Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [F:1][C:2]1[CH:7]=[C:6]([F:8])[C:5]([F:9])=[CH:4][C:3]=1[C:10]1[CH:25]=[CH:24][C:13]2[C@:14]3([CH3:23])[C@@H:19]([CH2:20][CH2:21][C:12]=2[CH:11]=1)[NH:18][C:17](=[O:22])[CH2:16][CH2:15]3.[C:26](O)(C)(C)C.CC(C)([O-])C.[K+].CI>C(OCC)(=O)C>[CH3:26][N:18]1[C@H:19]2[C@@:14]([CH3:23])([C:13]3[CH:24]=[CH:25][C:10]([C:3]4[CH:4]=[C:5]([F:9])[C:6]([F:8])=[CH:7][C:2]=4[F:1])=[CH:11][C:12]=3[CH2:21][CH2:20]2)[CH2:15][CH2:16][C:17]1=[O:22]
Reactant: C[C@]12CCC(=O)N[C@@H]1CCc1cc(-c3cc(F)c(F)cc3F)ccc12
Reactant: CC(C)(C)O
Agent: CC(C)(C)[O-]
Agent: [K+]
Solvent: CI
Solvent: CCOC(C)=O
Product: CN1C(=O)CC[C@]2(C)c3ccc(-c4cc(F)c(F)cc4F)cc3CC[C@@H]12
Temperature: 25 °C
Reaction time: 4 h
Yield: 89 %

Procedure:
A 15 mL round bottom flask was charged with (+)-(4aR)-(10bR)-8-(2,4,5-trifluorophenyl)-10b-methyl-1,2,3,4,4a,5,6,10b-octahydrobenzo[f]quinolin-3-one (43 mg, 0.12 mmol), 0.3 mL of t-butanol, and potassium t-butoxide (42 mg, 0.36 mmol). Methyl iodide (0.023 mL, 0.36 mmol) was added and the mixture was stirred at room temperature for 4 h. The mixture was diluted with ethyl acetate, and purified by silica gel chromatography (ethyl acetate eluent) to give 40 mg (89%) of the title compound as a foam. FDMS: m/e=359.
Reaction SMILES: [CH:1]([C:4]1[CH:9]=[CH:8][C:7]([S:10]([NH:13][C:14]2[CH:19]=[CH:18][C:17]([C@@H:20]3[CH2:24][CH2:23][NH:22][CH2:21]3)=[CH:16][CH:15]=2)(=[O:12])=[O:11])=[CH:6][CH:5]=1)([CH3:3])[CH3:2].[F:25][CH2:26][CH2:27][CH2:28]OS(C1C=CC(C)=CC=1)(=O)=O.C(N(CC)CC)C>CN(C)C=O>[CH:1]([C:4]1[CH:9]=[CH:8][C:7]([S:10]([NH:13][C:14]2[CH:19]=[CH:18][C:17]([C@@H:20]3[CH2:24][CH2:23][N:22]([CH2:28][CH2:27][CH2:26][F:25])[CH2:21]3)=[CH:16][CH:15]=2)(=[O:11])=[O:12])=[CH:6][CH:5]=1)([CH3:3])[CH3:2]
Reactant: Cc1ccc(S(=O)(=O)OCCCF)cc1
Reactant: CC(C)c1ccc(S(=O)(=O)Nc2ccc([C@@H]3CCNC3)cc2)cc1
Solvent: CN(C)C=O
Solvent: CCN(CC)CC
Product: CC(C)c1ccc(S(=O)(=O)Nc2ccc([C@@H]3CCN(CCCF)C3)cc2)cc1
Temperature: 50 °C
Reaction time: 1 h
Yield: 45.5 %

