Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]2[C:12](=[C:13]([NH:15][C:16]([CH:18]3[CH2:23][O:22][C:21]([CH3:25])([CH3:24])[CH2:20][N:19]3[CH2:26][CH:27]([NH2:30])[CH2:28][CH3:29])=[O:17])[CH:14]=1)[NH:11][C:10]1[CH:9]=[N:8][CH:7]=[CH:6][C:5]2=1.[CH3:31][C:32]1[N:40]=[CH:39][CH:38]=[CH:37][C:33]=1[C:34](O)=[O:35].CCN=C=NCCCN(C)C>N1C=CC=CC=1.O>[Cl:1][C:2]1[CH:3]=[C:4]2[C:12](=[C:13]([NH:15][C:16]([CH:18]3[CH2:23][O:22][C:21]([CH3:24])([CH3:25])[CH2:20][N:19]3[CH2:26][CH:27]([NH:30][C:34]([C:33]3[C:32]([CH3:31])=[N:40][CH:39]=[CH:38][CH:37]=3)=[O:35])[CH2:28][CH3:29])=[O:17])[CH:14]=1)[NH:11][C:10]1[CH:9]=[N:8][CH:7]=[CH:6][C:5]2=1
Reactant: Cc1ncccc1C(=O)O
Reactant: CCC(N)CN1CC(C)(C)OCC1C(=O)Nc1cc(Cl)cc2c1[nH]c1cnccc12
Agent: CCN=C=NCCCN(C)C
Solvent: c1ccncc1
Solvent: O
Product: CCC(CN1CC(C)(C)OCC1C(=O)Nc1cc(Cl)cc2c1[nH]c1cnccc12)NC(=O)c1cccnc1C
Temperature: 25 °C
Reaction time: 8 h
Yield: 80.5 %

Procedure:
To a solution of 4-(2-amino-butyl)-6,6-dimethyl-morpholine-3-carboxylic acid (6-chloro-9H-β-carbolin-8-yl)-amide (100 mg, 0.233 mmol) in pyridine (4 mL) was added 2-methyl-nicotinic acid (38.4 mg, 0.280 mmol) and EDCI (71.5 mg, 0.373 mmol). The solution was stirred overnight at room temperature, then diluted with water (5 mL). The mixture was poured into a separatory funnel and diluted further with water (20 mL). The mixture was extracted with EtOAc (2×20 mL), then the combined organic layers were washed with brine. The organic layer was dried over magnesium sulfate, filtered, and concentrated to yield a yellow-brown oil which was purified via column chromatography. The resulting yellow solid was dissolved in methanol (2 mL) and HCl in Et2O (2M, 2 mL) was added. The mixture was stirred for 5 minutes, then concentrated to yield 103 mg of 6,6-dimethyl-4-{2-[(2-methyl-pyridine-3-carbonyl)-amino]-butyl}-morpholine-3-carboxylic acid (6-chloro-9H-β-carbolin-8-yl)-amide (71% yield). 1H-NMR (DMSO-d6, 300 MHz) δ 13.31 (br s, 1); 11.41 (br s, 1); 11.14 (br s, 1); 9.44 (s, 1); 8.85 (d, 1); 8.73-8.64 (m, 3); 8.52 (s, 1); 8.32 (s, 1); 7.72 (s, 1); 4.64-3.55 (m, 6); 3.24-3.06 (m, 1); 2.95-2.81 (m, 1); 2.71 (s, 3); 1.89-1.74 (m, 1); 1.55-1.41 (m, 1); 1.32 (s, 3); 1.23 (s, 3); 0.93 (t, 3). NH4OAc standard conditions. DAD Rf=1.66 min. M+H=549.
Reaction SMILES: CCN(C(C)C)C(C)C.[OH:10][C:11]1[CH:16]=[CH:15][C:14]([CH2:17][C:18]([OH:20])=O)=[CH:13][CH:12]=1.C1C=CC2N(O)N=NC=2C=1.CCN=C=NCCCN(C)C.Cl.Cl.[CH2:44]([O:46][C:47](=[O:50])[CH2:48][NH2:49])[CH3:45]>CN(C=O)C.O>[CH2:44]([O:46][C:47](=[O:50])[CH2:48][NH:49][C:18](=[O:20])[CH2:17][C:14]1[CH:13]=[CH:12][C:11]([OH:10])=[CH:16][CH:15]=1)[CH3:45]
Reactant: CCOC(=O)CN
Reactant: O=C(O)Cc1ccc(O)cc1
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: O
Solvent: CN(C)C=O
Solvent: CCN(C(C)C)C(C)C
Product: CCOC(=O)CNC(=O)Cc1ccc(O)cc1
Temperature: 25 °C
Reaction time: 24 h
Yield: 106.6 %

