Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [F:1][C:2]1[CH:7]=[CH:6][C:5]([N:8]2[CH2:13][CH2:12][N:11]([S:14]([C:17]3[S:21][C:20]([N:22]4[CH2:26][CH2:25][CH2:24][CH:23]4[C:27](O)=[O:28])=[CH:19][CH:18]=3)(=[O:16])=[O:15])[C@H:10]([CH3:30])[CH2:9]2)=[C:4]([C:31]([F:34])([F:33])[F:32])[CH:3]=1.C1N=C[N:37](C(N2C=NC=C2)=O)C=1.[NH4+].[OH-].Cl>C1COCC1.C(OCC)(=O)C>[F:1][C:2]1[CH:7]=[CH:6][C:5]([N:8]2[CH2:13][CH2:12][N:11]([S:14]([C:17]3[S:21][C:20]([N:22]4[CH2:26][CH2:25][CH2:24][CH:23]4[C:27]([NH2:37])=[O:28])=[CH:19][CH:18]=3)(=[O:16])=[O:15])[C@H:10]([CH3:30])[CH2:9]2)=[C:4]([C:31]([F:33])([F:32])[F:34])[CH:3]=1
Reactant: C[C@@H]1CN(c2ccc(F)cc2C(F)(F)F)CCN1S(=O)(=O)c1ccc(N2CCCC2C(=O)O)s1
Reactant: O=C(n1ccnc1)n1ccnc1
Agent: Cl
Agent: [NH4+]
Agent: [OH-]
Solvent: CCOC(C)=O
Solvent: C1CCOC1
Product: C[C@@H]1CN(c2ccc(F)cc2C(F)(F)F)CCN1S(=O)(=O)c1ccc(N2CCCC2C(N)=O)s1
Temperature: 25 °C
Reaction time: 0.17 h
Yield: 31.6 %

Procedure:
Crude 1-(5-((R)-4-(4-fluoro-2-(trifluoromethyl)phenyl)-2-methylpiperazin-1-ylsulfonyl)thiophen-2-yl)pyrrolidine-2-carboxylic acid (570 mg, 1.094 mmol) charged to a reaction flask was dissolved in THF (23 mL). To it was added CDI (649 mg, 4.38 mmol) and the reaction mixture was heated to reflux for 1 hour. After cooling down to room temperature excess NH4OH (28% NH3)(23 ml) was added dropwise via addition funnel. The reaction mixture was left to stir at room temperature for 10 minutes, then it was diluted with ethyl acetate, acidified (pH acidic) using 10% HCl (aqueous) and stirred for 5 minutes. The layers were separated, and the organic layer washed with saturated brine, dried over MgSO4, concentrated. Crude product containing a significant amount of starting acid by TLC was subjected to the same reaction and work up conditions. After reaction completation crude was purified via flash column chromatography to yield 1-(5-((R)-4-(4-fluoro-2-(trifluoromethyl)phenyl)-2-methylpiperazin-1-ylsulfonyl)thiophen-2-yl)pyrrolidine-2-carboxamide as white solid (180 mg, 31% yield). HRMS: calcd for C21H24F4N4O3S2+H+, 521.12987. found (ESI-FTMS, [M+H]1+), 521.13026.
Reaction SMILES: [CH3:1][C:2]1[CH:7]=[CH:6][C:5]([NH:8][C:9](=[O:20])[C:10]2[CH:15]=[CH:14][CH:13]=[C:12]([C:16]([F:19])([F:18])[F:17])[CH:11]=2)=[CH:4][C:3]=1[C:21]1[N:22]=[C:23]([N:28]2[CH2:33][CH2:32][O:31][CH2:30][CH2:29]2)[C:24](=[O:27])[NH:25][CH:26]=1.[F:34][CH:35]([F:38])[CH2:36]I.C(=O)([O-])[O-].[K+].[K+]>>[F:34][CH:35]([F:38])[CH2:36][N:25]1[C:24](=[O:27])[C:23]([N:28]2[CH2:33][CH2:32][O:31][CH2:30][CH2:29]2)=[N:22][C:21]([C:3]2[CH:4]=[C:5]([NH:8][C:9](=[O:20])[C:10]3[CH:15]=[CH:14][CH:13]=[C:12]([C:16]([F:17])([F:19])[F:18])[CH:11]=3)[CH:6]=[CH:7][C:2]=2[CH3:1])=[CH:26]1
Reactant: Cc1ccc(NC(=O)c2cccc(C(F)(F)F)c2)cc1-c1c[nH]c(=O)c(N2CCOCC2)n1
Reactant: FC(F)CI
Agent: O=C([O-])[O-]
Agent: [K+]
Product: Cc1ccc(NC(=O)c2cccc(C(F)(F)F)c2)cc1-c1cn(CC(F)F)c(=O)c(N2CCOCC2)n1

Procedure:
Method 1 was followed using N-(4-methyl-3-(6-morpholino-5-oxo-4,5-dihydropyrazin-2-yl)phenyl)-3-(trifluoromethyl)benzamide (1.0 equiv.), 1,1-difluoro-2-iodoethane (1.2 equiv.) and potassium carbonate (2.0 equiv.) at 60° C. 1H NMR (400 MHz, <cd3od>) δ ppm 2.39 (s, 3H) 3.81 (d, J=5.09 Hz, 8H) 4.38 (td, J=14.09, 3.91 Hz, 2H) 6.02-6.44 (m, 1H) 7.14 (s, 1H) 7.26 (d, J=8.22 Hz, 1H) 7.59 (dd, J=8.22, 1.96 Hz, 1H) 7.67-7.79 (m, 2H) 7.89 (d, J=7.83 Hz, 1H) 8.16-8.34 (m, 1H). LCMS (m/z) (M+H)=523.3, Rt=1.05 min.
