Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: O[C:2]1[C:11]2[C:6](=[N:7][CH:8]=[CH:9][CH:10]=2)[N:5]([C:12]2[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=2)[C:4](=[O:18])[C:3]=1[C:19](=O)[CH2:20][CH2:21][C:22]1[CH:27]=[CH:26][C:25]([N+:28]([O-:30])=[O:29])=[CH:24][CH:23]=1.O.[NH2:33][NH2:34]>CN(C=O)C>[N+:28]([C:25]1[CH:26]=[CH:27][C:22]([CH2:21][CH2:20][C:19]2[C:3]3[C:4](=[O:18])[N:5]([C:12]4[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=4)[C:6]4[N:7]=[CH:8][CH:9]=[CH:10][C:11]=4[C:2]=3[NH:34][N:33]=2)=[CH:23][CH:24]=1)([O-:30])=[O:29]
Reactant: NN
Reactant: O=C(CCc1ccc([N+](=O)[O-])cc1)c1c(O)c2cccnc2n(-c2ccccc2)c1=O
Solvent: O
Solvent: CN(C)C=O
Product: O=c1c2c(CCc3ccc([N+](=O)[O-])cc3)n[nH]c2c2cccnc2n1-c1ccccc1
Yield: 97.2 %

Procedure:
To a suspension of 4-hydroxy-3-[1-oxo-3-(4-nitrophenyl)propyl]-1-phenyl-1,8-naphthyridin-2 (1H)-one (104 mg, 0.25 mmol, prepared in Synthetic Example 7) in DMF (2 ml) was added hydrazine monohydrate (80%, 40 μl, 11.0 mmol, 4.0 eq.), and the mixture was treated in the same manner as in Example 9 to give 3-[2-(4-nitrophenyl)ethyl]-5-phenyl-1H-pyrazolo[4,3-c][1,8]naphthyridin-4 (5H)-one (100 mg, 97%).
Reaction SMILES: Br[C:2]1[S:3][C:4]([C:8]([O:10][CH2:11][CH3:12])=[O:9])=[C:5]([CH3:7])[N:6]=1.[Cl:13][C:14]1[CH:19]=[CH:18][C:17](B(O)O)=[CH:16][N:15]=1.C(=O)([O-])[O-].[K+].[K+]>C1(C)C=CC=CC=1.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>[Cl:13][C:14]1[N:15]=[CH:16][C:17]([C:2]2[S:3][C:4]([C:8]([O:10][CH2:11][CH3:12])=[O:9])=[C:5]([CH3:7])[N:6]=2)=[CH:18][CH:19]=1
Reactant: CCOC(=O)c1sc(Br)nc1C
Reactant: OB(O)c1ccc(Cl)nc1
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: Cc1ccccc1
Solvent: CCO
Product: CCOC(=O)c1sc(-c2ccc(Cl)nc2)nc1C
Yield: 69.1 %

Procedure:
Ethyl 2-bromo-4-methyl-1,3-thiazole-5-carboxylate (1 g, 1.3 eq, 4 mmol) is added to a mixture of 2-chloro-5-pyridine boronic acid (0.48 g, 1 eq, 3.07 mmol), tetrakis(triphenylphosphine)palladium (0.18 g, 0.05 eq, 0.15 mmol) and an aqueous solution of 2 M potassium carbonate (3 ml, 2 eq, 6.14 mmol) in toluene/ethanol (18 ml, 2:1 v/v). The mixture is refluxed overnight and the solvent is evaporated, then taken up in ethyl acetate, and washed two times with an aqueous solution of sodium hydrogenocarbonate. The organic layer is dried over magnesium sulfate, filtered and concentrated under vacuum. Purification by chromatography over silicagel (eluent: dichloromethane 100%) affords 0.6 g of ethyl 2-(6-chloropyridin-3-yl)-4-methyl-1,3-thiazole-5-carboxylate i97.
Reaction SMILES: [Br:1][CH:2]([CH3:6])[C:3](Br)=[O:4].[C:7]([O:12][CH2:13][CH2:14][OH:15])(=[O:11])[C:8]([CH3:10])=[CH2:9].C(N(CC)CC)C.COC1C=CC(O)=CC=1>C(OCC)(=O)C>[C:7]([O:12][CH2:13][CH2:14][O:15][C:3](=[O:4])[CH:2]([Br:1])[CH3:6])(=[O:11])[C:8]([CH3:10])=[CH2:9]
Reactant: CC(Br)C(=O)Br
Reactant: C=C(C)C(=O)OCCO
Agent: COc1ccc(O)cc1
Solvent: CCN(CC)CC
Solvent: CCOC(C)=O
Product: C=C(C)C(=O)OCCOC(=O)C(C)Br
Reaction time: 8 h
Yield: 63.9 %

