Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [Cl:1][C:2]1[C:10]2[NH:9][N:8]=[CH:7][C:6]=2[C:5]2[CH2:11][N:12]([CH2:21][C:22]([F:25])([F:24])[F:23])[C:13](=[O:20])[C@H:14]([CH2:16][C:17](O)=[O:18])[CH2:15][C:4]=2[CH:3]=1.[NH:26]1[C:35]2[C:30](=[CH:31][CH:32]=[CH:33][CH:34]=2)[C:29]2([CH2:40][CH2:39][NH:38][CH2:37][CH2:36]2)[NH:28][C:27]1=[O:41].F[B-](F)(F)F.N1(OC(N(C)C)=[N+](C)C)C2C=CC=CC=2N=N1.C(N(CC)CC)C>ClCCl>[Cl:1][C:2]1[C:10]2[NH:9][N:8]=[CH:7][C:6]=2[C:5]2[CH2:11][N:12]([CH2:21][C:22]([F:24])([F:23])[F:25])[C:13](=[O:20])[C@H:14]([CH2:16][C:17](=[O:18])[N:38]3[CH2:37][CH2:36][C:29]4([C:30]5[C:35](=[CH:34][CH:33]=[CH:32][CH:31]=5)[NH:26][C:27](=[O:41])[NH:28]4)[CH2:40][CH2:39]3)[CH2:15][C:4]=2[CH:3]=1
Reactant: O=C1Nc2ccccc2C2(CCNCC2)N1
Reactant: O=C(O)C[C@@H]1Cc2cc(Cl)c3[nH]ncc3c2CN(CC(F)(F)F)C1=O
Agent: CN(C)C(On1nnc2ccccc21)=[N+](C)C
Agent: F[B-](F)(F)F
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: O=C1Nc2ccccc2C2(CCN(C(=O)C[C@@H]3Cc4cc(Cl)c5[nH]ncc5c4CN(CC(F)(F)F)C3=O)CC2)N1
Reaction time: 12 h
Yield: 79.8 %

Procedure:
To a solution of (S)-2-(4-chloro-8-oxo-9-(2,2,2-trifluoroethyl)-3,6,7,8,9,10-hexahydroazepino[3,4-e]indazol-7-yl)acetic acid (50 mg, 0.133 mmol) in dichloromethane (25 mL) was added 1′H-spiro[piperidine-4,4′-quinazolin]-2′(3′H)-one (31 mg, 0.14 mmol) followed by 2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium tetrafluoroborate (47 mg, 0.15 mmol) and triethylamine (1.0 mL). After 12 h, the reaction mixture was washed with aqueous NaHCO3 followed by 1.0 M HCl and dried (Na2SO4). The solvent was removed and the crude product was purified by flash chromatography using 7% MeOH in dichloromethane to give (S)-4-chloro-7-(2-oxo-2-(2′-oxo-2′,3′-dihydro-1′H-spiro[piperidine-4,4′-quinazoline]-1-yl)ethyl)-9-(2,2,2-trifluoroethyl)-6,7,9,10-tetrahydroazepino[3,4-e]indazol-8(3H)-one (61 mg, 79%) as a white powder. MS (ESI) 575 (M+H); Rf=2.133.
Reaction SMILES: [Br:1][C:2]1[CH:10]=[CH:9][C:5]([C:6](O)=[O:7])=[C:4]([CH3:11])[CH:3]=1.C(Cl)(=O)C(Cl)=O.CN.[CH2:20]([N:22](CC)CC)C>C(Cl)Cl.CN(C)C=O>[Br:1][C:2]1[CH:10]=[CH:9][C:5]([C:6]([NH:22][CH3:20])=[O:7])=[C:4]([CH3:11])[CH:3]=1
Reactant: Cc1cc(Br)ccc1C(=O)O
Reactant: CCN(CC)CC
Agent: CN
Agent: O=C(Cl)C(=O)Cl
Solvent: CN(C)C=O
Solvent: ClCCl
Product: CNC(=O)c1ccc(Br)cc1C
Temperature: 25 °C
Reaction time: 8 h
Yield: 93.4 %