Reaction SMILES: [CH2:1]([O:3][C:4]([N:6]1[C:15]2[C:10](=[CH:11][C:12]([CH3:17])=[N:13][C:14]=2[CH3:16])[C:9](=O)[CH2:8][CH:7]1[CH2:19][CH3:20])=[O:5])[CH3:2].[NH2:21][OH:22].Cl.N1C=CC=CC=1>>[CH2:1]([O:3][C:4]([N:6]1[C:15]2[C:10](=[CH:11][C:12]([CH3:17])=[N:13][C:14]=2[CH3:16])[C:9](=[N:21][OH:22])[CH2:8][CH:7]1[CH2:19][CH3:20])=[O:5])[CH3:2]
Reactant: CCOC(=O)N1c2c(cc(C)nc2C)C(=O)CC1CC
Reactant: NO
Agent: Cl
Solvent: c1ccncc1
Product: CCOC(=O)N1c2c(cc(C)nc2C)C(=NO)CC1CC

Procedure:
This compound can be prepared by reacting an ethanolic solution of 2-ethyl-6,8-dimethyl-4-oxo-3,4-dihydro-2H-[1,7]naphthyridine-1-carboxylic acid ethyl ester, with NH2OH.HCl (2-3 eqv) and pyridine (1-3 eqv), typically at reflux temperature for about 2 to about 6 h, followed by a typical workup procedure.
Reaction SMILES: ClCCl.[C:4]([OH:8])(=[O:7])[CH2:5]O.[Cl:9][C:10]1[CH:32]=[C:31]([C:33]([F:36])([F:35])[F:34])[CH:30]=[C:29]([F:37])[C:11]=1[O:12][C:13]1[CH:28]=[CH:27][C:16]2[N:17]([CH3:26])[C:18](=[O:25])[C:19]([CH3:24])([C:21]([OH:23])=[O:22])[O:20][C:15]=2[CH:14]=1>C(N(CC)CC)C>[Cl:9][C:10]1[CH:32]=[C:31]([C:33]([F:34])([F:35])[F:36])[CH:30]=[C:29]([F:37])[C:11]=1[O:12][C:13]1[CH:28]=[CH:27][C:16]2[N:17]([CH3:26])[C:18](=[O:25])[C:19]([CH3:24])([C:21]([O:23][CH2:5][C:4]([OH:8])=[O:7])=[O:22])[O:20][C:15]=2[CH:14]=1
Reactant: CN1C(=O)C(C)(C(=O)O)Oc2cc(Oc3c(F)cc(C(F)(F)F)cc3Cl)ccc21
Reactant: O=C(O)CO
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: CN1C(=O)C(C)(C(=O)OCC(=O)O)Oc2cc(Oc3c(F)cc(C(F)(F)F)cc3Cl)ccc21
Temperature: 25 °C
Reaction time: 1 h

Procedure:
To a dichloromethane solution (20 ml) of glycolic acid (0.3 g) and triethylamine (1.0 ml) was added an acid chloride (1.5 g) prepared as in Example 6 from 7-(2-chloro-6-fluoro-4-trifluoromethylphenoxy)-2,4-dimethyl-3,4-dihydro-3-oxo-2H-1,4-benzoxazine-2-carboxylic acid (Compound 25), and the mixture was stirred at room temperature for one hour. The reaction mixture was then concentrated under a reduced pressure, the residue was extracted twice with ethyl acetate (20 ml), and the extract was washed with water and then with saturated aqueous sodium chloride, and dried over magnesium sulfate, followed by evaporation of the solvent under a reduced pressure to obtain carboxymethyl 7-(2-chloro-6-fluoro-4-trifluoromethylphenoxy)-2,4-dimethyl-3,4-dihydro-3-oxo-2H-1,4-benzoxazine-2-carboxylate. The acid was dissolved in benzene (20 ml), thionyl chloride (0.9 g) was added thereto, and the mixture was heated under reflux for 3 hours. Then after an evaporation of the solvent under a reduced pressure, the residue was dissolved in dichloromethane (20 ml), ethylamine hydrochloride (0.6 g) and triethylamine (2 ml) were added thereto, and the mixture was stirred for one hour. The reaction mixture was then concentrated under a reduced pressure, and the residue was extracted twice with ethyl acetate (20 ml). The extract was washed with water and then with saturated aqueous sodium chloride, and dried over magnesium sulfate, followed by an evaporation of the solvent under a reduced pressure. The residue was purified by silica gel chromatography (eluant: n-hexane/ethyl acetate=3/1) to give 0.5 g of the title compound (colorless oil).