Procedure:
DIPEA (441 mg, 0.6 ml, 3.41 mmol) was added to a stirred solution of 4-hydroxyphenyl acetic acid (104 mg, 0.68 mmol) in DMF (4 mL). HOBT (101 mg, 0.748 mmol) and EDCI.HCl (245 mg, 1.28 mmol) were added at room temperature. After 2 minutes glycine ethyl ester hydrochloride (114.5 mg, 0.82 mmol) was added. The resulting mixture was stirred at room temperature for 24 hours. Water was then added, and the product was extracted with EtOAc. The organic layer was washed with brine, dried over Na2SO4 and concentrated under reduced pressure to afford 172 mg of [2-(4-hydroxy-phenyl)-acetyl amino]-acetic acid ethyl ester). LC-MS purity: 81.298%, HPLC purity 93.36%. 1H NMR (CDCl3): δ 7.1 (d, 2H), 6.8 (d, 2H), 6.0 (bs, 1H), 4.15 (q, 2H), 4.0 (d, 2H), 3.5 (s, 2H), 1.2 (t, 3H).
Reaction SMILES: Cl.Cl.[CH3:3][O:4][C:5](=[O:52])[C@@H:6]([NH:22][C:23]([C@@H:25]1[CH2:34][C:33]2[CH:32]=[C:31]3[O:35][CH2:36][C@H:37]([C:39]4[CH:44]=[CH:43][C:42]([C:45]5[CH:50]=[CH:49][CH:48]=[C:47]([Cl:51])[CH:46]=5)=[CH:41][CH:40]=4)[O:38][C:30]3=[CH:29][C:28]=2[CH2:27][NH:26]1)=[O:24])[CH2:7][C:8]1[CH:13]=[CH:12][C:11]([C:14]2[CH:19]=[CH:18][N:17]=[C:16]([CH3:20])[C:15]=2[CH3:21])=[CH:10][CH:9]=1.[CH3:53][C:54]1[O:55][C:56]([CH3:62])=[C:57]([C:59](O)=[O:60])[N:58]=1.CN(C(ON1N=NC2C=CC=CC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.CCN(C(C)C)C(C)C>C(Cl)Cl>[CH3:3][O:4][C:5](=[O:52])[C@@H:6]([NH:22][C:23]([C@@H:25]1[CH2:34][C:33]2[CH:32]=[C:31]3[O:35][CH2:36][C@H:37]([C:39]4[CH:40]=[CH:41][C:42]([C:45]5[CH:50]=[CH:49][CH:48]=[C:47]([Cl:51])[CH:46]=5)=[CH:43][CH:44]=4)[O:38][C:30]3=[CH:29][C:28]=2[CH2:27][N:26]1[C:59]([C:57]1[N:58]=[C:54]([CH3:53])[O:55][C:56]=1[CH3:62])=[O:60])=[O:24])[CH2:7][C:8]1[CH:13]=[CH:12][C:11]([C:14]2[CH:19]=[CH:18][N:17]=[C:16]([CH3:20])[C:15]=2[CH3:21])=[CH:10][CH:9]=1
Reactant: COC(=O)[C@H](Cc1ccc(-c2ccnc(C)c2C)cc1)NC(=O)[C@@H]1Cc2cc3c(cc2CN1)O[C@@H](c1ccc(-c2cccc(Cl)c2)cc1)CO3
Reactant: Cc1nc(C(=O)O)c(C)o1
Agent: CN(C)C(On1nnc2ccccc21)=[N+](C)C
Agent: Cl
Agent: F[P-](F)(F)(F)(F)F
Solvent: ClCCl
Solvent: CCN(C(C)C)C(C)C
Product: COC(=O)[C@H](Cc1ccc(-c2ccnc(C)c2C)cc1)NC(=O)[C@@H]1Cc2cc3c(cc2CN1C(=O)c1nc(C)oc1C)O[C@@H](c1ccc(-c2cccc(Cl)c2)cc1)CO3
Temperature: 25 °C
Reaction time: 2 h
Yield: 52.2 %

