Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [CH:1]1([NH:7][C:8](=[O:24])[NH:9][C:10]2[CH:15]=[CH:14][C:13]([C:16]3[CH:20]=[C:19]([C:21](O)=[O:22])[O:18][N:17]=3)=[CH:12][CH:11]=2)[CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1.Cl.[CH3:26][O:27][C:28](=[O:34])[C@@H:29]([NH2:33])[CH:30]([CH3:32])[CH3:31].[K+].[Br-]>>[CH3:26][O:27][C:28](=[O:34])[C@@H:29]([NH:33][C:21]([C:19]1[O:18][N:17]=[C:16]([C:13]2[CH:12]=[CH:11][C:10]([NH:9][C:8]([NH:7][CH:1]3[CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]3)=[O:24])=[CH:15][CH:14]=2)[CH:20]=1)=[O:22])[CH:30]([CH3:32])[CH3:31]
Reactant: COC(=O)[C@@H](N)C(C)C
Reactant: O=C(Nc1ccc(-c2cc(C(=O)O)on2)cc1)NC1CCCCC1
Agent: Cl
Agent: [Br-]
Agent: [K+]
Product: COC(=O)[C@@H](NC(=O)c1cc(-c2ccc(NC(=O)NC3CCCCC3)cc2)no1)C(C)C
Yield: 68 %

Procedure:
The title compound was prepared from 3-[4-(3-cyclohexyl-ureido)-phenyl]-isoxazole-5-carboxylic acid and (S)-2-amino-3-methyl-butyric acid methyl ester hydrochloride as set forth in Example 5 and was obtained in 68% yield. Mass (ES+): 443 (M++1); IR (KBr): 3382, 3345, 3290, 2932, 1746, 1665, 1652, 1543; 1H NMR (DMSO-d6) δ: 0.91 (2×d, 6H), 1.08-1.78 (4×m, 10H), 2.16 (m, 1H), 3.42 (br, 1H), 3.53 (s, 3H), 4.26 (t, 1H), 6.14 (d, 1H), 7.48 (d, 2H), 7.60 (s, 1H), 7.72 (d, 2H), 8.56 (s, 1H), 9.12 (d, 1H).
Reaction SMILES: [CH3:1][O:2][C:3]1[C:10]([C:11]2[S:12][CH:13]=[CH:14][CH:15]=2)=[CH:9][C:6]([CH:7]=O)=[C:5]([O:16][CH2:17][C:18]([N:20]2[CH2:25][CH2:24][O:23][CH2:22][CH2:21]2)=[O:19])[CH:4]=1.[C:26]([C:29]1[CH:37]=[CH:36][C:32]([C:33]([OH:35])=[O:34])=[CH:31][CH:30]=1)(=[O:28])[CH3:27]>>[CH3:1][O:2][C:3]1[C:10]([C:11]2[S:12][CH:13]=[CH:14][CH:15]=2)=[CH:9][C:6](/[CH:7]=[CH:27]/[C:26]([C:29]2[CH:37]=[CH:36][C:32]([C:33]([OH:35])=[O:34])=[CH:31][CH:30]=2)=[O:28])=[C:5]([O:16][CH2:17][C:18]([N:20]2[CH2:21][CH2:22][O:23][CH2:24][CH2:25]2)=[O:19])[CH:4]=1
Reactant: CC(=O)c1ccc(C(=O)O)cc1
Reactant: COc1cc(OCC(=O)N2CCOCC2)c(C=O)cc1-c1cccs1
Product: COc1cc(OCC(=O)N2CCOCC2)c(/C=C/C(=O)c2ccc(C(=O)O)cc2)cc1-c1cccs1
Yield: 70 %