Procedure:
0.215 g of 4-isopropyl-N-[4-((S)-pyrrolidin-3-yl)-phenyl]-benzenesulfonamide (0.0.62 mmol) and 0.16 g of toluene-4-sulfonic acid 3-fluoro-propyl ester (0.69 mmol) were dissolved in 5 ml of dimethylformamide, 0.43 ml of triethylamine added and the reaction stirred for 1 h at 50° C. Additional toluene-4-sulfonic acid 3-fluoro-propyl ester and triethylamine were added to drive the reaction to completion. After stirring at room temperature for 15 h, the solvent was evaporated, the residue re-dissolved in dichloromethane, and the organic layer washed with 1 N aqueous sodium hydroxide. The aqueous phase was extracted twice with dichloromethane, the organic layers combined, dried over magnesium sulfate, filtered and the solvent evaporated. The crude product was purified via silica gel chromatography (chromabond column) using dichloromethane/methanol 0-3%. Fractions containing the product were collected and the solvent evaporated to yield 0.115 g of the desired product.
Reaction SMILES: [H-].[Al+3].[Li+].[H-].[H-].[H-].[CH3:7][C:8]1[O:12][C:11]([C:13]2[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=2)=[N:10][C:9]=1[CH2:19][O:20][C:21]1[CH:26]=[C:25]([C:27](OC)=[O:28])[CH:24]=[CH:23][N:22]=1.O.O.O.O.O.O.O.O.O.O.S([O-])([O-])(=O)=O.[Na+].[Na+]>O1CCCC1>[CH3:7][C:8]1[O:12][C:11]([C:13]2[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=2)=[N:10][C:9]=1[CH2:19][O:20][C:21]1[CH:26]=[C:25]([CH2:27][OH:28])[CH:24]=[CH:23][N:22]=1
Reactant: COC(=O)c1ccnc(OCc2nc(-c3ccccc3)oc2C)c1
Agent: O=S(=O)([O-])[O-]
Agent: [Al+3]
Agent: [H-]
Solvent: O
Solvent: C1CCOC1
Product: Cc1oc(-c2ccccc2)nc1COc1cc(CO)ccn1
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 76.9 %

Procedure:
Lithium aluminium hydride (228 mg) was added to a solution of methyl 2-(5-methyl-2-phenyl-4-oxazolylmethoxy)-4-pyridinecarboxylate (1.95 g) in tetrahydrofuran (20 ml) at 0° C., which was stirred at room temperature for 30 minutes. Sodium sulfate decahydrate (1.93 g) was added to the reaction mixture, which was stirred at room temperature for 30 minutes. The precipitates were removed by filtration, the filtrate was concentrated. The resulting colorless crystals were collected by filtration to obtain 2-(5-methyl-2-phenyl-4-oxazolylmethoxy)-4-pyridylmethanol (1.37 g, yield 77%). This was recrystallized from ethyl acetate-hexane. Melting point: 100–101° C.
Reaction SMILES: N(C=CC=O)C1C=CC=CC=1.NC1C=CC=CC=1.[C:19]([CH2:21][C:22]([O:24][CH2:25][CH2:26][CH2:27][CH2:28][CH2:29][CH2:30][CH2:31][CH3:32])=[O:23])#[N:20].[C:33]([N:36]([C:50]1[CH:55]=[CH:54][CH:53]=[CH:52][CH:51]=1)/[CH:37]=[CH:38]/[CH:39]=C(\C#N)/C(OCCCC)=O)(=[O:35])[CH3:34]>C(OC(=O)C)(=O)C>[C:33]([N:36]([C:50]1[CH:51]=[CH:52][CH:53]=[CH:54][CH:55]=1)/[CH:37]=[CH:38]/[CH:39]=[C:21](\[C:19]#[N:20])/[C:22]([O:24][CH2:25][CH2:26][CH2:27][CH2:28][CH2:29][CH2:30][CH2:31][CH3:32])=[O:23])(=[O:35])[CH3:34]
Reactant: CCCCCCCCOC(=O)CC#N
Reactant: CCCCOC(=O)/C(C#N)=C/C=C/N(C(C)=O)c1ccccc1
Agent: O=CC=CNc1ccccc1
Solvent: CC(=O)OC(C)=O
Solvent: Nc1ccccc1
Product: CCCCCCCCOC(=O)/C(C#N)=C/C=C/N(C(C)=O)c1ccccc1
Yield: 79 %

Procedure:
3-Anilinoacrolein-aniline (27.7 g, 0.125 mol) and n-octyl cyanoacetate (26.3 ml, 0.125 mol) are heated in 70 ml of acetic anhydride at 115° C. for 2 hours while bubbling with nitrogen. After cooling, 80 ml of methanol are added and precipitation is allowed to take place. The solid obtained is filtered off and rinsed with methanol. Drying is carried out. 36.4 g of a yellow powder (yield: 79%) of butyl (2E,4E)-5-[acetyl(phenyl)amino]-2-cyanopenta-2,4-dienoate are recovered, which powder is used as is in the following stage.
Reaction SMILES: Br[C:2]1[CH:7]=[C:6]([S:8]([C:11]2[CH:16]=[CH:15][C:14]([NH2:17])=[CH:13][CH:12]=2)(=[O:10])=[O:9])[CH:5]=[C:4]([Br:18])[N:3]=1.[NH:19]1[CH2:24][CH2:23][NH:22][CH2:21][CH2:20]1.C(N(CC)CC)C>O1CCOCC1>[Br:18][C:4]1[CH:5]=[C:6]([S:8]([C:11]2[CH:16]=[CH:15][C:14]([NH2:17])=[CH:13][CH:12]=2)(=[O:10])=[O:9])[CH:7]=[C:2]([N:19]2[CH2:24][CH2:23][NH:22][CH2:21][CH2:20]2)[N:3]=1
Reactant: Nc1ccc(S(=O)(=O)c2cc(Br)nc(Br)c2)cc1
Reactant: C1CNCCN1
Solvent: CCN(CC)CC
Solvent: C1COCCO1
Product: Nc1ccc(S(=O)(=O)c2cc(Br)nc(N3CCNCC3)c2)cc1
Temperature: 40 °C
Reaction time: 72 h
Yield: 82.7 %