Procedure:
N,N-Dimethylformamide (10 uL) was added to a mixture of 4-bromo-2-methylbenzoic acid (1.0 g, 0.0046 mol) in oxalyl chloride (2.0 mL, 0.023 mol). The mixture was stirred at r.t. overnight. The volatiles were removed under reduced pressure. The residue was dissolved in methylene chloride (2 mL). To the solution was added to a mixture of methylamine (0.41 mL, 0.0093 mol) and triethylamine (1.3 mL, 0.0093 mol) in DCM (10 ml). After 30 min, the reaction mixture was quenched with aqueous sodium carbonate (10 mL) and extracted with DCM (3×20 mL). The organic layers were washed with brine, dried over Na2SO4, filtered. The solvents were removed under reduced pressure to give a crude product (980 mg, 92.4%). LCMS (M+H)+: m/z=228.1/230.2.
Reaction SMILES: [C:1](#[N:8])[CH2:2][CH2:3][CH2:4][CH2:5][C:6]#[N:7].[CH2:9]([NH2:12])[CH2:10][CH3:11]>>[C:6]([CH2:5][CH2:4][CH2:3][CH2:2][CH2:1][N:8]([CH2:4][CH2:5][CH3:6])[CH2:1][CH2:2][CH2:3][CH2:11][CH2:10][C:9]#[N:12])#[N:7]
Reactant: N#CCCCCC#N
Reactant: CCCN
Product: CCCN(CCCCCC#N)CCCCCC#N

Procedure:
116.0 g of adiponitrile and 15.7 mL of propylamine, (4 to 1 ratio of dinitrile to primary amine) were charged to a 300 cc autoclave along with 2.8 grams of catalyst (5 wt. % Pd on alumina powder). After purging with nitrogen, the reaction was pressurized to 50 psig with hydrogen and heating was commenced. Hydrogen was continuously replenished. After the temperature reached 110° C., stirring was increased to 1000 rpm and the hydrogen pressure was increased to 500 psig. The temperature and pressure were maintained for 1.5 hours. The product mixture comprised of 39% bis(cyanopentyl)aminopropane and 36% unconverted adiponitrile.
Reaction SMILES: [CH3:1][O:2][C:3]([C@H:5]1[CH2:10][CH2:9][C@H:8]([C:11]2[N:15]3[CH:16]=[CH:17][N:18]=[C:19]([NH2:20])[C:14]3=[C:13](Br)[N:12]=2)[CH2:7][CH2:6]1)=[O:4].[O:22]([C:29]1[CH:34]=[CH:33][C:32](B(O)O)=[CH:31][CH:30]=1)[C:23]1[CH:28]=[CH:27][CH:26]=[CH:25][CH:24]=1.O.O.[F-].[K+]>COCCOC.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>[CH3:1][O:2][C:3]([C@H:5]1[CH2:10][CH2:9][C@H:8]([C:11]2[N:15]3[CH:16]=[CH:17][N:18]=[C:19]([NH2:20])[C:14]3=[C:13]([C:32]3[CH:33]=[CH:34][C:29]([O:22][C:23]4[CH:28]=[CH:27][CH:26]=[CH:25][CH:24]=4)=[CH:30][CH:31]=3)[N:12]=2)[CH2:7][CH2:6]1)=[O:4]
Reactant: OB(O)c1ccc(Oc2ccccc2)cc1
Reactant: COC(=O)[C@H]1CC[C@H](c2nc(Br)c3c(N)nccn32)CC1
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: [F-]
Agent: [K+]
Solvent: COCCOC
Solvent: O
Product: COC(=O)[C@H]1CC[C@H](c2nc(-c3ccc(Oc4ccccc4)cc3)c3c(N)nccn32)CC1
Temperature: 100 °C

Procedure:
To a stirred mixture of trans-4-(8-amino-1-bromo-imidazo[1,5-a]pyrazin-3-yl)-cyclohexanecarboxylic acid methyl ester (2.00 g, 5.66 mmol) and 4-phenoxyphenylboronic acid (1.454 g, 6.7 mmol) in DME (25.00 mL) and H2O (8.3 mL) was added potassium fluoride dihydrate (1.865 g, 19.82 mmol). The mixture was bubbled with nitrogen for 5 min before Pd(PPh3)4 (330 mg, 0.28 mmol) was added to. The resulting mixture was refluxed overnight at 100° C. Solvent was removed under reduced pressure and the product was purified by flash chromatography (2% MeOH in DCM). 1H NMR (400 MHz, CD3OD) δ 1.59-1.87 (m, 4H), 2.02-2.18 (m, 4H), 2.41-2.53 (m, 1H), 3.09-3.19 (m, 1H), 3.68 (s, 3H), 6.94-7.20 (m, 6H), 7.32-7.44 (m, 2H), 7.52-7.63 (m, 3H). MS (ES+): m/z: 442.97 [MH+]. HPLC: tR=2.48 min (OpenLynx: polar—5 min).
Reaction SMILES: [C:1](=[S:11])([S:3][CH2:4][CH2:5][C:6]([F:10])=[C:7]([F:9])[F:8])[NH2:2].[CH2:12](OC(OCC)CCl)[CH3:13].O.C1(C)C=CC(S(O)(=O)=O)=CC=1>C(O)(=O)C>[F:10][C:6](=[C:7]([F:9])[F:8])[CH2:5][CH2:4][S:3][C:1]1[S:11][CH:12]=[CH:13][N:2]=1
Reactant: CCOC(CCl)OCC
Reactant: NC(=S)SCCC(F)=C(F)F
Agent: Cc1ccc(S(=O)(=O)O)cc1
Solvent: O
Solvent: CC(=O)O
Product: FC(F)=C(F)CCSc1nccs1
Temperature: 95 °C
Reaction time: 1.5 h