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[C:6]([F:8])[CH:5]=[CH:4][C:3]=1[S:9]([C@@H:12]1[CH2:16][C@@H:15]([C:17](O)=[O:18])[C@H:14]([C:20]([N:22]2[CH2:25][C:24]([F:27])([F:26])[CH2:23]2)=[O:21])[CH2:13]1)(=[O:11])=[O:10].[CH2:28]1[C:30]([NH2:33])([C:31]#[N:32])[CH2:29]1.Cl>>[C:31]([C:30]1([NH:33][C:17]([C@@H:15]2[CH2:16][C@@H:12]([S:9]([C:3]3[CH:4]=[CH:5][C:6]([F:8])=[CH:7][C:2]=3[Cl:1])(=[O:11])=[O:10])[CH2:13][C@H:14]2[C:20]([N:22]2[CH2:23][C:24]([F:27])([F:26])[CH2:25]2)=[O:21])=[O:18])[CH2:28][CH2:29]1)#[N:32]
Reactant: N#CC1(N)CC1
Reactant: O=C(O)[C@@H]1C[C@@H](S(=O)(=O)c2ccc(F)cc2Cl)C[C@H]1C(=O)N1CC(F)(F)C1
Agent: Cl
Product: N#CC1(NC(=O)[C@@H]2C[C@@H](S(=O)(=O)c3ccc(F)cc3Cl)C[C@H]2C(=O)N2CC(F)(F)C2)CC1

Procedure:
The title compound was prepared in analogy to Example 117, step 7, using (1R,2R,4S)-4-(2-Chloro-4-fluoro-benzenesulfonyl)-2-(3,3-difluoro-azetidine-1-carbonyl)-cyclopentanecarboxylic acid and 1-amino-cyclopropyl cyanic hydrochloride. Off-white solid. MS (EI): 490.1 (M+H)+.
Reaction SMILES: [CH:1]1([N:6]2[CH2:12][C:11]([F:14])([F:13])[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.F[P-](F)(F)(F)(F)F.CN(C(N(C)C)=[N+]1C2C(=NC=CC=2)[N+]([O-])=N1)C.C(N(C(C)C)C(C)C)C.[N:66]1([NH2:72])[CH2:71][CH2:70][CH2:69][CH2:68][CH2:67]1>O.C(=O)(O)[O-].[Na+].CN(C)C=O>[CH:1]1([N:6]2[CH2:12][C:11]([F:13])([F:14])[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:72][N:66]5[CH2:71][CH2:70][CH2:69][CH2:68][CH2:67]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)CC(F)(F)C(=O)N2C
Reactant: NN1CCCCC1
Agent: CN(C)C(N(C)C)=[N+]1N=[N+]([O-])c2ncccc21
Agent: F[P-](F)(F)(F)(F)F
Agent: O=C([O-])O
Solvent: O
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: COc1cc(C(=O)NN2CCCCC2)ccc1Nc1ncc2c(n1)N(C1CCCC1)CC(F)(F)C(=O)N2C
Reaction time: 0.08 h
Yield: 68 %

Procedure:
A mixture of 0.045 g (0.1 mmole) of 4-(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-ylamino)-3-methoxybenzoic acid (I-22), 0.042 g (0.110 mmole) of 1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium-3-oxide hexafluorophosphate, 0.052 ml (0.300 mmole) of ethyldiisopropyl amine and 1.0 mL of dimethylformamide was stirred for 5 minutes and then 0.012 g (0.12 mmole) piperidin-1-ylamine was added. The mixture was stirred for 3 hours, then diluted with 10 mL of water plus 2 mL of saturated aqueous sodium bicarbonate and then extracted 3 times with 10 mL of ethyl acetate. The combined extracts were washed with brine, dried over anhydrous magnesium sulfate, filtered and concentrated under reduced pressure. The residue was purified by reverse phase silica gel chromatography, eluting with water-acetonitrile (gradient, 0:100-80:20) to give 0.036 g of 4-(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-ylamino)-3-methoxy-N-piperidin-1-yl-benzamide (I-115) as a white solid.