Procedure:
2-Bromopropionyl bromide (18 g, 0.083 mol, 1 m.e) in ethyl acetate (30 mL) was added dropwise to a mixture of 2-hydroxyethyl methacrylate (HEMA) (16.26 g, 0.125 mol, 1.5 m.e) and triethylamine (9.26 g, 0.091 mol, 1.1 m.e) in ethyl acetate (80 mL) at 0° C. under a N2 environment. Hydroquinone monomethyl ether (MEHQ) was added as an inhibitor at this stage (−15 mg, 1.2×10−4 mol). The reaction mixture was stirred overnight, then filtered, further treated with more MEHQ (˜15 mg) and then evaporated to dryness to give a clear colourless oil (14 g, 0.053 mol, 63% yield). 1H NMR (200 MHz, CDCl3) δ 1.82 (d, J=8 Hz, 3H, CH3CH—), 1.95 (s, 3H, (CH3CCO—), 4.36-4.46 (m, 5H, 2× —CH2O— and —CHBr), 5.60 (br. s, 1H, vinyl), 6.13 (s, 1H, vinyl) ppm.
Reaction SMILES: [NH2:1][C:2]1[CH:3]=[CH:4][C:5]([N:8]2[CH2:13][CH2:12][C:11]([CH2:15][C:16]([O:18][CH3:19])=[O:17])([CH3:14])[CH2:10][CH2:9]2)=[N:6][CH:7]=1.C(N(CC)CC)C.Cl[C:28](=[O:33])[C:29]([O:31][CH3:32])=[O:30]>C(Cl)Cl>[CH3:19][O:18][C:16](=[O:17])[CH2:15][C:11]1([CH3:14])[CH2:12][CH2:13][N:8]([C:5]2[N:6]=[CH:7][C:2]([NH:1][C:28](=[O:33])[C:29]([O:31][CH3:32])=[O:30])=[CH:3][CH:4]=2)[CH2:9][CH2:10]1
Reactant: COC(=O)C(=O)Cl
Reactant: COC(=O)CC1(C)CCN(c2ccc(N)cn2)CC1
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: COC(=O)CC1(C)CCN(c2ccc(NC(=O)C(=O)OC)cn2)CC1
Temperature: 25 °C
Reaction time: 1.5 h
Yield: 100 %

Procedure:
To a solution of methyl [1-(5-aminopyridin-2-yl)-4-methylpiperidin-4-yl]acetate (3.29 g, 13.20 mmol) in DCM (100 mL) was added triethylamine (2.2 mL, 15.84 mmol) followed by methyl chlorooxoacetate (1.6 mL, 17.15 mmol) and the reaction mixture was allowed to stir at ambient temperature for 1.5 hrs. The reaction mixture was washed brine (2×100 mL), the aqueous layer was re extracted with DCM (50 mL) the organic washings were combined, dried and concentrated to leave the title compound as a brown gum (4.4 g, 13.2 mmol, 100%). 1H NMR δ 1.06 (s, 3H), 1.40-1.46 (m, 2H), 1.53-1.57 (m, 2H), 2.36 (s, 3H), 3.46-3.52 (m, 2H), 3.59 (s, 3H), 3.67-3.73 (m, 2H), 3.78 (s, 3H), 6.90 (d, 1H), 7.56 (d, 1H), 8.06 (s, 1H); MS m/e MH+ 350.
Reaction SMILES: C(N(CC)CC)C.[CH3:8][N:9]1[C:13]([C:14]([OH:16])=O)=[CH:12][N:11]=[CH:10]1.Cl.[CH3:18][NH:19][O:20][CH3:21].CCN=C=NCCCN(C)C>C(Cl)Cl>[CH3:21][O:20][N:19]([CH3:18])[C:14]([C:13]1[N:9]([CH3:8])[CH:10]=[N:11][CH:12]=1)=[O:16]
Reactant: CNOC
Reactant: Cn1cncc1C(=O)O
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: CON(C)C(=O)c1cncn1C
Temperature: 25 °C
Reaction time: 72 h