Procedure:
The title compound was prepared by condensing 4-methoxy-2-(2-morpholin-4-yl-2-oxo-ethoxy)-5-thiophen-2-yl-benzaldehyde (Ex-72A) and 4-acetylbenzoic acid in a similar manner as described in Ex-3. Orange solid, mp 231–233° C., 70% yield. 1H-NMR (300 MHz, DMSO-d6) δ 8.28–8.35 (m, 3H), 8.21 (s, 1H), 8.07–8.11 (m, 3H), 7.66 (d, 1H, J=3.3 Hz), 7.52 (d, 1H, J=5.1 Hz), 7.13 (dd, 1H, J=5.1, 3.3 Hz), 6.87 (s, 1H), 5.13 (s, 2H), 4.00 (s, 3H), 3.65 (brm, 4H), 3.54–3.55 (m, 4H). MS (EI) m/z=507 ([M]+, 100%). Anal. Calcd. for C27H25NO7S.½EtOH: C, 63.55; H, 5.61; N, 2.60; S, 5.95. Found: C, 63.13; H, 5.55; N, 2.53; S, 5.84.
Reaction SMILES: Cl[C:2]1[N:7]=[C:6]([O:8][CH2:9][C:10]([F:13])([F:12])[F:11])[CH:5]=[CH:4][N:3]=1.[CH3:14][N:15](C)C>C1(C)C=CC=CC=1>[C:14]([C:2]1[N:7]=[C:6]([O:8][CH2:9][C:10]([F:13])([F:12])[F:11])[CH:5]=[CH:4][N:3]=1)#[N:15]
Reactant: CN(C)C
Reactant: FC(F)(F)COc1ccnc(Cl)n1
Solvent: Cc1ccccc1
Product: N#Cc1nccc(OCC(F)(F)F)n1
Reaction time: 16 h
Yield: 77 %

Procedure:
The 2-chloro-4-(2,2,2-trifluoroethoxy)-pyrimidine (142 g) in toluene (330 ml) was added to trimethylamine (140 ml of a 45% aqueous solution) at 0° C. After stirring for 16 hours the organic phase was separated off. The aqueous phase was added to toluene (330 ml) then a solution potassium cyanide (44 g in 170 ml water) was added at 0° C. The reaction mixture was stirred for a further 16 hours and then the organic phase was separated, the aqueous was extracted with ether (2×200 ml) and the combined organic extracts were dried and concentrated to give 2-cyano-4-(2,2,2-trifluoroethoxy)-pyrimidine (73.5 g, 77% yield) as a yellow oil; 1H NMR (270 MHz): δ4.85(2H,q), 7.10(1H,d), 8.64(1H,d) ppm.
Reaction SMILES: [CH3:1][C@@H:2]1[CH2:6][O:5][C:4](=[O:7])[N:3]1[C:8]1[CH:16]=[CH:15][C:11]([C:12]([OH:14])=O)=[CH:10][CH:9]=1.[ClH:17].[CH2:18]([C:20]1[C:21]([N:27]2[CH2:32][CH2:31][NH:30][CH2:29][CH2:28]2)=[N:22][CH:23]=[C:24]([CH3:26])[CH:25]=1)[CH3:19]>>[ClH:17].[CH2:18]([C:20]1[C:21]([N:27]2[CH2:28][CH2:29][N:30]([C:12]([C:11]3[CH:10]=[CH:9][C:8]([N:3]4[C@H:2]([CH3:1])[CH2:6][O:5][C:4]4=[O:7])=[CH:16][CH:15]=3)=[O:14])[CH2:31][CH2:32]2)=[N:22][CH:23]=[C:24]([CH3:26])[CH:25]=1)[CH3:19]
Reactant: C[C@@H]1COC(=O)N1c1ccc(C(=O)O)cc1
Reactant: CCc1cc(C)cnc1N1CCNCC1
Agent: Cl
Product: CCc1cc(C)cnc1N1CCN(C(=O)c2ccc(N3C(=O)OC[C@H]3C)cc2)CC1
Yield: 66.8 %