Procedure:
0.275 g (0.0007 mol) of 4-(2,6-dibromopyridine-4-sulphonyl)-phenylamine was dissolved in 10 ml of dioxane and treated with 0.066 g (0.00077 mol) of piperazine and 1 ml of triethylamine. The mixture was stirred at 40° C. for 72 hrs. and the solvent was then removed. The residue was partitioned in ethyl acetate and water and the organic phase was extracted with sat. sodium chloride solution and dried over MgSO4 and filtered. After removal of the solvent the residue was chromatographed on silica gel with dichloromethane/methanol 9:1 and there was obtained 0.23 g (82%) of 4-(2-bromo-6-piperazin-1-ylpyridin-4-sulphonyl) -phenylamine as yellowish crystals; m.p.: 173-175° C.
Reaction SMILES: [CH3:1][N:2]1[C:15]([C:16]([O:18]C)=O)=[C:14]([OH:20])[C:5]2[N:6]([CH3:13])[C:7]3[CH:8]=[CH:9][CH:10]=[CH:11][C:12]=3[C:4]=2[S:3]1(=[O:22])=[O:21].[NH2:23][C:24]1[CH:29]=[CH:28][N:27]=[CH:26][N:25]=1>>[CH3:1][N:2]1[C:15]([C:16]([NH:23][C:24]2[CH:29]=[CH:28][N:27]=[CH:26][N:25]=2)=[O:18])=[C:14]([OH:20])[C:5]2[N:6]([CH3:13])[C:7]3[CH:8]=[CH:9][CH:10]=[CH:11][C:12]=3[C:4]=2[S:3]1(=[O:21])=[O:22]
Reactant: Nc1ccncn1
Reactant: COC(=O)C1=C(O)c2c(c3ccccc3n2C)S(=O)(=O)N1C
Product: CN1C(C(=O)Nc2ccncn2)=C(O)c2c(c3ccccc3n2C)S1(=O)=O
Yield: 86.5 %

Procedure:
Analogous to Example 45, 0.7 gm (2.1 millimols) of methyl 2,5-dihydro-2,5-dimethyl-4-hydroxy-1,2-thiazino[5,6-b]indole-3-carboxylate-1,1-dioxide and 0.24 gm (2.5 millimols) of 4-amino-pyrimidine were reacted, yielding 0.7 gm (86% of theory) of 2,5-dihydro-2,5-dimethyl-4-hydroxy-N-(4-pyrimidinyl)-1,2-thiazino[5,6-b]indole-3-carboxamide-1,1-dioxide; M.p.: 255° C. (decomposition).
Reaction SMILES: Cl[C:2]1[CH:7]=[CH:6][C:5]([C:8]([F:11])([F:10])[F:9])=[CH:4][N:3]=1.[CH2:12]([O:19][C:20]1[CH:21]=[C:22]([C:37]2[N:38]=[N:39][NH:40][N:41]=2)[CH:23]=[C:24]([N+:34]([O-:36])=[O:35])[C:25]=1[O:26][CH2:27][C:28]1[CH:33]=[CH:32][CH:31]=[CH:30][CH:29]=1)[C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1.C(=O)([O-])[O-].[K+].[K+]>C(#N)C.ClCCl>[CH2:12]([O:19][C:20]1[CH:21]=[C:22]([C:37]2[N:38]=[N:39][N:40]([C:2]3[CH:7]=[CH:6][C:5]([C:8]([F:11])([F:10])[F:9])=[CH:4][N:3]=3)[N:41]=2)[CH:23]=[C:24]([N+:34]([O-:36])=[O:35])[C:25]=1[O:26][CH2:27][C:28]1[CH:33]=[CH:32][CH:31]=[CH:30][CH:29]=1)[C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1
Reactant: FC(F)(F)c1ccc(Cl)nc1
Reactant: O=[N+]([O-])c1cc(-c2nn[nH]n2)cc(OCc2ccccc2)c1OCc1ccccc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: ClCCl
Solvent: CC#N
Product: O=[N+]([O-])c1cc(-c2nnn(-c3ccc(C(F)(F)F)cn3)n2)cc(OCc2ccccc2)c1OCc1ccccc1
Temperature: 25 °C