Procedure:
Triethylamine (5.51 mL, 39.646 mmol) was added slowly to a mixture of commercially available 1-methyl-1H-imidazole-5-carboxylic acid (2 g, 15.859 mmol), N,O-dimethylhydroxylamine hydrochloride (1.55 g, 15.859 mmol), and EDCI (3.65 g, 19.03 mmol) in CH2Cl2 (10 mL). The mixture was stirred at room temperature for 72 hours then quenched with saturated aqueous NaHCO3. Water (50 mL) was added followed by additional CH2Cl2. The mixture was stirred for 10 minutes and layers were separated. The CH2Cl2 layer was dried over Na2SO4, then filtered. The solvent was removed under reduced pressure and the residual oil chromatographed (CH2Cl2/EtOAc) to provide the product as a solid.
Reaction SMILES: Cl[C:2]1[CH:7]=[C:6]([N:8]([CH2:17][O:18][CH2:19][CH2:20][Si:21]([CH3:24])([CH3:23])[CH3:22])[CH2:9][O:10][CH2:11][CH2:12][Si:13]([CH3:16])([CH3:15])[CH3:14])[N:5]2[N:25]=[CH:26][CH:27]=[C:4]2[N:3]=1.CC1(C)C(C)(C)OB([C:36]2[CH2:41][CH2:40][N:39]([C:42]([O:44][C:45]([CH3:48])([CH3:47])[CH3:46])=[O:43])[CH2:38][CH:37]=2)O1.ClCCl.C([O-])([O-])=O.[Na+].[Na+]>COCCOC>[CH3:14][Si:13]([CH3:16])([CH3:15])[CH2:12][CH2:11][O:10][CH2:9][N:8]([CH2:17][O:18][CH2:19][CH2:20][Si:21]([CH3:24])([CH3:23])[CH3:22])[C:6]1[N:5]2[N:25]=[CH:26][CH:27]=[C:4]2[N:3]=[C:2]([C:36]2[CH2:41][CH2:40][N:39]([C:42]([O:44][C:45]([CH3:48])([CH3:47])[CH3:46])=[O:43])[CH2:38][CH:37]=2)[CH:7]=1
Reactant: C[Si](C)(C)CCOCN(COCC[Si](C)(C)C)c1cc(Cl)nc2ccnn12
Reactant: CC(C)(C)OC(=O)N1CC=C(B2OC(C)(C)C(C)(C)O2)CC1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: ClCCl
Solvent: COCCOC
Product: CC(C)(C)OC(=O)N1CC=C(c2cc(N(COCC[Si](C)(C)C)COCC[Si](C)(C)C)n3nccc3n2)CC1
Temperature: 100 °C
Reaction time: 8 h
Yield: 80 %

Procedure:
To a pressure tube was charged 5-chloro-N,N-bis((2-(trimethylsilyl)ethoxy)methyl)pyrazolo[1,5-a]pyrimidin-7-amine (Int-9d, 5.36 g, 12.5 mmol), tert-butyl 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-5,6-dihydropyridine-1(2H)-carboxylate (4.26 g, 13.8 mmol), [1,1′-bis(diphenylphosphino)ferrocene]dichloropalladium(II) complex with dichloromethane (1:1) (510 mg, 0.62 mmol), 2M Na2CO3 (30 ml) and DME (60 ml). The tube was degassed with Ar briefly, capped and heated at 100° C. with stirring overnight. After cooling, the reaction mixture was diluted with EtOAc and water, the organic layer was isolated, washed with brine and dried (MgSO4). After the solvent was removed under reduced pressure, the residue was purified on silica. Elution with EtOAc in hexanes (0-25%) gave tert-butyl 4-(7-(bis((2-(trimethylsilyl)ethoxy)methyl)amino)pyrazolo[1,5-a]pyrimidin-5-yl)-5,6-dihydropyridine-1(2H)-carboxylate (Int-9e) (5.76 g, 80%).
Reaction SMILES: [O:1]1[C:5]2[CH:6]=[CH:7][CH:8]=[CH:9][C:4]=2[N:3]=[C:2]1[C:10](OC)=[O:11].ClCC1C=CC=C(C)N=1>>[O:1]1[C:5]2[CH:6]=[CH:7][CH:8]=[CH:9][C:4]=2[N:3]=[C:2]1[CH:10]=[O:11]
Reactant: COC(=O)c1nc2ccccc2o1
Agent: Cc1cccc(CCl)n1
Product: O=Cc1nc2ccccc2o1
Yield: 35 %