Procedure:
3 g (14.9 mmol) of 3,4,4-trifluoro-3-butenyl dithiocarbamate in 15 ml of glacial acetic acid are admixed with 2.3 g (15.1 mmol) of chloroacetaldehyde diethyl acetal and 40 mg of p-toluenesulphonic acid monohydrate. The mixture is stirred at 95° C. for 1.5 h and, after cooling to room temperature, is then concentrated by evaporation under reduced pressure. The evaporation residue is taken up in dichloromethane and washed with 1 N sodium hydroxide solution, and the organic phase is removed, dried over Na2SO4 and concentrated by evaporation under reduced pressure. 2.8 g (81.5% of theory; purity by GC/MS: 97.7 area %) of an oil are obtained.
Reaction SMILES: [Se](=O)=O.[O:4]1CCOCC1.[S:10]([NH:14][C:15]1[S:16][CH:17]=[C:18]([CH2:20][C:21]([O:23][CH2:24][CH3:25])=[O:22])[N:19]=1)([CH3:13])(=[O:12])=[O:11]>O>[S:10]([NH:14][C:15]1[S:16][CH:17]=[C:18]([C:20](=[O:4])[C:21]([O:23][CH2:24][CH3:25])=[O:22])[N:19]=1)([CH3:13])(=[O:11])=[O:12]
Reactant: CCOC(=O)Cc1csc(NS(C)(=O)=O)n1
Reactant: C1COCCO1
Agent: O=[Se]=O
Solvent: O
Product: CCOC(=O)C(=O)c1csc(NS(C)(=O)=O)n1
Reaction time: 0.25 h

Procedure:
A mixture of selenium dioxide (11.1 g.), dioxane (250 ml.) and water (5 ml. was stirred for 15 minutes at 110° to 115° C. to give yellow solution. Ethyl 2-(2-mesylamino-1,3-thiazol-4-yl)acetate (26.4 g) was added thereto with stirring at the same temperature. After stirring for 1 hour, the reaction mixture was decanted with heating and cooled to precipitate yellow crystals. The crystals were collected by filtration, washed with dioxane and ether and dried to give ethyl 2-(2-mesylamino-1,3-thiazol-4-yl)glyoxylate (23.5 g.).
Reaction SMILES: [OH:1][C:2]1([C:8]2[CH:13]=[CH:12][CH:11]=[CH:10][CH:9]=2)[CH2:7][CH2:6][NH:5][CH2:4][CH2:3]1.[Cl:14][C:15]1[CH:16]=[C:17]([CH:22]([CH2:34][CH:35]=O)[CH2:23][N:24]([CH3:33])[C:25](=[O:32])[C:26]2[CH:31]=[CH:30][CH:29]=[CH:28][CH:27]=2)[CH:18]=[CH:19][C:20]=1[Cl:21].C([BH3-])#N.[Na+].C(=O)(O)[O-].[Na+]>CO.C(O)(=O)C>[Cl:14][C:15]1[CH:16]=[C:17]([CH:22]([CH2:34][CH2:35][N:5]2[CH2:6][CH2:7][C:2]([OH:1])([C:8]3[CH:13]=[CH:12][CH:11]=[CH:10][CH:9]=3)[CH2:3][CH2:4]2)[CH2:23][N:24]([CH3:33])[C:25](=[O:32])[C:26]2[CH:27]=[CH:28][CH:29]=[CH:30][CH:31]=2)[CH:18]=[CH:19][C:20]=1[Cl:21]
Reactant: CN(CC(CC=O)c1ccc(Cl)c(Cl)c1)C(=O)c1ccccc1
Reactant: OC1(c2ccccc2)CCNCC1
Agent: O=C([O-])O
Agent: [BH3-]C#N
Agent: [Na+]
Solvent: CO
Solvent: CC(=O)O
Product: CN(CC(CCN1CCC(O)(c2ccccc2)CC1)c1ccc(Cl)c(Cl)c1)C(=O)c1ccccc1
Temperature: 25 °C
Reaction time: 16 h
Yield: 46.4 %