Reaction SMILES: [C:1]([Br:5])(Br)(Br)Br.C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.[C:25]([O:29][C:30]([C@@:32]1([CH2:46][C:47](=C)[CH2:48]O)[CH2:36][C:35](=[O:37])[N:34]([C@@H:38]([C:40]2[CH:45]=[CH:44][CH:43]=[CH:42][CH:41]=2)[CH3:39])[CH2:33]1)=[O:31])([CH3:28])([CH3:27])[CH3:26]>ClCCl>[C:25]([O:29][C:30]([C@@:32]1([CH2:46][C:47](=[CH2:48])[CH2:1][Br:5])[CH2:36][C:35](=[O:37])[N:34]([C@@H:38]([C:40]2[CH:41]=[CH:42][CH:43]=[CH:44][CH:45]=2)[CH3:39])[CH2:33]1)=[O:31])([CH3:28])([CH3:27])[CH3:26]
Reactant: C=C(CO)C[C@]1(C(=O)OC(C)(C)C)CC(=O)N([C@H](C)c2ccccc2)C1
Reactant: BrC(Br)(Br)Br
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: ClCCl
Product: C=C(CBr)C[C@]1(C(=O)OC(C)(C)C)CC(=O)N([C@H](C)c2ccccc2)C1

Procedure:
Carbon tetrabromide (3.24 g, 9.77 mmol) and triphenylphosphine (2.57 g, 9.80 mmol) were added to a solution of (3S)-3-(3-hydroxy-2-methylene-1-propyl)-5-oxo-1-[(1R)-1-phenylethyl]pyrrolidine-3-carboxylic acid tert-butyl ester in dichloromethane (113 ml) under ice water-cooling in a nitrogen atmosphere. The mixture was stirred under ice water-cooling for 15 minutes and then concentrated under reduced pressure to remove the solvent. The resulting residue was purified by silica gel column chromatography (hexane:ethyl acetate=100:0→95:5→90:10→80:20→75:25→66:34) to give 3.22 g of the title compound as white crystals.
Reaction SMILES: [NH2:1][C:2]1[CH:7]=[C:6]([CH3:8])[CH:5]=[CH:4][C:3]=1[OH:9].[CH2:10]([O:12][C:13](OCC)([O:19]CC)[C:14](OCC)=O)[CH3:11]>>[CH2:10]([O:12][C:13]([C:14]1[O:9][C:3]2[CH:4]=[CH:5][C:6]([CH3:8])=[CH:7][C:2]=2[N:1]=1)=[O:19])[CH3:11]
Reactant: CCOC(=O)C(OCC)(OCC)OCC
Reactant: Cc1ccc(O)c(N)c1
Product: CCOC(=O)c1nc2cc(C)ccc2o1
Temperature: 110 °C
Reaction time: 8 h
Yield: 51.1 %

Procedure:
To 2-amino-4-methylphenol (1 g, 8.1 mmol) was added ethyl triethoxyacetate (5.4 g, 3 eq). The mixture was stirred at 110° C. overnight. The reaction mixture was cooled and triturated with hexane. Filtration gave 850 mg (91%) of 5-methyl-benzooxazole-2-carboxylic acid ethyl ester as a white solid.