Procedure:
2-chloro-5-(trifluoromethyl)pyridine (0.181 g, 1.00 mmol) was added to a stirred suspension of 5-(3,4-bis-benzyloxy-5-nitro-phenyl)-2H-tetrazole (0.4 g, 1.00 mmol) and potassium carbonate (0.14 g, 1 mmol) in acetonitrile (10 mL). The reaction mixture was stirred at room temperature till completion, then diluted with dichloromethane and washed with water. The organic phase was separated, dried over anhydrous magnesium sulphate, filtered and evaporated to dryness to leave a crude residue that was recrystallised from a dichloro-methane/isopropanol mixture to afford 2-(5-(3,4-bis(benzyloxy)-5-nitrophenyl)-2H-tetrazol-2-yl)-5-(trifluoromethyl)pyridine, 0.389 g (71%).
Reaction SMILES: [CH2:1]([O:3][C:4](=[O:23])[CH2:5][C:6]1[C:10]2[CH:11]=[CH:12][C:13](OS(C(F)(F)F)(=O)=O)=[CH:14][C:9]=2[S:8][CH:7]=1)[CH3:2].[CH3:24][CH2:25]O>[Cl-].[Na+].O.C1C=CC(P(C2C=CC=CC=2)[C-]2C=CC=C2)=CC=1.C1C=CC(P(C2C=CC=CC=2)[C-]2C=CC=C2)=CC=1.Cl[Pd]Cl.[Fe+2]>[CH2:1]([O:3][C:4](=[O:23])[CH2:5][C:6]1[C:10]2[CH:11]=[CH:12][C:13]([CH:24]=[CH2:25])=[CH:14][C:9]=2[S:8][CH:7]=1)[CH3:2]
Reactant: CCOC(=O)Cc1csc2cc(OS(=O)(=O)C(F)(F)F)ccc12
Reactant: CCO
Agent: Cl[Pd]Cl
Agent: [Fe+2]
Agent: [Cl-]
Solvent: O
Product: C=Cc1ccc2c(CC(=O)OCC)csc2c1
Temperature: 110 °C

Procedure:
To a mixture of ethyl(6-(((trifluoromethyl)sulfonyl)oxy)-1-benzothiophen-3-yl)acetate (600 mg) and EtOH (10 mL) were added potassium vinyl(trifluoro) borate (240 mg), PdCl2(dppf) (119 mg) and TEA (0.454 mL) at room temperature, and the mixture was heated to 110° C. with microwave irradiation for 15 min. The mixture was poured into brine at room temperature and extracted with EtOAc. The organic layer was separated, washed with brine, and dried over MgSO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (EtOAc/hexane) to give the title compound (320 mg).
Reaction SMILES: [C:1]([C:5]1[CH:10]=[CH:9][C:8]([C:11]2[C:20]3[C:15](=[C:16]([C:21]([F:24])([F:23])[F:22])[CH:17]=[CH:18][CH:19]=3)[N:14]=[CH:13][C:12]=2[C:25]([C:27]2[CH:32]=[CH:31][CH:30]=[CH:29][N:28]=2)=O)=[CH:7][CH:6]=1)([CH3:4])([CH3:3])[CH3:2].C1(C(C2C=NC3C(C=2C2C=CC=CC=2)=CC=CC=3C(F)(F)F)=O)C=CC=CC=1>>[C:1]([C:5]1[CH:6]=[CH:7][C:8]([C:11]2[C:20]3[C:15](=[C:16]([C:21]([F:22])([F:24])[F:23])[CH:17]=[CH:18][CH:19]=3)[N:14]=[CH:13][C:12]=2[CH2:25][C:27]2[CH:32]=[CH:31][CH:30]=[CH:29][N:28]=2)=[CH:9][CH:10]=1)([CH3:4])([CH3:2])[CH3:3]
Reactant: CC(C)(C)c1ccc(-c2c(C(=O)c3ccccn3)cnc3c(C(F)(F)F)cccc23)cc1
Agent: O=C(c1ccccc1)c1cnc2c(C(F)(F)F)cccc2c1-c1ccccc1
Product: CC(C)(C)c1ccc(-c2c(Cc3ccccn3)cnc3c(C(F)(F)F)cccc23)cc1