Procedure:
A solution of 4-hydroxy-4-phenyl-piperidine (1.99 g) in methanol (20 mL) was cooled to 0° C. and the pH was adjusted to 8 by adding acetic acid. To this solution was added N-[2-(3,4-dichlorophenyl)-4-oxobutyl]-N-methylbenzamide (3.57 g) in methanol (20 mL), and the resulting reaction mixture was treated with sodium cyanoborohydride (0.765 g). Upon warming to the room temperature, the reaction mixture was stirred for 16 hours and treated with saturated sodium bicarbonate solution. The solution was extracted with dichloromethane, dried (anhydrous sodium sulfate) and evaporated. The resulting material was purified by chromatography, with dichloromethane:methanol (90:10) as the eluent, to give the piperidine (2.42 g); NMR (CDCl3): 1.5-2.5 (m, 10), 2.68 (broad, 4), 3.47 (s, 3), 3.5-3.57 (m, 1), 6.8-7.5 (m, 13); MS: m/z=511(M+1). This material was used in the next step without further purification.
Reaction SMILES: [Br:1][C:2]1[N:3]=[C:4]2[C:10]([C:11]([OH:13])=O)=[CH:9][N:8]([CH2:14][O:15][CH2:16][CH2:17][Si:18]([CH3:21])([CH3:20])[CH3:19])[C:5]2=[N:6][CH:7]=1.[C:22]([NH2:26])([CH3:25])([CH3:24])[CH3:23].CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F>CN(C=O)C>[Br:1][C:2]1[N:3]=[C:4]2[C:10]([C:11]([NH:26][C:22]([CH3:25])([CH3:24])[CH3:23])=[O:13])=[CH:9][N:8]([CH2:14][O:15][CH2:16][CH2:17][Si:18]([CH3:21])([CH3:20])[CH3:19])[C:5]2=[N:6][CH:7]=1
Reactant: C[Si](C)(C)CCOCn1cc(C(=O)O)c2nc(Br)cnc21
Reactant: CC(C)(C)N
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CN(C)C=O
Product: CC(C)(C)NC(=O)c1cn(COCC[Si](C)(C)C)c2ncc(Br)nc12
Temperature: 25 °C
Reaction time: 72 h
Yield: 86 %

Procedure:
In a 100 ml round-bottomed flask, 2-bromo-5-(2-trimethylsilanyl-ethoxymethyl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid (1.00 g, 2.69 mmol) was dissolved in DMF (6 ml). tert-Butylamine (1.7 ml, 16.2 mmol) was added followed by HATU (1.12 g, 2.95 mmol). The yellow suspension was stirred at room temperature for 72 h then quenched with water and extracted with a mixture of diethyl ether and EtOAc. The organic layers were washed twice with water and once with brine then combined, dried over sodium sulfate, filtered and concentrated. The residue was triturated with petroleum ether to afford 989 mg (86%) of 2-bromo-N-tert-butyl-5-((2-(trimethylsilyl)ethoxy)methyl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide as an off-white powder. 1H NMR (CDCl3, 300 MHz): δ (ppm) 8.40 (s, 1H), 8.31 (s, 1H), 7.86 (s, 1H), 5.65 (s, 2H), 3.46-3.58 (m, 2H), 1.54 (s, 9H), 0.84-0.98 (m, 2H), −0.04 (s, 9H).
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]([CH3:13])([CH3:12])[C:9]([OH:11])=O)=[CH:4][CH:3]=1.[NH2:14][CH2:15][CH2:16][CH2:17][N:18]1[CH2:23][CH2:22][CH:21]([C:24]2[CH:25]=[C:26]([NH:30][C:31](=[O:34])[CH2:32][CH3:33])[CH:27]=[CH:28][CH:29]=2)[CH2:20][CH2:19]1>>[Cl:1][C:2]1[CH:3]=[CH:4][C:5]([C:8]([CH3:13])([CH3:12])[C:9]([NH:14][CH2:15][CH2:16][CH2:17][N:18]2[CH2:23][CH2:22][CH:21]([C:24]3[CH:29]=[CH:28][CH:27]=[C:26]([NH:30][C:31](=[O:34])[CH2:32][CH3:33])[CH:25]=3)[CH2:20][CH2:19]2)=[O:11])=[CH:6][CH:7]=1
Reactant: CC(C)(C(=O)O)c1ccc(Cl)cc1
Reactant: CCC(=O)Nc1cccc(C2CCN(CCCN)CC2)c1
Product: CCC(=O)Nc1cccc(C2CCN(CCCNC(=O)C(C)(C)c3ccc(Cl)cc3)CC2)c1