Procedure:
(S)-2-{[(3S,8S)-3-(3′-Chloro-biphenyl-4-yl)-2,3,6,7,8,9-hexahydro-[1,4]dioxino[2,3-g]isoquinoline-8-carbonyl]-amino}-3-[4-(2,3-dimethyl-pyridin-4-yl)-phenyl]-propionic acid methyl ester bis hydrochloride (0.025 g), 2,5-dimethyl-oxazole-4-carboxylic acid (0.010 g), HBTU (0.027 g) in DCM (3.0 mL), DIEA (0.019 g) was added. The reaction mixture was stirred at room temperature for 2.0 hours, poured onto a silica gel column and eluted with 1% MeOH, 1:1 hexanes-EtOAc to provide (S)-2-{[(3S,8S)-3-(3′-Chloro-biphenyl-4-yl)-7-(2,5-dimethyl-oxazole-4-carbonyl)-2,3,6,7,8,9-hexahydro-[1,4]dioxino[2,3-g]isoquinoline-8-carbonyl]-amino}-3-[4-(2,3-dimethyl-pyridin-4-yl)-phenyl]-propionic acid methyl ester (0.0139 g).
Reaction SMILES: [Br:1][C:2]1[CH:3]=[C:4]2[C:8](=[CH:9][CH:10]=1)[N:7]([S:11]([C:14]1[CH:15]=[C:16]3[C:20](=[CH:21][CH:22]=1)[NH:19][C:18](=[O:23])[CH2:17]3)(=[O:13])=[O:12])[CH2:6][CH2:5]2.[N:24]1([CH2:29][CH2:30][O:31][C:32]2[CH:33]=[C:34]3[C:38](=[CH:39][CH:40]=2)[NH:37][C:36]([CH:41]=O)=[CH:35]3)[CH2:28][CH2:27][CH2:26][CH2:25]1>>[Br:1][C:2]1[CH:3]=[C:4]2[C:8](=[CH:9][CH:10]=1)[N:7]([S:11]([C:14]1[CH:15]=[C:16]3[C:20](=[CH:21][CH:22]=1)[NH:19][C:18](=[O:23])[C:17]3=[CH:41][C:36]1[NH:37][C:38]3[C:34]([CH:35]=1)=[CH:33][C:32]([O:31][CH2:30][CH2:29][N:24]1[CH2:28][CH2:27][CH2:26][CH2:25]1)=[CH:40][CH:39]=3)(=[O:12])=[O:13])[CH2:6][CH2:5]2
Reactant: O=C1Cc2cc(S(=O)(=O)N3CCc4cc(Br)ccc43)ccc2N1
Reactant: O=Cc1cc2cc(OCCN3CCCC3)ccc2[nH]1
Product: O=C1Nc2ccc(S(=O)(=O)N3CCc4cc(Br)ccc43)cc2C1=Cc1cc2cc(OCCN3CCCC3)ccc2[nH]1

Procedure:
5-(5-Bromo-2,3-dihydro-indole-1-sulfonyl)-1,3-dihydro-indol-2-one was condensed with 5-(2-pyrrolidin-1-yl-ethoxy)-1H-indole-2-carbaldehyde to give the title compound.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([C:9]2([C:25]([F:28])([F:27])[F:26])[O:13][N:12]=[C:11]([C:14]3[CH:19]=[CH:18][C:17]([C:20]4([F:24])[CH2:23][NH:22][CH2:21]4)=[CH:16][CH:15]=3)[CH2:10]2)[CH:5]=[C:6]([Cl:8])[CH:7]=1.C(N(CC)CC)C.[C:36](OC(=O)C)(=[O:38])[CH3:37]>ClCCl.O>[Cl:1][C:2]1[CH:3]=[C:4]([C:9]2([C:25]([F:27])([F:26])[F:28])[O:13][N:12]=[C:11]([C:14]3[CH:19]=[CH:18][C:17]([C:20]4([F:24])[CH2:23][N:22]([C:36](=[O:38])[CH3:37])[CH2:21]4)=[CH:16][CH:15]=3)[CH2:10]2)[CH:5]=[C:6]([Cl:8])[CH:7]=1
Reactant: CC(=O)OC(C)=O
Reactant: FC1(c2ccc(C3=NOC(c4cc(Cl)cc(Cl)c4)(C(F)(F)F)C3)cc2)CNC1
Solvent: CCN(CC)CC
Solvent: O
Solvent: ClCCl
Product: CC(=O)N1CC(F)(c2ccc(C3=NOC(c4cc(Cl)cc(Cl)c4)(C(F)(F)F)C3)cc2)C1
Temperature: 25 °C
Reaction time: 8 h
Yield: 91 %