Procedure:
The title compound was prepared from methyl benzoxazole-2-carboxylate by the method of part (ii), above, on a 0.041 molar scale; yield 35% as a yellow oil. 1H-NMR(CDCl3)ppm(delta): 7.3-8.1 (m, 4H), 10.0 (s, 1H).
Reaction SMILES: Br[C:2]1[CH:35]=[CH:34][C:5]([CH2:6][C:7]2[N:8]([C:20]3[CH:21]=[C:22]([N:26]4[S:30](=[O:32])(=[O:31])[NH:29][C:28](=[O:33])[CH2:27]4)[CH:23]=[CH:24][CH:25]=3)[CH:9]=[C:10]([C:12]3[CH:17]=[CH:16][C:15]([Cl:18])=[CH:14][C:13]=3[Cl:19])[N:11]=2)=[CH:4][CH:3]=1.[CH3:36][CH:37]([CH3:44])[CH2:38][CH:39]=[CH:40]B(O)O>>[Cl:19][C:13]1[CH:14]=[C:15]([Cl:18])[CH:16]=[CH:17][C:12]=1[C:10]1[N:11]=[C:7]([CH2:6][C:5]2[CH:4]=[CH:3][C:2]([CH:40]=[CH:39][CH2:38][CH:37]([CH3:44])[CH3:36])=[CH:35][CH:34]=2)[N:8]([C:20]2[CH:21]=[C:22]([N:26]3[S:30](=[O:32])(=[O:31])[NH:29][C:28](=[O:33])[CH2:27]3)[CH:23]=[CH:24][CH:25]=2)[CH:9]=1
Reactant: CC(C)CC=CB(O)O
Reactant: O=C1CN(c2cccc(-n3cc(-c4ccc(Cl)cc4Cl)nc3Cc3ccc(Br)cc3)c2)S(=O)(=O)N1
Product: CC(C)CC=Cc1ccc(Cc2nc(-c3ccc(Cl)cc3Cl)cn2-c2cccc(N3CC(=O)NS3(=O)=O)c2)cc1

Procedure:
5-{3-[2-(4-Bromo-benzyl)-4-(2,4-dichloro-phenyl)-imidazol-1-yl]-phenyl}-1,2,5-thiadiazolidine-3-one-1,1-dioxide (59 mg, 0.1 mmol) was treated as described in general procedure G using 4-methyl-1-pentenylboronic acid (39 mg, 0.3 mmol) to give 5-(3-{4-(2,4-dichloro-phenyl)-2-[4-(4-methyl-pent-1-enyl)-benzyl]-imidazol-1-yl}-phenyl)-1,2,5-thiadiazolidine-3-one-1,1-dioxide.
Reaction SMILES: [CH:1]([O:4][S:5]([C:8]1[C:17]([N:18]=[N:19][C:20]2[CH:25]=[CH:24][C:23]([O:26][CH3:27])=[CH:22][CH:21]=2)=[C:16]([OH:28])[C:15]2[C:10](=[CH:11][C:12]([NH2:29])=[CH:13][CH:14]=2)[CH:9]=1)(=[O:7])=[O:6])([CH3:3])[CH3:2].C(N(C(C)C)CC)(C)C.[CH3:39][O:40][C:41]1[CH:49]=[CH:48][CH:47]=[C:46]([O:50][CH3:51])[C:42]=1[C:43](Cl)=[O:44]>ClCCl>[CH:1]([O:4][S:5]([C:8]1[C:17]([N:18]=[N:19][C:20]2[CH:25]=[CH:24][C:23]([O:26][CH3:27])=[CH:22][CH:21]=2)=[C:16]([OH:28])[C:15]2[C:10](=[CH:11][C:12]([NH:29][C:43](=[O:44])[C:42]3[C:46]([O:50][CH3:51])=[CH:47][CH:48]=[CH:49][C:41]=3[O:40][CH3:39])=[CH:13][CH:14]=2)[CH:9]=1)(=[O:6])=[O:7])([CH3:3])[CH3:2]
Reactant: COc1cccc(OC)c1C(=O)Cl
Reactant: COc1ccc(N=Nc2c(S(=O)(=O)OC(C)C)cc3cc(N)ccc3c2O)cc1
Solvent: ClCCl
Solvent: CCN(C(C)C)C(C)C
Product: COc1ccc(N=Nc2c(S(=O)(=O)OC(C)C)cc3cc(NC(=O)c4c(OC)cccc4OC)ccc3c2O)cc1
Reaction time: 14 h