Procedure:
Example 7 was prepared from 2-(4-chlorophenyl)-2-methylpropanoic acid and N-{3-[1-(3-aminopropyl)-4-piperidinyl]phenyl}propanamide according to the procedures described in Scheme 10: 1H NMR (400 MHz, CDCl3) δ 7.86 (s, 1H), 7.50 (s, 1H), 7.34–7.19 (m, 6H), 6.96 (d, 1H, J=7.8 Hz), 6.72–6.67 (m, 1H), 3.42 (q, 2H, J=7.1 Hz), 3.31 (q, 3H, J=5.4 Hz), 2.49–2.35 (m, 5H), 2.08–1.95 (m, 2H), 1.82–1.74 (m, 2H), 1.71–1.62 (m, 3H), 1.56 (s, 6H), 1.24 (t, 3H, J=7.8 Hz); ESMS m/e: 470.3 (M+H)+.
Reaction SMILES: [Cl:1][C:2]1[CH:23]=[CH:22][C:5]([CH2:6][N:7]2[CH:12]=[C:11]([C:13]3[CH:18]=[CH:17][C:16]([CH2:19][OH:20])=[CH:15][CH:14]=3)[CH:10]=[CH:9][C:8]2=[O:21])=[CH:4][CH:3]=1.I[CH2:25][CH3:26]>>[Cl:1][C:2]1[CH:3]=[CH:4][C:5]([CH2:6][N:7]2[CH:12]=[C:11]([C:13]3[CH:18]=[CH:17][C:16]([CH2:19][O:20][CH2:25][CH3:26])=[CH:15][CH:14]=3)[CH:10]=[CH:9][C:8]2=[O:21])=[CH:22][CH:23]=1
Reactant: CCI
Reactant: O=c1ccc(-c2ccc(CO)cc2)cn1Cc1ccc(Cl)cc1
Product: CCOCc1ccc(-c2ccc(=O)n(Cc3ccc(Cl)cc3)c2)cc1
Yield: 40.8 %

Procedure:
According to Scheme 25 Method A: The title compound was prepared from 1-(4-chlorobenzyl)-5-(4-(hydroxymethyl)phenyl)pyridin-2(1H)-one (1 eq, 2.50 mmol, 0.80 g) and iodoethane (3 eq, 7.40 mmol, 1.10 g)) according to the procedure described for Example 34 Step 3. The crude product was purified by flash chromatography over silica gel (AIT Flashsmart prepacked column 5 g SiO2) using CH2Cl2/MeOH 99/1 as eluent to afford 1-(4-chlorobenzyl)-5-(4-(ethoxymethyl)phenyl)pyridin-2(1H)-one (1.02 mmol, 0.36 g, 41%) as a yellow solid.
Reaction SMILES: [CH3:1][S:2][C:3]1[CH:8]=[CH:7][C:6]([CH2:9][C:10](=[O:12])[CH3:11])=[CH:5][CH:4]=1.[CH:13](=O)[C:14]1[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=1.N1CCCCC1>C1C=CC=CC=1>[C:14]1([CH:13]=[C:9]([C:6]2[CH:7]=[CH:8][C:3]([S:2][CH3:1])=[CH:4][CH:5]=2)[C:10](=[O:12])[CH3:11])[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=1
Reactant: O=Cc1ccccc1
Reactant: CSc1ccc(CC(C)=O)cc1
Solvent: c1ccccc1
Solvent: C1CCNCC1
Product: CSc1ccc(C(=Cc2ccccc2)C(C)=O)cc1

Procedure:
A solution of 1-(4-methylthiophenyl)-2-propanone [G. Y. Lesher, U.S. Pat. No. 4,517,192, May 14, 1985; L. M. Werfel et al, J. Med. Chem., 29, 924-36 (1986)] (11.2 g, 0.062 mol) and benzaldehyde (6.6 g, 0.062 mol) in benzene (75 ml) containing piperidine (200 mg) was heated at reflux for 24 hours. After cooling, the solvent was removed and the residue was purified by chromatography on silica gel using mixtures of ethyl acetate and toluene to give the ketone. This material was recrystallized from ethyl acetate and hexane to give 14 g (82%) of pure ketone as a crystalline solid: mp 91°-93° C. Anal. Calc'd. for C17H16OS (268.38): C, 76.08; H, 6.01; S, 11.95. Found: C, 76.15; H, 6.08; S, 11.79.
Reaction SMILES: [CH:1]1([N:6]2[CH2:12][C:11]3([CH2:14][CH2:13]3)[C:10](=[O:15])[N:9]([CH3:16])[C:8]3[CH:17]=[N:18][C:19]([NH:21][C:22]4[CH:30]=[CH:29][C:25]([C:26](O)=[O:27])=[CH:24][C:23]=4[O:31][CH3:32])=[N:20][C:7]2=3)[CH2:5][CH2:4][CH2:3][CH2:2]1.CCN(C(C)C)C(C)C.CN(C(ON1N=NC2C=CC=CC1=2)=[N+](C)C)C.[B-](F)(F)(F)F.[CH2:64]([N:66]1[CH2:72][CH2:71][CH2:70][N:69]([CH:73]2[CH2:78][CH2:77][CH:76]([NH2:79])[CH2:75][CH2:74]2)[CH2:68][CH2:67]1)[CH3:65]>CN(C=O)C>[CH:1]1([N:6]2[CH2:12][C:11]3([CH2:14][CH2:13]3)[C:10](=[O:15])[N:9]([CH3:16])[C:8]3[CH:17]=[N:18][C:19]([NH:21][C:22]4[CH:30]=[CH:29][C:25]([C:26]([NH:79][CH:76]5[CH2:75][CH2:74][CH:73]([N:69]6[CH2:70][CH2:71][CH2:72][N:66]([CH2:64][CH3:65])[CH2:67][CH2:68]6)[CH2:78][CH2:77]5)=[O:27])=[CH:24][C:23]=4[O:31][CH3:32])=[N:20][C:7]2=3)[CH2:5][CH2:4][CH2:3][CH2:2]1
Reactant: COc1cc(C(=O)O)ccc1Nc1ncc2c(n1)N(C1CCCC1)CC1(CC1)C(=O)N2C
Reactant: CCN1CCCN(C2CCC(N)CC2)CC1
Agent: CN(C)C(On1nnc2ccccc21)=[N+](C)C
Agent: F[B-](F)(F)F
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: CCN1CCCN(C2CCC(NC(=O)c3ccc(Nc4ncc5c(n4)N(C4CCCC4)CC4(CC4)C(=O)N5C)c(OC)c3)CC2)CC1
Temperature: 25 °C
Reaction time: 2 h