Procedure:
This compound was prepared using the procedure of Example 31 substituting [4-(4-tert-butylphenyl)-8-(trifluoromethyl)quinolin-3-yl](pyridin-2-yl)methanone. of Example 18 for 2 phenyl[4-phenyl-8-(trifluoromethyl)quinolin-3-yl]methanone. MS (ESI) m/z 421 ([M+H]+); Anal. Calcd for C26H23F3N2: C, 74.27; H, 5.51; N, 6.66. Found: C, 73.94; H, 5.30; N, 6.53.
Reaction SMILES: C(OC([NH:8][CH2:9][CH2:10][CH2:11][CH2:12][C:13]([C:24]1[N:25]=[CH:26][N:27]([CH2:29][C:30]2[S:31][C:32]([CH:35]3[CH2:37][CH2:36]3)=[N:33][N:34]=2)[CH:28]=1)(C(OCC)=O)[C:14]([O:16]CC)=[O:15])=O)(C)(C)C>Cl>[NH2:8][CH2:9][CH2:10][CH2:11][CH2:12][CH:13]([C:24]1[N:25]=[CH:26][N:27]([CH2:29][C:30]2[S:31][C:32]([CH:35]3[CH2:37][CH2:36]3)=[N:33][N:34]=2)[CH:28]=1)[C:14]([OH:16])=[O:15]
Reactant: CCOC(=O)C(CCCCNC(=O)OC(C)(C)C)(C(=O)OCC)c1cn(Cc2nnc(C3CC3)s2)cn1
Agent: Cl
Product: NCCCCC(C(=O)O)c1cn(Cc2nnc(C3CC3)s2)cn1
Temperature: 95 °C
Reaction time: 8 h

Procedure:
0.140 g (261 μmol) of diethyl 2-(4-tert-butoxycarbonylaminobutyl)-2-[1-(5-cyclopropyl-[1,3,4]thiadiazol-2-ylmethyl)-1H-imidazol-4-yl]malonate was suspended in 10 ml of semi-concentrated hydrochloric acid, and the mixture was heated with stirring at 95° C. for 8 h. The reaction mixture was concentrated under reduced pressure and purified by preparative HPLC, and the product-containing fractions were freeze-dried and then taken up in 2.5 eq of 1N hydrochloric acid and freeze-dried and taken up in water and freeze-dried. The preparation was then purified once more by preparative HPLC, and the product-containing fractions were freeze-dried. This gave 35 mg (32%) of the title compound as trifluoroacetic acid salt.
Reaction SMILES: [CH2:1]([N:8]1[CH2:14][CH2:13][CH2:12][C:11]2([CH2:23][C:22](=[O:24])[C:21]3[C:16](=[CH:17][CH:18]=[C:19](/[CH:25]=[CH:26]/[C:27](O)=[O:28])[CH:20]=3)[O:15]2)[CH2:10][CH2:9]1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[NH2:30][O:31][CH:32]1[CH2:37][CH2:36][CH2:35][CH2:34][O:33]1>>[CH2:1]([N:8]1[CH2:14][CH2:13][CH2:12][C:11]2([CH2:23][C:22](=[O:24])[C:21]3[C:16](=[CH:17][CH:18]=[C:19](/[CH:25]=[CH:26]/[C:27]([NH:30][O:31][CH:32]4[CH2:37][CH2:36][CH2:35][CH2:34][O:33]4)=[O:28])[CH:20]=3)[O:15]2)[CH2:10][CH2:9]1)[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: NOC1CCCCO1
Reactant: O=C(O)/C=C/c1ccc2c(c1)C(=O)CC1(CCCN(Cc3ccccc3)CC1)O2
Product: O=C(/C=C/c1ccc2c(c1)C(=O)CC1(CCCN(Cc3ccccc3)CC1)O2)NOC1CCCCO1

Procedure:
(±)-(E)-3-[1′-Benzyl-4-oxo-spiro(chromane-2,4′-azepane)-6-yl]-acrylic acid (490 mg, 1.15 mmol) was reacted with NH2OTHP following the procedure described in Example 22, Step C, giving (E)-3-[1′-benzyl-4-oxo-spiro(chromane-2,4′-azepane)-6-yl]-N-(tetrahydro-pyran-2-yloxy)-acrylamide (270 mg).
Reaction SMILES: Cl.[Cl:2][C:3]1[C:12]([Cl:13])=[C:11]2[C:6]([CH:7]=[CH:8][N:9]=[CH:10]2)=[CH:5][CH:4]=1>[Pt]=O.CO>[Cl:2][C:3]1[C:12]([Cl:13])=[C:11]2[C:6]([CH2:7][CH2:8][NH:9][CH2:10]2)=[CH:5][CH:4]=1
Reactant: Clc1ccc2ccncc2c1Cl
Agent: O=[Pt]
Agent: Cl
Solvent: CO
Product: Clc1ccc2c(c1Cl)CNCC2