Reaction SMILES: [C:1]([C:5]1[O:9][N:8]=[C:7]([NH:10][C:11]([NH:13][C:14]2[CH:19]=[CH:18][C:17]([C:20]3[N:21]=[C:22]4[N:26]([CH:27]=3)[C:25]3[CH:28]=[CH:29][C:30]([O:32][CH2:33][CH2:34]Cl)=[CH:31][C:24]=3[S:23]4)=[CH:16][CH:15]=2)=[O:12])[CH:6]=1)([CH3:4])([CH3:3])[CH3:2].[CH2:36]([CH2:38][NH2:39])[OH:37].C(=O)([O-])[O-].[K+].[K+].[I-].[Na+]>CN(C=O)C>[C:1]([C:5]1[O:9][N:8]=[C:7]([NH:10][C:11]([NH:13][C:14]2[CH:19]=[CH:18][C:17]([C:20]3[N:21]=[C:22]4[N:26]([CH:27]=3)[C:25]3[CH:28]=[CH:29][C:30]([O:32][CH2:33][CH2:34][NH:39][CH2:38][CH2:36][OH:37])=[CH:31][C:24]=3[S:23]4)=[CH:16][CH:15]=2)=[O:12])[CH:6]=1)([CH3:4])([CH3:3])[CH3:2]
Reactant: CC(C)(C)c1cc(NC(=O)Nc2ccc(-c3cn4c(n3)sc3cc(OCCCl)ccc34)cc2)no1
Reactant: NCCO
Agent: O=C([O-])[O-]
Agent: [I-]
Agent: [K+]
Solvent: CN(C)C=O
Product: CC(C)(C)c1cc(NC(=O)Nc2ccc(-c3cn4c(n3)sc3cc(OCCNCCO)ccc34)cc2)no1

Procedure:
A mixture of 1-(5-tert-butyl-isoxazol-3-yl)-3-{4-[7-(2-chloro-ethoxy)-benzo[d]imidazo[2,1-b]thiazol-2-yl]-phenyl}-urea (1 equivalent), ethanolamine (1-3 equivalents), potassium carbonate (2-5 equivalents) and sodium iodide (2-5 equivalents) in anhydrous DMF is stirred at temperatures between rt and 80° C. until the reaction is substantially complete as monitored by LCMS or TLC. The mixture is partitioned between water and either dichloromethane or a mixture of isopropanol and dichloromethane. The separated aqueous layer is further extracted with dichloromethane or a mixture of isopropanol and dichloromethane, and the combined organic layers are washed with water or brine, then dried over magnesium sulfate, filtered, and concentrated under reduced pressure. The residue is purified by preparative reverse-phase HPLC or silica gel flash chromatography to afford 1-(5-tert-butyl-isoxazol-3-yl)-3-(4-{7-[2-(2-hydroxy-ethylamino)-ethoxy]-benzo[d]imidazo[2,1-b]thiazol-2-yl}-phenyl)-urea (I-2).
Reaction SMILES: [NH2:1][C@H:2]([C:15]([N:17]1[CH2:63][CH2:62][CH2:61][C@H:18]1[C:19]([N:21]1[CH2:60][CH2:59][CH2:58][C@H:22]1[C:23]([NH:25][C@H:26]([C:52]([C:54]([CH3:57])([CH3:56])[CH3:55])=[O:53])[CH2:27][CH2:28][CH2:29][NH:30][C:31](=[NH:51])[NH:32][S:33]([C:36]1[C:49]([CH3:50])=[C:47]([CH3:48])[C:46]2[O:45][C:42]([CH3:44])([CH3:43])[CH2:41][CH2:40][C:39]=2[C:37]=1[CH3:38])(=[O:35])=[O:34])=[O:24])=[O:20])=[O:16])[CH2:3][CH2:4][CH2:5][CH2:6][NH:7][C:8]([O:10][C:11]([CH3:14])([CH3:13])[CH3:12])=[O:9].