Procedure:
To a solution of 5-(3,5-dichlorophenyl)-3-(4-(3-fluoroazetidin-3-yl)phenyl)-5-(trifluoromethyl)-4,5-dihydroisoxazole (Preparation 15, 200 mg, 0.462 mMol) in dichloromethane (3 mL) was added triethylamine (0.192 mL) followed by acetic anhydride (50.2 μL). The reaction was allowed to stir at room temperature overnight. The solution was diluted with water and allowed to stir for 10 minutes. The mixture was passed through an ISCO Phase Separator. A stream of nitrogen was blown onto the organics then placed under high vacuum to form a white foam 200 mg (91% yield) 1H NMR (400 MHz, CDCl3-d) δ ppm 2.01 (s, 3H) 3.73 (d, 1H) 3.92 (qd, 1H) 4.12 (d, 1H) 4.32-4.56 (m, 3H) 4.59-4.70 (m, 1H) 7.46 (t, 1H) 7.52-7.59 (m, 4H) 7.76 (d, 2H), LC/MS retention time=3.510 min; MS calculated for (C21H16Cl2F4N2O2), 474.052; found 475.0 M+H.
Reaction SMILES: [CH:1]1([C@@:6]([OH:16])([C:10]2[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=2)[C:7]([OH:9])=O)[CH2:5][CH2:4][CH2:3][CH2:2]1.C(OC([N:24]1[CH2:29][CH2:28][CH:27]([NH2:30])[CH2:26][CH2:25]1)=O)(C)(C)C.CCN(C(C)C)C(C)C.C1C=CC2N(O)N=NC=2C=1.CCN=C=NCCCN(C)C>C(Cl)Cl>[NH2:30][CH:27]1[CH2:28][CH2:29][N:24]([C:7](=[O:9])[C@:6]([CH:1]2[CH2:2][CH2:3][CH2:4][CH2:5]2)([OH:16])[C:10]2[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=2)[CH2:25][CH2:26]1
Reactant: O=C(O)[C@](O)(c1ccccc1)C1CCCC1
Reactant: CC(C)(C)OC(=O)N1CCC(N)CC1
Agent: CCN=C=NCCCN(C)C
Agent: On1nnc2ccccc21
Solvent: CCN(C(C)C)C(C)C
Solvent: ClCCl
Product: NC1CCN(C(=O)[C@](O)(c2ccccc2)C2CCCC2)CC1
Temperature: 25 °C
Reaction time: 12 h
Yield: 66.7 %

Procedure:
To a stirred solution of (R)-cyclopentylhydroxyphenyl acetic acid (1.0 g, 4.54 mmol) in DCM (50 mL) was added t-butoxycarbonyl-4-aminopiperidine (0.9 g, 4.5 mmol). DIPEA (2.4 mL, 1.4 mmol) and HOBt (1.0 g, 6.8 mmol) were added to the mixture, followed by EDCI (1.0 g, 5.5 mmol). The mixture was stirred at room temperature for 12 hours. The mixture was then washed with 1N NaOH (50 mL), 1N HCl (50 mL), and then saturated aqueous NaCl (50 mL). The organic layer was dried over MgSO4 and filtered. The solvent was removed by rotary evaporation. To the crude material was added a solution of 20% TFA/DCM and the reaction was stirred for 2 hours at room temperature. The solvent was removed by rotary evaporation. DCM (50 mL) was added and the mixture was then washed with saturated sodium bicarbonate (50 mL). The organic layer was removed, dried over MgSO4 and filtered. The crude material was purified by silica gel chromatography (10% MeOH/DCM with 1% NH3 (aq)) to afford the title compound as a white powder (920 mg, 3.0 mmol).
Reaction SMILES: C(NC(C)C)(C)C.C([Li])CCC.[S:13]1[CH:17]=[CH:16][CH:15]=[C:14]1[C:18]#[N:19].CN(C)[CH:22]=[O:23].C(O)(=O)CC(CC(O)=O)(C(O)=O)O>O1CCCC1.O>[C:18]([C:14]1[S:13][C:17]([CH:22]=[O:23])=[CH:16][CH:15]=1)#[N:19]
Reactant: N#Cc1cccs1
Reactant: CN(C)C=O
Agent: O=C(O)CC(O)(CC(=O)O)C(=O)O
Agent: [Li]CCCC
Solvent: CC(C)NC(C)C
Solvent: O
Solvent: C1CCOC1
Product: N#Cc1ccc(C=O)s1
Reaction time: 0.08 h
Yield: 50.3 %

Procedure:
A solution of diisopropylamine (35.3 ml, 0.251 moles) in tetrahydrofuran (500 ml) was cooled to −78° C. under a nitrogen blanket. To this was added 1.6M n-butyllithium in hexanes (157 ml, 0.251 moles) and allowed to stir for 5 min. Then slowly added thiopene-2-carbonitrile (21.33 ml, 0.229 moles) in tetrahydrofuran (115 ml) and allowed to stir. After 45 min. was added N,N-dimethylformamide (88.66 ml, 1.145 moles) at −78° C. Citric acid (40 g) was added after 2 h. followed by water (240 ml) and stirred for 18 h. The reaction was concentrated in vacuo, transferred to a separatory funnel, diluted with brine, and extracted twice with ether. The combined ether layers were washed with brine, dried over magnesium sulfate, filtered, and the solvent removed in vacuo. Chromatography yielded 15.8 g (50%) of 2-cyano-5-formylthiophene (EX-55A) as a brown solid: 1H NMR (300 MHZ, CDCl3) d 10.02 (s, 1H), 7.79 (m, 1H), 7.30 (m, 1H).
Reaction SMILES: [CH3:1][C:2]([C:4]1[CH:5]=[CH:6][CH:7]=[C:8]([OH:10])[CH:9]=1)=[O:3].C(=O)([O-])[O-].[K+].[K+].[CH2:17](Br)[C:18]1[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=1>CC(C)=O>[CH2:17]([O:10][C:8]1[CH:9]=[C:4]([C:2](=[O:3])[CH3:1])[CH:5]=[CH:6][CH:7]=1)[C:18]1[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=1
Reactant: CC(=O)c1cccc(O)c1
Reactant: BrCc1ccccc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC(C)=O
Product: CC(=O)c1cccc(OCc2ccccc2)c1
Reaction time: 24 h
Yield: 98 %