Procedure:
7-Amino-4-hydroxy-3-(4-methoxy-phenylazo)-napthalene-2-sulfonic acid isopropyl ester (Example 6, 200 mg, 0.48 mmol) was dissolved in dichloromethane (3 mL) and diisopropylethylamine (160 μL, 114 mg, 0.96 mmol) under nitrogen. 2,6-dimethoxybenzoyl chloride (120 mg, 0.60 mmol) was added and the solution was allowed to stir for 14 h. The resulting suspension was filtered to provide the title -compound (100 mg, 0.17 mmol, 36%) as a red solid: NMR (DMSO-d6): δ 16.30 (s, 1H), 10.81 (s, 1H), 8.35 (s, 1H), 8.21 (d, J=9 Hz, 1H), 7.92 (d, J=9 Hz, 1H), 7.82 (s, 1H), 7.73 (d, J=9 Hz, 2H), 7.21 (t, J=9 Hz, 1H), 7.07 (d, J=9 Hz, 2H), 6.67 (d, J=9 Hz, 2H), 4.72 (m, 1H), 3.87 (s, 3H), 3.82 (s, 6H), 1.32 (d, J=3 Hz, 6H); Analytical HPLC: 88% pure; MS (ES-NEG): [M−H] 578; Anal. Calc. for C29H29N3O8S: C, 60.09, H, 5.04, N, 7.25. Found: C, 57.26, H, 4.82, N, 7.09.
Reaction SMILES: N(C(OCC)=O)=NC(OCC)=O.[F:13][C:14]1[C:22]([O:23][C:24]2[C:33]3[C:28](=[CH:29][C:30]([OH:36])=[C:31]([O:34][CH3:35])[CH:32]=3)[N:27]=[N:26][CH:25]=2)=[CH:21][CH:20]=[C:19]2[C:15]=1[CH:16]=[C:17]([CH3:37])[NH:18]2.[C:38]([CH2:40][N:41]1[CH2:46][CH2:45][N:44]([CH2:47][CH2:48][CH2:49]O)[CH2:43][CH2:42]1)#[N:39].C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1>C(Cl)Cl>[C:38]([CH2:40][N:41]1[CH2:42][CH2:43][N:44]([CH2:47][CH2:48][CH2:49][O:36][C:30]2[CH:29]=[C:28]3[C:33]([C:24]([O:23][C:22]4[C:14]([F:13])=[C:15]5[C:19](=[CH:20][CH:21]=4)[NH:18][C:17]([CH3:37])=[CH:16]5)=[CH:25][N:26]=[N:27]3)=[CH:32][C:31]=2[O:34][CH3:35])[CH2:45][CH2:46]1)#[N:39]
Reactant: N#CCN1CCN(CCCO)CC1
Reactant: COc1cc2c(Oc3ccc4[nH]c(C)cc4c3F)cnnc2cc1O
Agent: CCOC(=O)N=NC(=O)OCC
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: ClCCl
Product: COc1cc2c(Oc3ccc4[nH]c(C)cc4c3F)cnnc2cc1OCCCN1CCN(CC#N)CC1
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 23.1 %

Procedure:
Diethyl azodicarboxylate (0.095 ml, 0.6 mmol) was added dropwise to a suspension of 4-(4-fluoro-2-methylindol-5-yloxy)-7-hydroxy-6-methoxycinnoline (0.1 g, 0.3 mmol), prepared as described in Example 4), 3-(4-cyanomethylpiperazin-1-yl)propan-1-ol (0.085 g, 0.45 mmol) and triphenylphosphine (0.155 g, 0.6 mmol) in methylene chloride (2.5 ml). The mixture was stirred for 30 minutes at ambient temperature. Further 3-(4-cyanomethylpiperazin-1-yl)propan-1-ol (0.085 g, 0.45 mmol), triphenylphosphine (0.155 g, 0.6 mmol) and diethyl azodicarboxylate (0.095 ml, 0.6 mmol) were added. The mixture was stirred for 30 minutes and the volatiles were removed under vacuum. The residue was purified by column chromatography eluting with ethylacetate/methylene chloride (1/1) followed by methanol/ethyl acetate/methylene chloride (5/45/50 followed by 10/40/50 and 10/0/90). The fractions containing the expected product were combined and evaporated to give 7-(3-(4-cyanomethylpiperazin-1-yl)propoxy)-4-(4-fluoro-2-methylindol-5-yloxy)-6-methoxycinnoline (0.035 g, 24%).
Reaction SMILES: [CH2:1]([O:8][C:9]([CH:11]([CH2:16][CH2:17][C:18]([O:20][CH2:21][C:22]1[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=1)=[O:19])[CH2:12][PH:13](=[O:15])[OH:14])=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[CH2:28](O)[C:29]1[CH:34]=[CH:33][CH:32]=[CH:31][CH:30]=1.CN(C1C=CC=CN=1)C.C1(N=C=NC2CCCCC2)CCCCC1>O1CCCC1>[CH2:1]([O:8][C:9]([CH:11]([CH2:16][CH2:17][C:18]([O:20][CH2:21][C:22]1[CH:23]=[CH:24][CH:25]=[CH:26][CH:27]=1)=[O:19])[CH2:12][P:13]([CH2:28][C:29]1[CH:34]=[CH:33][CH:32]=[CH:31][CH:30]=1)(=[O:14])[OH:15])=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: O=C(CCC(C[PH](=O)O)C(=O)OCc1ccccc1)OCc1ccccc1
Reactant: OCc1ccccc1
Agent: C(=NC1CCCCC1)=NC1CCCCC1
Agent: CN(C)c1ccccn1
Solvent: C1CCOC1
Product: O=C(CCC(CP(=O)(O)Cc1ccccc1)C(=O)OCc1ccccc1)OCc1ccccc1
Yield: 48.5 %