[NH:64]([C:76]([O:78][CH2:79][CH:80]1[C:92]2[C:87](=[CH:88][CH:89]=[CH:90][CH:91]=2)[C:86]2[C:81]1=[CH:82][CH:83]=[CH:84][CH:85]=2)=[O:77])[C@H:65]([C:73](O)=[O:74])[C@@H:66]([CH3:72])[O:67][C:68]([CH3:71])([CH3:70])[CH3:69].CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.CCN(C(C)C)C(C)C>C(Cl)Cl.C(OCC)(=O)C>[NH:64]([C:76]([O:78][CH2:79][CH:80]1[C:92]2[C:87](=[CH:88][CH:89]=[CH:90][CH:91]=2)[C:86]2[C:81]1=[CH:82][CH:83]=[CH:84][CH:85]=2)=[O:77])[C@H:65]([C:73]([NH:1][C@H:2]([C:15]([N:17]1[CH2:63][CH2:62][CH2:61][C@H:18]1[C:19]([N:21]1[CH2:60][CH2:59][CH2:58][C@H:22]1[C:23]([NH:25][C@H:26]([C:52]([C:54]([CH3:55])([CH3:57])[CH3:56])=[O:53])[CH2:27][CH2:28][CH2:29][NH:30][C:31](=[NH:51])[NH:32][S:33]([C:36]1[C:49]([CH3:50])=[C:47]([CH3:48])[C:46]2[O:45][C:42]([CH3:43])([CH3:44])[CH2:41][CH2:40][C:39]=2[C:37]=1[CH3:38])(=[O:35])=[O:34])=[O:24])=[O:20])=[O:16])[CH2:3][CH2:4][CH2:5][CH2:6][NH:7][C:8]([O:10][C:11]([CH3:13])([CH3:12])[CH3:14])=[O:9])=[O:74])[C@@H:66]([CH3:72])[O:67][C:68]([CH3:70])([CH3:71])[CH3:69]
Reactant: Cc1c(C)c(S(=O)(=O)NC(=N)NCCC[C@H](NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@@H](N)CCCCNC(=O)OC(C)(C)C)C(=O)C(C)(C)C)c(C)c2c1OC(C)(C)CC2
Reactant: C[C@@H](OC(C)(C)C)[C@H](NC(=O)OCC1c2ccccc2-c2ccccc21)C(=O)O
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CCN(C(C)C)C(C)C
Solvent: CCOC(C)=O
Solvent: ClCCl
Product: Cc1c(C)c(S(=O)(=O)NC(=N)NCCC[C@H](NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@@H](NC(=O)OCC2c3ccccc3-c3ccccc32)[C@@H](C)OC(C)(C)C)C(=O)C(C)(C)C)c(C)c2c1OC(C)(C)CC2
Temperature: 25 °C
Reaction time: 20 h

Procedure:
H-Lys(Boc)-Pro-Pro-Arg(Pmc)-t-Bu (3.55 g, 3.86m mmol) was added to a solution of the activated acid prepared from Fmoc-Thr(t-Bu)-OH (1.6 g, 4 mmol) and HATU (1.9 g, 5 mmol) and DIEA (1.29 g, 10 mmol) in dry CH2Cl2 (25 ml) and stirred for 20 h at RT. The reaction mixture was then diluted with ethyl acetate (200 ml) and washed with saturated sodium carbonate (2×200 ml), water (2×200 ml) and dried (sodium sulfate). The solution was filtered and the solvents were removed under reduced pressure to leave behind a paste. The paste was chromatographed over flash silica gel (400 g). Elution with 2% methanol in chloroform furnished the product as a colorless foam. Yield: 3.5 g (70%).
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C@@:8]2([OH:34])[CH2:13][CH2:12][N:11]([C:14](=[O:31])[CH2:15][C@H:16]([NH:18][C:19]([C:21]3[CH:22]=[C:23]([CH:28]=[CH:29][CH:30]=3)[C:24]([O:26]C)=[O:25])=[O:20])[CH3:17])[CH2:10][C:9]2([CH3:33])[CH3:32])=[CH:4][CH:3]=1.C(O)(C(F)(F)F)=O>O.CC#N>[Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C@@:8]2([OH:34])[CH2:13][CH2:12][N:11]([C:14](=[O:31])[CH2:15][C@H:16]([NH:18][C:19]([C:21]3[CH:22]=[C:23]([CH:28]=[CH:29][CH:30]=3)[C:24]([OH:26])=[O:25])=[O:20])[CH3:17])[CH2:10][C:9]2([CH3:33])[CH3:32])=[CH:4][CH:3]=1
Reactant: COC(=O)c1cccc(C(=O)N[C@H](C)CC(=O)N2CC[C@](O)(c3ccc(Cl)cc3)C(C)(C)C2)c1
