CH3:23])[CH3:24])=[CH:16][N:15]=3)[O:11][N:10]=2)[CH:6]=[C:5]([CH3:25])[C:4]=1[O:26][CH2:28][CH2:29][OH:30])[CH3:2]
Reactant: OCCBr
Reactant: CCc1cc(-c2noc(-c3cc(C)c(CC(C)C)cn3)n2)cc(C)c1O
Agent: [Na+]
Agent: [OH-]
Solvent: CC(C)O
Solvent: CCOC(C)=O
Product: CCc1cc(-c2noc(-c3cc(C)c(CC(C)C)cn3)n2)cc(C)c1OCCO
Reaction time: 6 h
Yield: 79.8 %

Procedure:
To a solution of the compound of Example 32 (1.00 g, 2.85 mmol) in isopropanol (10 mL) and 3 M aq. NaOH (3 mL), 2-bromo-ethanol (1.42 g, 11.4 mmol) is added. The mixture is stirred at 60° C. for 24 h before another portion of 2-bromo-ethanol (176 mg, 1.41 mmol) is added. Stirring is continued at 60° C. for 6 h. The mixture is diluted with EA and washed with water. The org. extract is dried over MgSO4, filtered and concentrated. The crude product is purified by CC on silica gel eluting with heptane:EA 4:1 to 3:1 to give the title compound (900 mg) as a colourless oil; LC-MS: tR=1.10 min, [M+H]+=396.09.
Reaction SMILES: Br[C:2]1[C:3]([N:21]2[CH2:26][CH2:25][C:24]([CH3:28])([CH3:27])[CH2:23][CH2:22]2)=[C:4]([C@H:10]([O:16][C:17]([CH3:20])([CH3:19])[CH3:18])[C:11]([O:13][CH2:14][CH3:15])=[O:12])[C:5]([CH3:9])=[N:6][C:7]=1[CH3:8].[N:29]1[CH:34]=[CH:33][C:32]([CH2:35][O:36][C:37]2[CH:42]=[CH:41][C:40](B(O)O)=[CH:39][CH:38]=2)=[CH:31][CH:30]=1.C([O-])([O-])=O.[Na+].[Na+]>CN(C=O)C.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:17]([O:16][C@@H:10]([C:4]1[C:5]([CH3:9])=[N:6][C:7]([CH3:8])=[C:2]([C:40]2[CH:39]=[CH:38][C:37]([O:36][CH2:35][C:32]3[CH:33]=[CH:34][N:29]=[CH:30][CH:31]=3)=[CH:42][CH:41]=2)[C:3]=1[N:21]1[CH2:26][CH2:25][C:24]([CH3:28])([CH3:27])[CH2:23][CH2:22]1)[C:11]([O:13][CH2:14][CH3:15])=[O:12])([CH3:20])([CH3:19])[CH3:18]
Reactant: CCOC(=O)[C@@H](OC(C)(C)C)c1c(C)nc(C)c(Br)c1N1CCC(C)(C)CC1
Reactant: OB(O)c1ccc(OCc2ccncc2)cc1
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: CN(C)C=O
Product: CCOC(=O)[C@@H](OC(C)(C)C)c1c(C)nc(C)c(-c2ccc(OCc3ccncc3)cc2)c1N1CCC(C)(C)CC1
Reaction time: 9 h
Yield: 52.3 %

Procedure:
A mixture of (S)-ethyl 2-(5-bromo-4-(4,4-dimethylpiperidin-1-yl)-2,6-dimethylpyridin-3-yl)-2-(tert-butoxy)acetate (0.02 g, 0.044 mmol), (4-(pyridin-4-ylmethoxy)phenyl)boronic acid (0.020 g, 0.088 mmol) and 2M Na2CO3 (0.055 ml, 0.110 mmol) in DMF (1 mL) was degassed for 3 min. Then, Pd(Ph3P)4 (5.07 mg, 4.39 μmol) was degassed for 1 min and placed in a pre-heated oil bath at 90° C. After 9 h, cooled and purified by prep-HPLC to afford (S)-ethyl 2-(tert-butoxy)-2-(4-(4,4-dimethylpiperidin-1-yl)-2,6-dimethyl-5-(4-(pyridin-4-ylmethoxy)phenyl)pyridin-3-yl)acetate (0.013 g, 0.023 mmol, 52.9% yield) as brown paste. LCMS (M+H)=560.4.