Procedure:
The above prepared 7,8-dichloroisoquinoline hydrochloride was reduced in two portions, using 0.7 g. of platinum oxide in 100 cc. of methanol, for 1 hour at ambient temperature. The mixture was filtered and concentrated. The residue was converted to the base using ammonium hydroxide and was extracted into ether. The extract was dried with magnesium sulfate, filtered and concentrated to give, as the residue, 7,8-dichloro-1,2,3,4-tetrahydroisoquinoline.
Reaction SMILES: [Cl:1][C:2]1[N:10]=[C:9]2[C:5]([N:6]=[CH:7][N:8]2[CH:11]2[CH2:15][CH2:14][CH2:13][CH2:12]2)=[C:4](Cl)[N:3]=1.[Cl:17][C:18]1[CH:23]=[CH:22][CH:21]=[C:20]([Cl:24])[C:19]=1[NH:25][NH2:26]>C(N(CC)CC)C>[Cl:1][C:2]1[N:10]=[C:9]2[C:5]([N:6]=[CH:7][N:8]2[CH:11]2[CH2:15][CH2:14][CH2:13][CH2:12]2)=[C:4]([NH:26][NH:25][C:19]2[C:18]([Cl:17])=[CH:23][CH:22]=[CH:21][C:20]=2[Cl:24])[N:3]=1
Reactant: Clc1nc(Cl)c2ncn(C3CCCC3)c2n1
Reactant: NNc1c(Cl)cccc1Cl
Solvent: CCN(CC)CC
Product: Clc1nc(NNc2c(Cl)cccc2Cl)c2ncn(C3CCCC3)c2n1

Procedure:
2-Chloro-6-[2,6-dichlorophenylhydrazino]-9-cyclopentylpurine is prepared from 2,6-dichloro-9-cyclopentylpurine, 2,6-dichlorophenylhydrazine, and triethylamine essentially as described above in Example 1, Scheme A, step b.
Reaction SMILES: C(OC([N:8]1[CH2:13][CH2:12][CH:11]([C:14]2[CH:19]=[CH:18][C:17]([C:20]3[CH:25]=[CH:24][C:23]([S:26]([CH2:29][CH3:30])(=[O:28])=[O:27])=[CH:22][CH:21]=3)=[CH:16][N:15]=2)[CH2:10][CH2:9]1)=O)(C)(C)C.C(O)(C(F)(F)F)=O.[OH-].[Na+]>C(Cl)Cl>[CH2:29]([S:26]([C:23]1[CH:24]=[CH:25][C:20]([C:17]2[CH:18]=[CH:19][C:14]([CH:11]3[CH2:12][CH2:13][NH:8][CH2:9][CH2:10]3)=[N:15][CH:16]=2)=[CH:21][CH:22]=1)(=[O:28])=[O:27])[CH3:30]
Reactant: CCS(=O)(=O)c1ccc(-c2ccc(C3CCN(C(=O)OC(C)(C)C)CC3)nc2)cc1
Agent: [Na+]
Agent: [OH-]
Solvent: ClCCl
Solvent: O=C(O)C(F)(F)F
Product: CCS(=O)(=O)c1ccc(-c2ccc(C3CCNCC3)nc2)cc1
Reaction time: 4 h
Yield: 83.5 %

Procedure:
5-(4-Ethanesulfonylphenyl)-3′,4′,5′,6′-tetrahydro-2′H-[2,4′]bipyridinyl-1′-carboxylic acid tert-butyl ester (0.76 g, 1.675 mmol) was dissolved in DCM (12 mL) and TFA (4 mL) was added. The reaction mixture was stirred for 4 hours. 1N NaOH (20 mL) was added and the DCM phase was washed and dried with Na2CO3, filtered and evaporation gave 462 mg (79%) white crystalline compound.
Reaction SMILES: C(OC([NH:8][C:9]1[N:10]=[C:11]([C:15]([O:17][CH3:18])=[O:16])[N:12]([CH3:14])[CH:13]=1)=O)(C)(C)C.Cl.[C:20]([O:24][C:25]([NH:27][C:28]1[N:29]=[C:30]([C:34]([OH:36])=O)[N:31]([CH3:33])[CH:32]=1)=[O:26])([CH3:23])([CH3:22])[CH3:21].C(Cl)CCl.CCN(C(C)C)C(C)C>C(O)C.C1(C)C=CC=CC=1.CC(N(C)C)=O>[C:20]([O:24][C:25]([NH:27][C:28]1[N:29]=[C:30]([C:34]([NH:8][C:9]2[N:10]=[C:11]([C:15]([O:17][CH3:18])=[O:16])[N:12]([CH3:14])[CH:13]=2)=[O:36])[N:31]([CH3:33])[CH:32]=1)=[O:26])([CH3:21])([CH3:22])[CH3:23]
Reactant: COC(=O)c1nc(NC(=O)OC(C)(C)C)cn1C
Reactant: Cn1cc(NC(=O)OC(C)(C)C)nc1C(=O)O
Agent: Cl
Solvent: CC(=O)N(C)C
Solvent: CCN(C(C)C)C(C)C
Solvent: Cc1ccccc1
Product: COC(=O)c1nc(NC(=O)c2nc(NC(=O)OC(C)(C)C)cn2C)cn1C
Reaction time: 0.5 h
Yield: 71.5 %