Solvent: CC#N
Solvent: O=C(O)C(F)(F)F
Solvent: O
Product: C[C@H](CC(=O)N1CC[C@](O)(c2ccc(Cl)cc2)C(C)(C)C1)NC(=O)c1cccc(C(=O)O)c1

Procedure:
Example 8 was prepared from methyl 3-((R)-4-((S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl)-4-oxobutan-2-ylcarbamoyl)benzoate using the conditions described in Example 6. MS (ESI+)=473.2 (M+H)+. 1H NMR (CD3OD, 500 MHz) (NMR shows several rotamers) δ ppm 8.54 (t, J=1.6 Hz, 0.6 H), 8.46 (t, J=1.6 Hz, 0.4 H), 8.22 (d, J=7.7 Hz, 0.6 H), 8.17 (d, J=7.7 Hz, 0.4 H), 8.08 (d, J=8.2 Hz, 0.6 H), 8.02 (d, J=7.7 Hz, 0.4 H), 7.61 (t, J=7.7 Hz, 0.6 H), 7.57 (t, J=7.7 Hz, 0.4 H), 7.47 (d, J=8.8 Hz, 0.8 H), 7.32-7.25 (m, 2 H), 7.23 (d, J=8.3 Hz, 1.2 H), 4.64-4.46 (m, 1.4 H), 4.10 (dt, J=13.2, 2.5 Hz, 0.6 H), 4.04 (dd, J=12.6, 2.2 Hz, 0.6 H), 3.67-3.53 (m, 1.4 H), 3.17-3.03 (m, 1.6 H), 2.97 (dd, J=14.9, 6.1 Hz, 0.4 H), 2.67-2.46 (m, 2 H), 1.57-1.47 (m, 1 H), 1.40 (d, J=6.6 Hz, 1.8 H), 1.34 (d, J=6.6 Hz, 1.2 H), 0.83 (s, 1.2 H), 0.82 (s, 1.2 H), 0.76 (s, 1.8 H), 0.66 (s, 1.8 H); HPLC Method: Inj. Vol.=5 uL, Start % B=10, 12 Min. 100%, 15 Min. 100%, Flow Rate=1 ml/min, Wavelength 1=220, Wavelength 2=254, Solvent A=0.05% TFA in H2O:MeCN (95:5), Solvent B=0.05% TFA in H2O:MeCN (5:95), Col-1: Sunfire C18 3.5 um, 4.6×150 mm; Retention Time=10.92 min., Col-2: Xbridge Phenyl 3.5 um, 4.6×150 mm; Retention Time=10.45 min.
Reaction SMILES: [F:1][C:2]1[CH:30]=[C:29]([N+:31]([O-])=O)[CH:28]=[CH:27][C:3]=1[O:4][C:5]1[CH:10]=[CH:9][N:8]=[C:7]2[CH:11]=[C:12]([C:14]3[N:19]=[CH:18][C:17]([CH2:20][N:21]4[CH2:26][CH2:25][O:24][CH2:23][CH2:22]4)=[CH:16][CH:15]=3)[S:13][C:6]=12.[Cl-].[NH4+]>O.C(O)C.[Fe]>[F:1][C:2]1[CH:30]=[C:29]([CH:28]=[CH:27][C:3]=1[O:4][C:5]1[CH:10]=[CH:9][N:8]=[C:7]2[CH:11]=[C:12]([C:14]3[CH:15]=[CH:16][C:17]([CH2:20][N:21]4[CH2:22][CH2:23][O:24][CH2:25][CH2:26]4)=[CH:18][N:19]=3)[S:13][C:6]=12)[NH2:31]
Reactant: O=[N+]([O-])c1ccc(Oc2ccnc3cc(-c4ccc(CN5CCOCC5)cn4)sc23)c(F)c1
Agent: [Fe]
Agent: [Cl-]
Agent: [NH4+]
Solvent: O
Solvent: CCO
Product: Nc1ccc(Oc2ccnc3cc(-c4ccc(CN5CCOCC5)cn4)sc23)c(F)c1
Temperature: 80 °C
Yield: 33.7 %

Procedure:
A mixture of the nitro compound 358 (432 mg, 0.926 mmol), iron powder (440 mg, 7.87 mmol), and ammonium chloride (42.6 mg, 0.796 mmol) in a mixture of water (3.00 mL) and ethanol (6 mL) was heated to 80° C. for 30 min. The reaction mixture was then filtered while hot through a pad of Celite. The filtrate was concentrated and the residue was purified using Biotage (eluent 0-20% EtOAc/MeOH, 10 g SNAP column) to afford the amine 359 (136 mg, 0.312 mmol, 33.6% yield) as a white solid. MS: 437 (MH)+.