Procedure:
To a solution of 2,4-di-(benzyloxycarbonyl)butyl phosphinic acid (6) (19.3 g, 49.4 mmol) in tetrahydrofuran was added benzyl alcohol (5.3 g, 49.3 mmol) and dimethylamino in tetrahydrofuran was added benzyl alcohol (5.3 g, 49.3 mmol) and dimethylamino pyridine (0.5 g). Dicylcohexylcarbodiimide (DCC, 12 g, 58 mmol) was added and a white precipitate formed. After 30 minutes the white suspension was filtered and the filtrate evaporated under reduced pressure. The clear and colorless oil was purified by flash chromatography and eluted with 1:1 Hex./EtOAc to give 2,4-di(benzyloxycarbonyl)butylbenzylphosphinic acid (7) (11.5 g, 47%) as a clear and colorless oil. Rf. 0.16 (1:1 Hex./EtOAc);
Reaction SMILES: [B:1]([C:4]1[CH:5]=[C:6]([CH:10]=[CH:11][C:12]=1[O:13][CH3:14])[C:7](O)=[O:8])([OH:3])[OH:2].CN.[CH3:17][N:18](C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.CN1CCOCC1>CN(C=O)C>[CH3:14][O:13][C:12]1[CH:11]=[CH:10][C:6]([C:7](=[O:8])[NH:18][CH3:17])=[CH:5][C:4]=1[B:1]([OH:3])[OH:2]
Reactant: COc1ccc(C(=O)O)cc1B(O)O
Reactant: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: CN
Agent: F[P-](F)(F)(F)(F)F
Solvent: CN(C)C=O
Solvent: CN1CCOCC1
Product: CNC(=O)c1ccc(OC)c(B(O)O)c1
Temperature: 25 °C
Reaction time: 20 h
Yield: 56.9 %

Procedure:
3-Borono-4-methoxybenzoic acid (2.5 g, 12.50 mmol) was dissolved in DMF (6 ml) and 12.50 ml methylamine (2 M solution in THF, 25 mmol) was added followed by HATU (4.75 mg, 12.5 mmol) and NMM (1.375, 12.50 mmol). The reaction mixture was stirred at RT for 20 hours and concentrated. The crude material was added to 50 ml water and extracted 3 times with EtOAc. The combined organic phases were dried (Na2SO4), filtered and concentrated. The crude material was triturated in EtOAc and filtered. The residue was purified by chromatography (Silicagel, CH2Cl2/MeOH 95:5) to give 1.92 g (7.11 mmol, 56.9% yield) of the title compound as a colorless solid. LCMS: (M+H)=210; tR=0.50 min (LC-MS 1). TLC: Rf=0.27 (CH2Cl2/MeOH 95:5). HPLC: tR=3.76 min (HPLC 3). 1H-NMR (d6-DMSO, 600.13 MHz) δ ppm 8.29 (bs, 1H), 8.03 (s, 1H), 7.87 (d, 1H), 7.85 (s, 2H) 7.02 (d, 1H), 3.84 (s, 3H), 2.75 (d, 3H).
Reaction SMILES: Cl[C:2]1[N:7]=[CH:6][N:5]=[C:4]([NH:8][C:9]2[CH:10]=[C:11]([CH:16]=[CH:17][CH:18]=2)[C:12]([NH:14][CH3:15])=[O:13])[CH:3]=1.Cl.[F:20][C:21]1[CH:31]=[CH:30][C:24]([O:25][CH:26]2[CH2:29][NH:28][CH2:27]2)=[CH:23][CH:22]=1.C(N(CC)C(C)C)(C)C>CC(O)C>[F:20][C:21]1[CH:31]=[CH:30][C:24]([O:25][CH:26]2[CH2:27][N:28]([C:2]3[N:7]=[CH:6][N:5]=[C:4]([NH:8][C:9]4[CH:10]=[C:11]([CH:16]=[CH:17][CH:18]=4)[C:12]([NH:14][CH3:15])=[O:13])[CH:3]=3)[CH2:29]2)=[CH:23][CH:22]=1
Reactant: Fc1ccc(OC2CNC2)cc1
Reactant: CNC(=O)c1cccc(Nc2cc(Cl)ncn2)c1
Agent: Cl
Solvent: CCN(C(C)C)C(C)C
Solvent: CC(C)O
Product: CNC(=O)c1cccc(Nc2cc(N3CC(Oc4ccc(F)cc4)C3)ncn2)c1
Temperature: 84 °C
Yield: 100 %