Procedure:
3-Hydroxyacetophenone (136.15 g, 1 mol), potassium carbonate (414.63 g, 2 mol), KI (33.2 g, 0.2 mol), and benzyl bromide (171.04 g, 1 mol) were dissolved in acetone and the reaction mixture was refluxed while stirring for 24 hours, followed by washing with brine. The reaction mixture was extracted with ethyl acetate, the extract was dried over anhydrous magnesium sulfate, concentrated, and the resulting residue was purified by column chromatography (ethyl acetate:hexane=1:3) to obtain 1-(3-benzyloxyphenyl)ethanone (221.8 g, yield 98%) in an oil state.
Reaction SMILES: [F:1][C:2]1[CH:3]=[C:4]([OH:9])[CH:5]=[CH:6][C:7]=1[F:8].BrC1C=C(O)C=CC=1.[C:18]1([CH:24]([C:36]2[CH:41]=[CH:40][CH:39]=[CH:38][CH:37]=2)[N:25]2[C:33]3[C:28](=[CH:29][CH:30]=[CH:31][CH:32]=3)[C:27](=[O:34])[C:26]2=[O:35])[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=1.FC(F)(F)C1OC(CN2C3C(=CC=CC=3)C(=O)C2=O)=CC=1>>[F:1][C:2]1[C:7]([F:8])=[CH:6][C:5]([C:27]2([OH:34])[C:28]3[C:33](=[CH:32][CH:31]=[CH:30][CH:29]=3)[N:25]([CH:24]([C:18]3[CH:19]=[CH:20][CH:21]=[CH:22][CH:23]=3)[C:36]3[CH:41]=[CH:40][CH:39]=[CH:38][CH:37]=3)[C:26]2=[O:35])=[C:4]([OH:9])[CH:3]=1
Reactant: Oc1ccc(F)c(F)c1
Reactant: O=C1C(=O)N(C(c2ccccc2)c2ccccc2)c2ccccc21
Agent: O=C1C(=O)N(Cc2ccc(C(F)(F)F)o2)c2ccccc21
Agent: Oc1cccc(Br)c1
Product: O=C1N(C(c2ccccc2)c2ccccc2)c2ccccc2C1(O)c1cc(F)c(F)cc1O

Procedure:
Following the procedure as described in PREPARATION 2A and making non-critical variations using 3,4-difluorophenol to replace 3-bromophenol, and 1-(diphenylmethyl)-1H-indole-2,3-dione to replace 1-((5-(trifluoromethyl)furan-2-yl)methylindoline-2,3-dione, 3-(4,5-difluoro-2-hydroxyphenyl)-1-(diphenylmethyl)-3-hydroxy-1,3-dihydro-2H-indol-2-one was obtained (61%) as a colorless solid: 1H NMR (300 MHz, CDCl3) δ9.23 (br s, 1H), 7.47-7.44 (m, 1H), 7.35-7.21 (m, 9H), 7.18-7.11 (m, 2H), 6.90 (s, 1H), 6.83 (dd, J=11.2, 6.9 Hz, 1H), 6.67 (dd, J=11.2, 8.7 Hz, 1H), 6.56-6.51 (m, 1H), 4.13 (br s, 1H); MS (ES+) m/z 426.2 (M−17).
Reaction SMILES: [CH3:1][C:2]1[CH:3]=[CH:4][C:5]2[C:9]3([CH2:13][CH2:12][CH2:11][CH2:10]3)[O:8][B:7]([OH:14])[C:6]=2[CH:15]=1.C1C(=O)N([Br:23])C(=O)C1>C(Cl)(Cl)(Cl)Cl>[Br:23][CH2:1][C:2]1[CH:3]=[CH:4][C:5]2[C:9]3([CH2:13][CH2:12][CH2:11][CH2:10]3)[O:8][B:7]([OH:14])[C:6]=2[CH:15]=1
Reactant: O=C1CCC(=O)N1Br
Reactant: Cc1ccc2c(c1)B(O)OC21CCCC1
Solvent: ClC(Cl)(Cl)Cl
Product: OB1OC2(CCCC2)c2ccc(CBr)cc21
Temperature: 25 °C
Yield: 71.2 %