Reaction SMILES: Br[CH2:2][CH2:3][CH2:4][N:5]1[C:9]2[CH:10]=[CH:11][CH:12]=[CH:13][C:8]=2[N:7]([C:14]2[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=2)[S:6]1(=[O:21])=[O:20].[C:22]([N:29]1[CH2:34][CH2:33][NH:32][CH2:31][CH2:30]1)([O:24][C:25]([CH3:28])([CH3:27])[CH3:26])=[O:23].C(=O)([O-])[O-].[Na+].[Na+]>C(O)C>[O:20]=[S:6]1(=[O:21])[N:5]([CH2:4][CH2:3][CH2:2][N:32]2[CH2:31][CH2:30][N:29]([C:22]([O:24][C:25]([CH3:28])([CH3:27])[CH3:26])=[O:23])[CH2:34][CH2:33]2)[C:9]2[CH:10]=[CH:11][CH:12]=[CH:13][C:8]=2[N:7]1[C:14]1[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=1
Reactant: O=S1(=O)N(CCCBr)c2ccccc2N1c1ccccc1
Reactant: CC(C)(C)OC(=O)N1CCNCC1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: CCO
Product: CC(C)(C)OC(=O)N1CCN(CCCN2c3ccccc3N(c3ccccc3)S2(=O)=O)CC1
Temperature: 90 °C
Yield: 96 %

Procedure:
A mixture of 1-(3-bromopropyl)-3-phenyl-1,3-dihydro-2,1,3-benzothiadiazole 2,2-dioxide (prepared in an analogous manner as described in general procedure V), 1-Boc-piperazine (624 mg, 3.35 mmol, 6 equiv.), sodium carbonate (granular, 355 mg, 3.35 mmol, 6 equiv.), and ethanol (5 mL) in a sealed reaction vessel was heated at 90° C. for 8 h. After cooling, solid sodium carbonate was removed by decantation, and the supernatant was concentrated and re-dissolved in ethyl acetate (15 mL). The resulting solution was washed with water, dried (anhydrous sodium sulfate), and concentrated. The crude oil was pre-adsorbed onto Florisil and purified via Isco flash column chromatography (4-g redisep silica gel column, 5-60% ethyl acetate/hexane) to give 252 mg (96%) of tert-butyl 4-[3-(2,2-dioxido-3-phenyl-2,1,3-benzothiadiazol-1(3H)-yl)propyl]piperazine-1-carboxylate as a viscous, brown liquid. MS (ESI) m/z 473.1 ([M+H]+).
Reaction SMILES: CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.C(N(CC)CC)C.[CH2:32]([C:40]1[C:41]([C:53]([F:56])([F:55])[F:54])=[C:42]2[C:46]3=[C:47]([CH2:49][NH:50][CH2:51][CH2:52][N:45]3[CH:44]=[CH:43]2)[CH:48]=1)[CH2:33][C:34]1[CH:39]=[CH:38][CH:37]=[CH:36][CH:35]=1.Cl.[C:58]([NH:65][CH2:66][C:67](O)=[O:68])([O:60][C:61]([CH3:64])([CH3:63])[CH3:62])=[O:59]>C1COCC1>[O:68]=[C:67]([CH:51]1[NH:50][CH2:49][C:47]2=[C:46]3[C:42](=[C:41]([C:53]([F:56])([F:55])[F:54])[C:40]([CH2:32][CH2:33][C:34]4[CH:35]=[CH:36][CH:37]=[CH:38][CH:39]=4)=[CH:48]2)[CH:43]=[CH:44][N:45]3[CH2:52]1)[CH2:66][NH:65][C:58](=[O:59])[O:60][C:61]([CH3:63])([CH3:62])[CH3:64]
Reactant: FC(F)(F)c1c(CCc2ccccc2)cc2c3c1ccn3CCNC2
Reactant: CC(C)(C)OC(=O)NCC(=O)O
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: Cl
Agent: F[P-](F)(F)(F)(F)F
Solvent: C1CCOC1
Solvent: CCN(CC)CC
Product: CC(C)(C)OC(=O)NCC(=O)C1Cn2ccc3c(C(F)(F)F)c(CCc4ccccc4)cc(c32)CN1
Reaction time: 8 h

Procedure:
HATU (172 mg, 0.45 mmol) and triethylamine (1.97 mmol) was added to a mixture of 6-phenethyl-7-(trifluoromethyl)-1,2,3,4-tetrahydro-[1,4]diazepino[6,7,1-hi]indole (prepared as described in Example 2 above, 150 mg, 0.39 mmol) and N-Boc-glycine hydrochloride (72 mg, 0.41 mmol) in THF (7 mL). After stirring overnight, the resulting mixture was partitioned between ethyl acetate and water. The organic phase was washed sequentially with NaHCO3 (sat'd., aq) and brine, then dried and concentrated. The resulting residue was purified by reverse-phase chromatography to yield tert-butyl (2-oxo-2-(6-phenethyl-7-(trifluoromethyl)-3,4-dihydro-[1,4]diazepino[6,7,1-hi]indol-2(1H)-yl)ethyl)carbamate (200 mg, MS m/z 502 (MH+).