Procedure:
4-(9′-Cyclopentyl-5′-methyl-6′-oxo-5′,6′,8′,9′-tetrahydrospiro[cyclopropane-1,7′-pyrimido[4,5-b][1,4]diazepine]-2′-ylamino)-3-methoxybenzoic acid (Intermediate 5) (44 mg, 0.1 mmol, 1 eq), DIPEA (35 μl, 0.2 mmol, 2 eq) and TBTU (36 mg, 0.12 mmol, 1.2 eq) were added to 1 mL DMF and the resulting solution was stirred at rt for 20 min before the addition of 4-(4-ethyl-1,4-diazepan-1-yl)cyclohexanamine (Intermediate 15) as the trihydrochloride salt (32 mg, 0.1 mmol, 1 eq) and DIPEA (53 μL, 0.3 mmol, 3 eq). The RM was then stirred at rt for 2 hours before purifying by preparative RP-HPLC-MS (Preparative—2) to provide 4-(9′-cyclopentyl-5′-methyl-6′-oxo-5′,6′,8′,9′-tetrahydrospiro[cyclopropane-1,7′-pyrimido[4,5-b][1,4]diazepine]-2′-ylamino)-N-(4-(4-ethyl-1,4-diazepan-1-yl)cyclohexyl)-3-methoxybenzamide as a mixture cis and trans isomers (white solid, 10 mg, 16%).
Reaction SMILES: [N+:1]([C:4]1[CH:5]=[C:6]([CH:20]=[CH:21][CH:22]=1)[NH:7][C:8]1[CH:19]=[CH:18][CH:17]=[CH:16][C:9]=1[C:10]([NH:12][CH2:13][C:14]#[CH:15])=[O:11])([O-:3])=[O:2].[O:23]1CCC[CH2:24]1.[H-].[Na+].ClC(Cl)(Cl)C(N1C=CN=C1)=O>O>[N+:1]([C:4]1[CH:5]=[C:6]([N:7]2[C:8]3[C:9](=[CH:16][CH:17]=[CH:18][CH:19]=3)[C:10](=[O:11])[N:12]([CH2:13][C:14]#[CH:15])[C:24]2=[O:23])[CH:20]=[CH:21][CH:22]=1)([O-:3])=[O:2]
Reactant: C1CCOC1
Reactant: C#CCNC(=O)c1ccccc1Nc1cccc([N+](=O)[O-])c1
Agent: O=C(n1ccnc1)C(Cl)(Cl)Cl
Agent: [H-]
Agent: [Na+]
Solvent: O
Product: C#CCn1c(=O)c2ccccc2n(-c2cccc([N+](=O)[O-])c2)c1=O
Temperature: 25 °C
Reaction time: 0.5 h