Procedure:
Methyl 4-(tert-butoxycarbonylamino)-1-methyl-1H-imidazole-2-carboxylate (2.50 g, 9.80 mmol) in 30 ml of EtAc was added 6 ml of HCl (conc.). After stirred for 30 min, the mixture was diluted with ethanol and toluene, concentrated and co-evaporated with ethanol/toluene (1:1, 3×50 ml) to dryness compound without further purification. To the dryness compound was added 4-(tert-butoxycarbonylamino)-1-methyl-1H-imidazole-2-carboxylic acid (2.36 g, 9.8 mmol), EDC (5.90 g, 30.7 mmol), DIPEA (1.70 ml, 9.8 mmol) and 80 ml of DMA. The mixture was stirred under Ar overnight, concentrated, diluted with THF/EtAc (1:2, 150 ml), and washed 1M NaH2PO4/NaCl (conc) and NaHCO3 (conc) separately. The organic solvent layer was separated and dried over MgSO4, filtered, concentrated and purified on SiO2 chromatography eluted with EtAc/DCM (1:25 to 1:15) to afford 2.65 g (71.5%) of the title product. 1H NMR (DMSO) 11.17 (s, 1H), 10.48 (s, 1H), 7.58 (s, 1H), 7.32 (s, 1H), 4.01 (s, 3H), 3.94 (s, 3H), 3.92 (s, 3H), 1.45 (s, 9H); 13C NMR 160.60, 157.30, 135.92, 135.45, 132.86, 126.12, 114.83, 79.50, 52.70, 35.58, 34.92, 28.08; MS m/z+401.8 (M+Na).
Reaction SMILES: N1C=CC=CC=1.[C:7](OC(=O)C)(=[O:9])[CH3:8].[C:14]([C:18]1[CH:26]=[C:22]([C:23]([OH:25])=[O:24])[C:21]([OH:27])=[CH:20][CH:19]=1)([CH3:17])([CH3:16])[CH3:15]>C(Cl)Cl>[C:7]([O:27][C:21]1[CH:20]=[CH:19][C:18]([C:14]([CH3:17])([CH3:15])[CH3:16])=[CH:26][C:22]=1[C:23]([OH:25])=[O:24])(=[O:9])[CH3:8]
Reactant: CC(=O)OC(C)=O
Reactant: CC(C)(C)c1ccc(O)c(C(=O)O)c1
Solvent: c1ccncc1
Solvent: ClCCl
Product: CC(=O)Oc1ccc(C(C)(C)C)cc1C(=O)O
Temperature: 25 °C
Reaction time: 2 h

Procedure:
Pyridine (0.034 mL) and acetic anhydride (0.034 mL) were sequentially added to a methylene chloride (0.54 mL) solution of 5-tert-butylsalicylic acid (0.054 g), followed by stirring at room temperature for 2 hours. The solvent was evaporated under reduced pressure, and 1 mol/L hydrochloric acid and ethyl acetate were added to the residue. The organic layer was separated, washed with a saturated aqueous solution of sodium chloride, and dried over anhydrous magnesium sulfate, and the solvent was evaporated under reduced pressure. The obtained residue was purified by silica gel column chromatography [eluent: 100-90% chloroform/methanol] to obtain 0.049 g of 2-acetoxy-5-tert-butylbenzoic acid as a white solid.
Reaction SMILES: [NH:1]1[CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1.F[C:8]1[CH:17]=[CH:16][C:11]([C:12]([O:14][CH3:15])=[O:13])=[CH:10][C:9]=1[N+:18]([O-:20])=[O:19]>CN(C=O)C.C(OCC)(=O)C>[N+:18]([C:9]1[CH:10]=[C:11]([CH:16]=[CH:17][C:8]=1[N:1]1[CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1)[C:12]([O:14][CH3:15])=[O:13])([O-:20])=[O:19]
Reactant: COC(=O)c1ccc(F)c([N+](=O)[O-])c1
Reactant: C1CCNCC1
Solvent: CCOC(C)=O
Solvent: CN(C)C=O
Product: COC(=O)c1ccc(N2CCCCC2)c([N+](=O)[O-])c1
Temperature: 25 °C
Reaction time: 1 h