Procedure:
To 3-(6-chloropyrimidin-4-ylamino)-N-methylbenzamide (90.0 mg, 0.343 mmol) and 3-(4-fluorophenoxy)azetidine hydrochloride (73.3 mg, 0.360 mmol) in a disposable sealed tube at RT was added 2-propanol (2 mL) followed by N,N-diisopropylethylamine (0.179 mL, 1.028 mmol). The resulting reaction mixture was heated to 84° C. for 51 h, cooled to RT, concentrated, purified using MPLC (5 g cartridge, 12 g column, 0 to 65% 90/10 CH2Cl2-MeOH in CH2Cl2) giving 3-(6-(3-(4-fluorophenoxy)azetidin-1-yl)pyrimidin-4-ylamino)-N-methylbenzamide (135.0 mg).
Reaction SMILES: CN1C=CN=C1.[CH:7]1([CH2:12][C@H:13]([CH2:34][N:35]([CH:44]=[O:45])[O:36][CH2:37][C:38]2[CH:43]=[CH:42][CH:41]=[CH:40][CH:39]=2)[C:14]([N:16]2[C@H:20]([C:21](O)=[O:22])[CH2:19][CH2:18][N:17]2[C:24]([O:26][CH2:27][C:28]2[CH:33]=[CH:32][CH:31]=[CH:30][CH:29]=2)=[O:25])=[O:15])[CH2:11][CH2:10][CH2:9][CH2:8]1.S(Cl)(C)(=O)=O.[CH3:51][C@H:52]1[CH2:57][N:56]([CH3:58])[CH2:55][CH2:54][N:53]1[C:59]1[N:64]=[C:63]([NH2:65])[CH:62]=[CH:61][N:60]=1>ClCCl>[CH:7]1([CH2:12][C@H:13]([CH2:34][N:35]([CH:44]=[O:45])[O:36][CH2:37][C:38]2[CH:43]=[CH:42][CH:41]=[CH:40][CH:39]=2)[C:14]([N:16]2[C@H:20]([C:21]([NH:65][C:63]3[CH:62]=[CH:61][N:60]=[C:59]([N:53]4[CH2:54][CH2:55][N:56]([CH3:58])[CH2:57][C@@H:52]4[CH3:51])[N:64]=3)=[O:22])[CH2:19][CH2:18][N:17]2[C:24]([O:26][CH2:27][C:28]2[CH:29]=[CH:30][CH:31]=[CH:32][CH:33]=2)=[O:25])=[O:15])[CH2:8][CH2:9][CH2:10][CH2:11]1
Reactant: C[C@H]1CN(C)CCN1c1nccc(N)n1
Reactant: O=CN(C[C@@H](CC1CCCC1)C(=O)N1[C@H](C(=O)O)CCN1C(=O)OCc1ccccc1)OCc1ccccc1
Agent: CS(=O)(=O)Cl
Agent: Cn1ccnc1
Solvent: ClCCl
Product: C[C@H]1CN(C)CCN1c1nccc(NC(=O)[C@@H]2CCN(C(=O)OCc3ccccc3)N2C(=O)[C@H](CC2CCCC2)CN(C=O)OCc2ccccc2)n1
Temperature: 0 °C
Reaction time: 0.67 h
Yield: 58.2 %

Procedure:
1-Methylimidazole (133 μl, 1.674 mmol) was added into the solution of (3S)-2-[(2R)-3-cyclopentyl-2-({formyl[(phenylmethyl)oxy]amino}methyl)propanoyl]-1-{[(phenylmethyl)oxy]carbonyl}-3-pyrazolidinecarboxylic acid (300 mg, 0.558 mmol) in dichloromethane (DCM) (4 ml). The resulting solution was cooled to 0° C., and then mesyl chloride (45.4 μl, 0.586 mmol) was added dropwise at 0° C. To the reaction mixture was added 2-[(25)-2,4-dimethyl-1-piperazinyl]-4-pyrimidinamine (127 mg, 0.614 mmol). After stirring for 1 h 40 min at ambient temperature, the reaction solution was purified by RP-HPLC to yield phenylmethyl (3S)-2-[(2R)-3-cyclopentyl-2-({formyl[(phenylmethyl)oxy]amino}methyl)propanoyl]-3-[({2-[(2S)-2,4-dimethyl-1-piperazinyl]-4-pyrimidinyl}amino)carbonyl]-1-pyrazolidinecarboxylate (236 mg, 0.325 mmol, 58% yield). MS (ES+) m/z 515.4 (MH+). MS (ES+) m/z 727.3 (MH+).
Reaction SMILES: C[Si]([N-][Si](C)(C)C)(C)C.[Na+].[C:11]([O:15][C:16]([N:18]1[CH2:24][CH2:23][C:22]2[C:25]([S:30][CH2:31][C:32]#[N:33])=[C:26]([Cl:29])[CH:27]=[CH:28][C:21]=2[CH2:20][CH2:19]1)=[O:17])([CH3:14])([CH3:13])[CH3:12].Br[CH2:35][CH2:36]Br.CN(C=O)C>C1(C)C=CC=CC=1>[C:11]([O:15][C:16]([N:18]1[CH2:24][CH2:23][C:22]2[C:25]([S:30][C:31]3([C:32]#[N:33])[CH2:36][CH2:35]3)=[C:26]([Cl:29])[CH:27]=[CH:28][C:21]=2[CH2:20][CH2:19]1)=[O:17])([CH3:14])([CH3:13])[CH3:12]
Reactant: BrCCBr
Reactant: CC(C)(C)OC(=O)N1CCc2ccc(Cl)c(SCC#N)c2CC1
Agent: C[Si](C)(C)[N-][Si](C)(C)C
Agent: [Na+]
Solvent: Cc1ccccc1
Solvent: CN(C)C=O
Product: CC(C)(C)OC(=O)N1CCc2ccc(Cl)c(SC3(C#N)CC3)c2CC1
Temperature: 38 °C
Reaction time: 0.17 h
Yield: 62.1 %