Procedure:
To a solution of 3.0 g of 2-(m-nitroanilino)-N-propargylbenzamide and 25 ml of dry tetrahydrofuran was added 1.0 g of approximately 55 % sodium hydride, and the solution was stirred for 30 minutes at room temperature. To this was added dropwise 2.1 g of 1-trichloroacetylimidazole and the mixture was refluxed for one hour. After the reaction was complete, the solvent was distilled off from the resulting mixture under reduced pressure. To the residue thus obtained was added water to yield a crude product. This product was recrystallized from methanol to yield 2.8 g of 1-(m-nitrophenyl) -3-propargylquinazoline-2,4(1H, 3H)-dione as colorless needles, melting at 222°-223° C.
Reaction SMILES: Cl[C:2]1[C:7]([C:8]#[N:9])=[CH:6][C:5]([C:10]2[C:19]3[C:14](=[CH:15][C:16]([S:20]([NH:23][C:24]4[S:25][CH:26]=[N:27][N:28]=4)(=[O:22])=[O:21])=[CH:17][CH:18]=3)[CH:13]=[CH:12][N:11]=2)=[C:4]([O:29][CH3:30])[CH:3]=1.[F:31][C:32]([F:43])([F:42])[C:33]1[CH:34]=[C:35](B(O)O)[CH:36]=[CH:37][CH:38]=1.C1(P(C2CCCCC2)C2C=CC=CC=2C2C(OC)=CC=CC=2OC)CCCCC1.P([O-])([O-])([O-])=O.[K+].[K+].[K+]>C(Cl)Cl>[C:8]([C:7]1[CH:6]=[C:5]([C:10]2[C:19]3[C:14](=[CH:15][C:16]([S:20]([NH:23][C:24]4[S:25][CH:26]=[N:27][N:28]=4)(=[O:21])=[O:22])=[CH:17][CH:18]=3)[CH:13]=[CH:12][N:11]=2)[C:4]([O:29][CH3:30])=[CH:3][C:2]=1[C:37]1[CH:36]=[CH:35][CH:34]=[C:33]([C:32]([F:43])([F:42])[F:31])[CH:38]=1)#[N:9]
Reactant: COc1cc(Cl)c(C#N)cc1-c1nccc2cc(S(=O)(=O)Nc3nncs3)ccc12
Reactant: OB(O)c1cccc(C(F)(F)F)c1
Agent: COc1cccc(OC)c1-c1ccccc1P(C1CCCCC1)C1CCCCC1
Agent: O=P([O-])([O-])[O-]
Agent: [K+]
Solvent: ClCCl
Product: COc1cc(-c2cccc(C(F)(F)F)c2)c(C#N)cc1-c1nccc2cc(S(=O)(=O)Nc3nncs3)ccc12
Temperature: 120 °C

Procedure:
A vial was charged with 1-(4-chloro-5-cyano-2-methoxyphenyl)-N-(1,3,4-thiadiazol-2-yl)isoquinoline-6-sulfonamide (EXAMPLE 337, 69.8 mg, 0.152 mmol) (3-(trifluoromethyl)phenyl)boronic acid (57.9 mg, 0.305 mmol), dicyclohexyl(2′,6′-dimethoxy-[1,1′-biphenyl]-2-yl)phosphine (3.13 mg, 7.62 μmol), chloro(2-dicyclohexylphosphino-2′,6′-dimethoxy-1,1′-biphenyl)[2-(2-aminoethylphenyl)]palladium(ii) dichloromethane (11.55 mg, 0.015 mmol) and potassium phosphate (162 mg, 0.762 mmol). The vial was flushed with Ar (g), then 1,4-dioxane (693 μl) and water (69.3 μl) were added. The vial was sealed and heated in a Biotage Initiator microwave reactor for 1 h at 120° C. The mixture was extracted with EtOAc, MeOH-EtOAc, and MeOH-DCM. The combined organic extracts were concentrated. The residue was purified by chromatography on silica gel (12-g Redi-Sep Gold column, 0-7.5% MeOH/DCM) to give an off-white solid. The solid was taken up in DCM and filtered. The collected solid was washed with DCM (2×), dried under a stream of N2 (g), and dried under vacuum to give 1-(2-cyano-5-methoxy-3′-(trifluoromethyl)-[1,1′-biphenyl]-4-yl)-N-(1,3,4-thiadiazol-2-yl)isoquinoline-6-sulfonamide as a white solid. 1H NMR (400 MHz, DMSO-d6) δ=8.80 (s, 1H), 8.73 (d, J=5.7 Hz, 1H), 8.62-8.55 (m, 1H), 8.17 (d, J=5.6 Hz, 1H), 8.11-8.04 (m, 2H), 7.98 (s, 1H), 7.96-7.78 (m, 3H), 7.51 (s, 1H), 7.19 (br. s., 1H), 3.83 (s, 3H). m/z (ESI) 567.9 (M+H)+.
Reaction SMILES: C(N[C:5]1[C:14]2[C:9](=[CH:10][C:11]([O:15][CH3:16])=[CH:12][CH:13]=2)[C:8]([C:17]2[CH:22]=[CH:21][CH:20]=[CH:19][CH:18]=2)=[C:7]([C:23]#[N:24])[N:6]=1)C=C.[NH:25]1[CH2:29][CH2:28][C@@H:27]([OH:30])[CH2:26]1>>[OH:30][C@@H:27]1[CH2:28][CH2:29][N:25]([C:5]2[C:14]3[C:9](=[CH:10][C:11]([O:15][CH3:16])=[CH:12][CH:13]=3)[C:8]([C:17]3[CH:22]=[CH:21][CH:20]=[CH:19][CH:18]=3)=[C:7]([C:23]#[N:24])[N:6]=2)[CH2:26]1
Reactant: O[C@@H]1CCNC1
Reactant: C=CCNc1nc(C#N)c(-c2ccccc2)c2cc(OC)ccc12
Product: COc1ccc2c(N3CC[C@@H](O)C3)nc(C#N)c(-c3ccccc3)c2c1