Procedure:
To a solution of 6-methyl-1H-spiro[benzo[c][1,2]oxaborole-3,1′-cyclopentan]-1-ol (1.2 g, 6.0 mmol) in CCl4 (10 mL) under nitrogen was added NBS (1.07 g, 6.0 mmol) and BPO (145 mg, 0.6 mmol). The mixture was heated at reflux for 2 h under the light from a Sun lamp, and then it was cooled to rt, washed with aqueous NaHCO3 and brine, dried over Na2SO4 and concentrated under vacuum. The residue was purified on column chromatography to provide the product (1.2 g, yield 71.7%).
Reaction SMILES: [Cl:1][CH2:2][C:3](=[O:8])[CH2:4][C:5](Cl)=[O:6].O>ClCCl.FC(F)(F)S([O-])(=O)=O.[Sc+3].FC(F)(F)S([O-])(=O)=O.FC(F)(F)S([O-])(=O)=O>[Cl:1][CH2:2][C:3]1[O:8][C:3]([CH2:2][Cl:1])=[CH:4][C:5](=[O:6])[CH:4]=1
Reactant: O=C(Cl)CC(=O)CCl
Agent: O=S(=O)([O-])C(F)(F)F
Agent: [Sc+3]
Solvent: ClCCl
Solvent: O
Product: O=c1cc(CCl)oc(CCl)c1
Yield: 0.1 %

Procedure:
4-Chloroacetoacetyl chloride (14.8 g, 33.4 mol) in dichloromethane (35% strength solution) and scandium trifluoromethanesulphonate (1.45 g, 2.5 mol) were stirred at 25° C. for 6.5 days under a nitrogen atmosphere. Water (10 g, 0.55 mol) was then added and the organic phase was concentrated. 4.2 g of product were obtained (according to GC 68% crude product). After chromatography on a silica gel column, 0.7 g of pure product corresponding to a yield of 10.8% were obtained.
Reaction SMILES: [I-:1].[CH3:2][NH+:3]1[CH:7]=[CH:6][N:5]([CH3:8])[CH:4]1[CH3:9].[N:10]1[CH:15]=[CH:14][CH:13]=[CH:12][C:11]=1[CH:16]=O>[OH-].[K+].C(O)C>[I-:1].[CH3:2][NH+:3]1[CH:7]=[CH:6][N:5]([CH3:8])[CH:4]1[CH:9]=[CH:16][C:11]1[CH:12]=[CH:13][CH:14]=[CH:15][N:10]=1
Reactant: O=Cc1ccccn1
Reactant: CC1N(C)C=C[NH+]1C
Agent: [I-]
Agent: [K+]
Agent: [OH-]
Solvent: CCO
Product: CN1C=C[NH+](C)C1C=Cc1ccccn1

Procedure:
A mixture of 12.0 g of 1,2,3-trimethyl-1H-imidazolium iodide and 12 ml of 2-pyridinecarboxaldehyde in 40 ml of 10% potassium hydroxide in absolute ethanol is refluxed for 15 minutes. The resulting solid is filtered off and crystallized from absolute ethanol to yield 3.5 g of the title compound, melting point 306° C.
Reaction SMILES: C([Li])CCC.C(OO)(C)(C)C.[C:12]1([CH:18]([C:79]2[CH:84]=[CH:83][CH:82]=[CH:81][CH:80]=2)[C@H:19]([NH:60][C:61](=[O:78])[C@H:62]([CH2:74][CH:75]([CH3:77])[CH3:76])[NH:63][C:64]([O:66][CH2:67][C:68]2[CH:73]=[CH:72][CH:71]=[CH:70][CH:69]=2)=[O:65])[CH:20]=[CH:21][S:22]([CH:25]=[CH:26][C@@H:27]([NH:41][C:42](=[O:59])[C@H:43]([CH2:55][CH:56]([CH3:58])[CH3:57])[NH:44][C:45]([O:47][CH2:48][C:49]2[CH:54]=[CH:53][CH:52]=[CH:51][CH:50]=2)=[O:46])[CH:28]([C:35]2[CH:40]=[CH:39][CH:38]=[CH:37][CH:36]=2)[C:29]2[CH:34]=[CH:33][CH:32]=[CH:31][CH:30]=2)(=[O:24])=[O:23])[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1.CCOC(C)=O>C1COCC1>[C:29]1([CH:28]([C:35]2[CH:36]=[CH:37][CH:38]=[CH:39][CH:40]=2)[C:27]([NH:41][C:42](=[O:59])[C@H:43]([CH2:55][CH:56]([CH3:57])[CH3:58])[NH:44][C:45]([O:47][CH2:48][C:49]2[CH:54]=[CH:53][CH:52]=[CH:51][CH:50]=2)=[O:46])=[CH:26][CH2:25][S:22]([CH2:21][CH:20]=[C:19]([NH:60][C:61](=[O:78])[C@H:62]([CH2:74][CH:75]([CH3:77])[CH3:76])[NH:63][C:64]([O:66][CH2:67][C:68]2[CH:69]=[CH:70][CH:71]=[CH:72][CH:73]=2)=[O:65])[CH:18]([C:12]2[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=2)[C:79]2[CH:80]=[CH:81][CH:82]=[CH:83][CH:84]=2)(=[O:23])=[O:24])[CH:34]=[CH:33][CH:32]=[CH:31][CH:30]=1
Reactant: CC(C)C[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@H](C=CS(=O)(=O)C=C[C@@H](NC(=O)[C@H](CC(C)C)NC(=O)OCc1ccccc1)C(c1ccccc1)c1ccccc1)C(c1ccccc1)c1ccccc1
Agent: CC(C)(C)OO
Agent: [Li]CCCC
Solvent: CCOC(C)=O
Solvent: C1CCOC1
Product: CC(C)C[C@H](NC(=O)OCc1ccccc1)C(=O)NC(=CCS(=O)(=O)CC=C(NC(=O)[C@H](CC(C)C)NC(=O)OCc1ccccc1)C(c1ccccc1)c1ccccc1)C(c1ccccc1)c1ccccc1
Temperature: 25 °C
Yield: 63 %