Procedure:
Piperidine (1.24 ml) was added to a solution of methyl 4-fluoro-3-nitrobenzoate (1.00 g) in DMF (20 ml) and the mixture was stirred at room temperature for 1 hour. The reaction mixture was diluted with ethyl acetate, sequentially washed with water and brine, and dried over anhydrous sodium sulfate. The filtrate was concentrated under reduced pressure and the residue was purified by silica gel column chromatography to obtain the title compound (1.50 g).
Reaction SMILES: [OH-].[Na+].C([O:5][C:6](=[O:27])[CH2:7][C:8]([CH:22]1[CH2:26][CH2:25][CH2:24][CH2:23]1)([OH:21])[CH2:9][CH2:10][NH:11][C:12](=[O:20])[CH2:13][CH2:14][C:15]1[O:16][CH:17]=[CH:18][CH:19]=1)C>C(Cl)Cl>[CH:22]1([C:8]([OH:21])([CH2:9][CH2:10][NH:11][C:12](=[O:20])[CH2:13][CH2:14][C:15]2[O:16][CH:17]=[CH:18][CH:19]=2)[CH2:7][C:6]([OH:27])=[O:5])[CH2:23][CH2:24][CH2:25][CH2:26]1
Reactant: CCOC(=O)CC(O)(CCNC(=O)CCc1ccco1)C1CCCC1
Agent: [Na+]
Agent: [OH-]
Solvent: ClCCl
Product: O=C(O)CC(O)(CCNC(=O)CCc1ccco1)C1CCCC1
Temperature: 25 °C
Yield: 36.6 %

Procedure:
A solution of NaOH (0.3 M, 1.6 mL, 0.49 mmol) was added to 3-cyclopentyl-5-(3-furan-2-yl-propionylamino)-3-hydroxy-pentanoic acid ethyl ester (86 mg, 0.245 mmol) from Step 1 below and stirred at room temperature until complete by HPLC. The reaction was diluted with 10 mL CH2Cl2, and washed with 10 mL saturated NH4Cl. The aqueous layer was extracted with 2×10 mL CH2Cl2, and the organic layers were combined. After concentrating by rotary evaporation, the residue was purified by flash chromatography to give the desired compound (29 mg, 37% yield). 1H NMR (CDCl3) δ: 1.39-1.75 (m, 8H), 2.00-2.09 (m, 2H), 2.39-2.52 (m, 5H), 2.90 (t, J=7.45 Hz, 2H), 3.29-3.40 (m, 2H), 5.96 (s, 1H), 6.2 (s, 1H), 6.31 (br, 1H), 7.23 (s, 1H). MS (ESI): 322 (M−H).
Reaction SMILES: [O:1]=[CH:2][C@@H:3]([C@H:5]([C@@H:7]([C@@H:9]([CH2:11][OH:12])[OH:10])[OH:8])[OH:6])[OH:4].[C:13]([OH:18])(=[O:17])[C@@H:14]([CH3:16])[OH:15]>>[C:13]([O-:18])(=[O:17])[CH:14]([CH3:16])[OH:15].[O:1]=[CH:2][C@@H:3]([C@H:5]([C@@H:7]([C@@H:9]([CH2:11][OH:12])[OH:10])[OH:8])[OH:6])[OH:4]
Reactant: C[C@@H](O)C(=O)O
Agent: O=C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO
Product: CC(O)C(=O)[O-]

Procedure:
Fermentation of glucose to D-lactic acid under aerobic growth condition by an evolved E. coli mutant deficient in three terminal oxidases is reported in this work. Cytochrome oxidases (cydAB, cyoABCD, cbdAB) were removed from the E. coli K12 MG1655 genome resulting in the ECOM3 (E. coli Cytochrome Oxidase Mutant) strain. Removal of cytochrome oxidases reduced the oxygen uptake rate of the knock-out strain by nearly 85%. Moreover, the knock-out strain was initially incapable of growing on M9 minimal media. After subjecting the ECOM3 strain to adaptive evolution on glucose M9 medium for 60 days, the growth rate equivalent to anaerobic wild type E. coli was achieved. Our findings demonstrate that three independently adaptively evolved ECOM3 populations acquired different phenotypes: one produced lactate as a sole fermentation product while the other two strains exhibited a mixed acid fermentation under oxic growth conditions with lactate remaining as the major product. The homofermenting strain showed the D-lactate yield of 0.8 g/g from glucose. Gene expression and in silico model-based analysis was employed to identify perturbed pathways and explain phenotypic behavior. Significant upregulation of ygiN and sodAB explain the remaining oxygen uptake that was observed in evolved ECOM3 strains. E. coli strains exemplified herein showed the ability to produce lactate as a fermentation product from glucose as well as undergo mixed-acid fermentation during aerobic (oxic conditions) growth.