Procedure:
Following the procedure for 1-(allylamino)-6-methoxy-4-phenylisoquinoline-3-carbonitrile, using (R)-3-pyrrolidinol in place of allylamine, the title compound was synthesized.
Reaction SMILES: [F:1]C1C=CC=CC=1C(Cl)=O.[CH3:11][O:12][C:13]1[CH:14]=[C:15]2[C:20](=[CH:21][C:22]=1[O:23][CH3:24])[N:19]=[CH:18][CH:17]=[C:16]2[O:25][C:26]1[CH:32]=[CH:31][C:29]([NH2:30])=[C:28](F)[CH:27]=1.[F:34][C:35]1[CH:40]=[CH:39][CH:38]=[CH:37][C:36]=1[C:41]([N:43]=[C:44]=[S:45])=[O:42]>C1(C)C=CC=CC=1.C(O)C>[F:34][C:35]1[CH:40]=[CH:39][CH:38]=[CH:37][C:36]=1[C:41]([N:43]=[C:44]=[S:45])=[O:42].[CH3:11][O:12][C:13]1[CH:14]=[C:15]2[C:20](=[CH:21][C:22]=1[O:23][CH3:24])[N:19]=[CH:18][CH:17]=[C:16]2[O:25][C:26]1[CH:32]=[CH:31][C:29]([NH:30][C:44]([NH:43][C:41](=[O:42])[C:36]2[CH:37]=[CH:38][CH:39]=[CH:40][C:35]=2[F:34])=[S:45])=[CH:28][C:27]=1[F:1]
Reactant: COc1cc2nccc(Oc3ccc(N)c(F)c3)c2cc1OC
Reactant: O=C(Cl)c1ccccc1F
Agent: O=C(N=C=S)c1ccccc1F
Solvent: Cc1ccccc1
Solvent: CCO
Product: COc1cc2nccc(Oc3ccc(NC(=S)NC(=O)c4ccccc4F)cc3F)c2cc1OC
Temperature: 25 °C
Reaction time: 2 h
Yield: 86 %

Procedure:
2-Fluoro-1-benzenecarbonyl isothiocyanate was prepared using commercially available 2-fluoro-1-benzenecarbonyl chloride (80 mg) as a starting compound according to the description of the literature. 4-[(6,7-Dimethoxy-4-quinolyl)oxy]-2-fluoroaniline (50 mg) was dissolved in toluene (5 ml) and ethanol (1 ml) to prepare a solution. A solution of 2-fluoro-1-benzenecarbonyl isothiocyanate in ethanol (1 ml) was then added to the solution, and the mixture was stirred at room temperature for 2 hr. The reaction solution was concentrated, and the residue was purified by chromatography on silica gel using chloroform/acetone for development to give the title compound (68 mg, yield 86%).
Reaction SMILES: Cl[C:2]1[CH:7]=[CH:6][C:5]([O:8][CH3:9])=[CH:4][CH:3]=1.[C:10]1(B(O)O)[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=1>>[CH3:9][O:8][C:5]1[CH:6]=[CH:7][C:2]([C:10]2[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=2)=[CH:3][CH:4]=1
Reactant: COc1ccc(Cl)cc1
Reactant: OB(O)c1ccccc1
Product: COc1ccc(-c2ccccc2)cc1
Yield: 80.3 %

Procedure:
Bromobenzene (79 mg, 0.50 mmol) reacted with 4-methoxyphenylboronic acid (99 mg, 0.65 mmol) using 1 mol % of Pd(dba)2/Ph5FcP(t-Bu)2 and KF (87 mg, 1.50 mmol) in THF solvent at room temperature to give the title compound (87 mg, 95%) as a white solid. The reaction of 4-chloroanisole (71 mg, 0.50 mmol) with phenylboronic acid (92 mg, 0.75 mmol) gave the title compound (74 mg, 80%) using 1/2 mol % of Pd(dba)2/Ph5FcP(t-Bu)2 and KF in THF solvent at 40° C. 1H-NMR (400 MHz, CDCl3): δ 7.61 (m, 4H), 7.48 (t, 2H, J=7.6 Hz), 7.37 (app.t, 1H, J=7.2 Hz), 7.04 (d, 2H, J=8.8 Hz), 3.90 (s, 3H). 13C{1H}-NMR (100 MHz, CDCl3): δ 159.09, 140.76, 133.69, 128.66, 128.08, 126.67, 126.60, 114.14, 55.26. GC/MS(EI): m/z 184 (M+). Anal. Calcd for C13H12O: C, 84.75; H, 6.56. Found: C, 84.86; H, 6.76.