Procedure:
Butyllithium (3.63 ml, 6.17 mmol, 1.7 M in pentane) was added dropwise to a solution of tert-butylhydroperoxide (2.55 ml, 8.42 mmol, 3.3 M in toluene) in freshly distilled THF (80 ml) at −78° C. under argon. A solution of Cbz-Leu-Phe-VS-Ph (3.00 g, 5.61 mmol) in dry THF (30 ml) was added dropwise. The reaction was continued to stir at −20° C. for 45 minutes (TLC Hex/EtOAc 1:1). The reaction was quenched with saturated aqueous ammonium chloride (50 ml) and allowed to warm to room temperature. The organic layer was separated, and the aqueous layer was extracted with ethyl acetate (3×30 ml). The extracts were then washed with aqueous sodium sulfite (10%, 3×20 ml). The combined organic layers were dried (MgSO4) and evaporated to give Cbz-Leu-Phe-AS-Ph as a white powder, yield 63%. 1H-NMR (CDCl3) δ 0.8-0.9 (2d, 6H, 2×Leu-CH3), 1.4-1.6 (m, 2H, Leu-CH2), 3.8 (s, 2H, CH2-Phe), 3.9 (d, 2H, CH2—SO2), 4.1 (m, 1H, α-H), 4.8 (t, 1H, CH═), 4.9-5.0 (b, 1H, NH), 5.1 (m, 2H, Cbz), 7.1-7.4 (m, 10H, 2×Ph), 7.5-7.7 (m, 5H, SO2-Ph), 8.4 (b, 1H, NH). 13C NMR (400 MHz, CDCl3)δ 172.1, 156.3, 144.4, 140.8, 135.7, 134.2, 133.6, 131.2, 129.5, 129.4×2, 129.3, 128.8×2, 128.7, 128.6, 128.4, 128.3, 127.8, 127.3, 126.9, 106.3, 67.6, 56.0, 55.6, 41.7, 40.4, 22.1, 21.0, 18.4. MS (FAB+) m/z 535 (M+1, 100%). Anal. Calcd. for C30H34N2O5S: C, 67.39; H, 6.56; N, 5.43. Found: C, 67.41; H, 6.56; N, 5.43.
Reaction SMILES: Cl[C:2]1[N:7]=[C:6]2[N:8]([CH2:11][CH3:12])[N:9]=[CH:10][C:5]2=[C:4]([N:13]2[CH2:19][CH:18]3[O:20][CH:15]([CH2:16][CH2:17]3)[CH2:14]2)[N:3]=1.[NH2:21][C:22]1[CH:27]=[CH:26][C:25](B(O)O)=[CH:24][CH:23]=1.C([O-])([O-])=O.[Na+].[Na+]>C1(C)C=CC=CC=1.C(O)C>[CH:15]12[O:20][CH:18]([CH2:17][CH2:16]1)[CH2:19][N:13]([C:4]1[N:3]=[C:2]([C:25]3[CH:26]=[CH:27][C:22]([NH2:21])=[CH:23][CH:24]=3)[N:7]=[C:6]3[N:8]([CH2:11][CH3:12])[N:9]=[CH:10][C:5]=13)[CH2:14]2
Reactant: CCn1ncc2c(N3CC4CCC(C3)O4)nc(Cl)nc21
Reactant: Nc1ccc(B(O)O)cc1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: CCO
Solvent: Cc1ccccc1
Product: CCn1ncc2c(N3CC4CCC(C3)O4)nc(-c3ccc(N)cc3)nc21
Temperature: 25 °C