Procedure:
Add sodium bis(trimethylsilyl)amide (5.4 mL, 5.4 mmol, 1M solution in THF) at room temperature under nitrogen to a solution of 3-tert-butoxycarbonyl-7-chloro-6-(1-cyano-methylthio)-2,3,4,5-tetrahydro-1H-benzo[d]azepine (380 mg, 1.1 mmol) in anhydrous toluene (4 mL). Stir the solution for 10 min, then add quickly 1,2-dibromoethane (2.8 mL, 32.4 mmol) followed by anhydrous DMF (4 mL). An exothermic reaction was observed and the reaction temperature increased to 38° C. Stir the mixture for 15 min at ambient temperature, then quench with methanol (2 mL). Concentrate in vacuo and purify by chromatography on silica gel eluting with hexane/EtOAc (9:1) to obtain 3-tert-butoxycarbonyl-7-chloro-6-(1-cyano-cyclopropylthio)-2,3,4,5-tetrahydro-1H-benzo[d]azepine (259 mg).
Reaction SMILES: [NH:1]1[C:9]2[C:4](=[C:5]([C:10]3[N:11]=[C:12]([N:26]4[CH2:31][CH2:30][O:29][CH2:28][CH2:27]4)[C:13]4[S:18][C:17]([CH2:19][N:20]5[CH2:25][CH2:24][NH:23][CH2:22][CH2:21]5)=[CH:16][C:14]=4[N:15]=3)[CH:6]=[CH:7][CH:8]=2)[CH:3]=[CH:2]1.[CH2:32]([O:36][CH2:37][CH2:38][CH2:39][CH3:40])[CH:33]1[O:35][CH2:34]1>CN(C)C=O>[CH2:37]([O:36][CH2:32][CH:33]([OH:35])[CH2:34][N:23]1[CH2:22][CH2:21][N:20]([CH2:19][C:17]2[S:18][C:13]3[C:12]([N:26]4[CH2:27][CH2:28][O:29][CH2:30][CH2:31]4)=[N:11][C:10]([C:5]4[CH:6]=[CH:7][CH:8]=[C:9]5[C:4]=4[CH:3]=[CH:2][NH:1]5)=[N:15][C:14]=3[CH:16]=2)[CH2:25][CH2:24]1)[CH2:38][CH2:39][CH3:40]
Reactant: CCCCOCC1CO1
Reactant: c1cc(-c2nc(N3CCOCC3)c3sc(CN4CCNCC4)cc3n2)c2cc[nH]c2c1
Solvent: CN(C)C=O
Product: CCCCOCC(O)CN1CCN(Cc2cc3nc(-c4cccc5[nH]ccc45)nc(N4CCOCC4)c3s2)CC1

Procedure:
To a stirred solution of 2-(1H-indol-4-yl)-4-morpholin-4-yl-6-piperazin-1-ylmethyl-thieno[3,2-d]pyrimidine (50 mg) in N,N-dimethylformamide (3 mL) at r.t. was added 0.1 M Na2HPO4 pH 6.8 buffer (0.5 mL) and butyl glycidyl ether (18 μL) and the resulting cloudy mixture was heated at 55° C. for 3 days with 2 extra equivalents of butyl glycidyl ether (18 μL) added during this time. The reaction mixture was partitioned between EtOAc (15 mL) and brine (15 mL), the organic layer was dried (Na2SO4), concentrated and the residue purified by flash chromatography (silica; 96:4 EtOAc/MeOH as eluent) to give an off-white solid (38 mg).