Procedure:
3-(6-chloro-1-ethyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl)-8-oxa-3-azabicyclo[3.2.1]octane (3.08 g, 10.5 mmol) was dissolved in toluene (95 mL) and ethanol (55 mL). 4-Aminophenylboronic acid, pinacol ester (2.53 g, 11.55 mmol) was added followed by the addition of a 2M aqueous solution of Na2CO3 (21 mL). The mixture was degassed by bubbling a stream of nitrogen through the solution and tetrakis(triphenylphosphine)palladium (606 mg) was added. The mixture was heated under reflux for 16 h, cooled to room temperature and concentrated. The mixture was dissolved in ethyl acetate and washed with brine. The organic phase was dried over MgSO4 and filtered over magnesol. The aqueous phase was extracted with ethyl acetate, which was dried over MgSO4. The combined organic phases were concentrated. The crude product was applied to a silica gel column and eluted with ethyl acetate in hexanes (30-100%) to give 3.6 g of the title compound. HRMS: 351.1925 [M+H]. For [M+H]+ mass error=−0.3 mDa or −0.92 ppm.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:10]=[CH:9][C:6]([CH2:7]Br)=[CH:5][CH:4]=1.[Br:11][C:12]1[N:17]=[C:16]([C:18]([O:20][CH3:21])=[O:19])[C:15]([OH:22])=[CH:14][CH:13]=1.C([O-])([O-])=O.[K+].[K+]>CC(C)=O>[Br:11][C:12]1[N:17]=[C:16]([C:18]([O:20][CH3:21])=[O:19])[C:15]([O:22][CH2:7][C:6]2[CH:9]=[CH:10][C:3]([O:2][CH3:1])=[CH:4][CH:5]=2)=[CH:14][CH:13]=1
Reactant: COC(=O)c1nc(Br)ccc1O
Reactant: COc1ccc(CBr)cc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC(C)=O
Product: COC(=O)c1nc(Br)ccc1OCc1ccc(OC)cc1
Temperature: 25 °C

Procedure:
4-Methoxybenzyl bromide (0.095 g, 0.47 mmol) was added dropwise to a suspension of methyl 6-bromo-3-hydroxypicolinate (26B) (0.100 g, 0.43 mmol) and K2CO3 (0.089 g, 0.65 mmol) in anhydrous acetone (2.5 mL). The reaction mixture was heated at reflux for 3.5 hours, cooled to rt, and concentrated under reduced pressure. Water was added and the mixture extracted with DCM. The organic phases were washed with 1 M NaOH, brine, dried over MgSO4, filtered, and concentrated under reduced pressure. The concentrate was purified by column chromatography on silica gel eluting with a gradient of PE:EtOAc 84:16 to 72:28, to provide the desired product methyl 6-bromo-3-(4-methoxybenzyloxy)picolinate (40A).
Reaction SMILES: [N:1]1([C:7]2[CH:8]=[CH:9][C:10]3[N:11]([C:13]([C:16]([F:19])([F:18])[F:17])=[N:14][N:15]=3)[N:12]=2)[CH2:6][CH2:5][NH:4][CH2:3][CH2:2]1.[CH3:20][O:21][C:22]1[CH:23]=[C:24]([CH:27]=[CH:28][CH:29]=1)[CH:25]=O>>[CH3:20][O:21][C:22]1[CH:23]=[C:24]([CH2:25][N:4]2[CH2:3][CH2:2][N:1]([C:7]3[CH:8]=[CH:9][C:10]4[N:11]([C:13]([C:16]([F:17])([F:18])[F:19])=[N:14][N:15]=4)[N:12]=3)[CH2:6][CH2:5]2)[CH:27]=[CH:28][CH:29]=1
Reactant: FC(F)(F)c1nnc2ccc(N3CCNCC3)nn12
Reactant: COc1cccc(C=O)c1
Product: COc1cccc(CN2CCN(c3ccc4nnc(C(F)(F)F)n4n3)CC2)c1

Procedure:
Reductive amination of 6-(piperazin-1-yl)-3-(trifluoromethyl)-[1,2,4]triazolo[4,3-b]pyridazine with 3-methoxybenzaldehyde was carried out according to General Synthetic Method 5. The crude product was purified by hplc using a Waters XBridge Prep C18 OBD column (5μ silica, 19 mm diameter, 100 mm length) eluted with decreasingly polar mixtures of water (containing 1% aqueous ammonia) and acetonitrile as eluents to give 6-[4-[(3-methoxyphenyl)methyl]piperazin-1-yl]-3-(trifluoromethyl)-[1,2,4]triazolo[4,3-b]pyridazine.