Procedure:
By reaction and treatment in the same manner as in Example 87 and using (R)-4-(4-methyl-2-oxooxazolidin-3-yl)benzoic acid (332 mg) described in Preparation Example 37 and 1-(3-ethyl-5-methylpyridin-2-yl)piperazine hydrochloride (363 mg) described in Preparation Example 54, the title compound (446 mg) was obtained.
Reaction SMILES: Br[C:2]1[CH:7]=[CH:6][C:5]([CH2:8][C@@H:9]([NH:13][C:14]([O:16][C:17]([CH3:20])([CH3:19])[CH3:18])=[O:15])[C:10]([OH:12])=[O:11])=[CH:4][CH:3]=1.[Cl:21][C:22]1[CH:23]=[C:24](B(O)O)[CH:25]=[CH:26][CH:27]=1.C([O-])([O-])=O.[Na+].[Na+]>COCCOC.CCOC(C)=O.C1C=CC([P]([Pd]([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)[P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1>[C:17]([O:16][C:14]([NH:13][C@H:9]([CH2:8][C:5]1[CH:6]=[CH:7][C:2]([C:26]2[CH:25]=[CH:24][CH:23]=[C:22]([Cl:21])[CH:27]=2)=[CH:3][CH:4]=1)[C:10]([OH:12])=[O:11])=[O:15])([CH3:20])([CH3:19])[CH3:18]
Reactant: OB(O)c1cccc(Cl)c1
Reactant: CC(C)(C)OC(=O)N[C@H](Cc1ccc(Br)cc1)C(=O)O
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: [Na+]
Solvent: COCCOC
Solvent: CCOC(C)=O
Product: CC(C)(C)OC(=O)N[C@H](Cc1ccc(-c2cccc(Cl)c2)cc1)C(=O)O
Temperature: 25 °C

Procedure:
(R)-3-(4-Bromo-phenyl)-2-tert-butoxycarbonylamino-propionic acid (4.0 g, 11.6 mmol), 3-chlorophenylboronic acid (2.36 g, 15.11 mmol), Pd(PPh3)4 (0.067 g, 0.058 mmol) and 2M Na2CO3 aqueous solution (8.0 mL) are refluxed in 1,2-dimethoxyethane (70 mL) for 2.5 h under N2 atmosphere. After cooling to room temperature, the reaction mixture is diluted with EtOAc and washed with 1M HCl and brine. The organic layer is dried over Na2SO4 and concentrated. The residue is purified by flash column chromatography (silica gel, DCM/10% MeOH in DCM=100:0 to 0:100). to give (R)-2-tert-butoxycarbonylamino-3-(3′-chloro-biphenyl-4-yl)-propionic acid (containing impurities). HPLC retention time=1.56 minutes (condition A): MS (m+1)=376.
Reaction SMILES: [CH3:1][O:2][CH2:3][C@H:4]([CH3:31])[O:5][C:6]1[CH:7]=[C:8]([C:23]2[NH:27][C:26]([C:28](O)=[O:29])=[CH:25][CH:24]=2)[CH:9]=[C:10]([O:12][Si:13]([CH:20]([CH3:22])[CH3:21])([CH:17]([CH3:19])[CH3:18])[CH:14]([CH3:16])[CH3:15])[CH:11]=1.[NH2:32][C@H:33]([CH2:37][OH:38])[C@@H:34]([CH3:36])[OH:35].[Cl-].COC1N=C(OC)N=C([N+]2(C)CCOCC2)N=1>CO>[OH:38][CH2:37][C@@H:33]([NH:32][C:28]([C:26]1[NH:27][C:23]([C:8]2[CH:9]=[C:10]([O:12][Si:13]([CH:14]([CH3:15])[CH3:16])([CH:20]([CH3:22])[CH3:21])[CH:17]([CH3:18])[CH3:19])[CH:11]=[C:6]([O:5][C@@H:4]([CH3:31])[CH2:3][O:2][CH3:1])[CH:7]=2)=[CH:24][CH:25]=1)=[O:29])[C@H:34]([OH:35])[CH3:36]
Reactant: C[C@@H](O)[C@H](N)CO
Reactant: COC[C@H](C)Oc1cc(O[Si](C(C)C)(C(C)C)C(C)C)cc(-c2ccc(C(=O)O)[nH]2)c1
Agent: COc1nc(OC)nc([N+]2(C)CCOCC2)n1
Agent: [Cl-]
Solvent: CO
Product: COC[C@H](C)Oc1cc(O[Si](C(C)C)(C(C)C)C(C)C)cc(-c2ccc(C(=O)N[C@H](CO)[C@@H](C)O)[nH]2)c1
Temperature: 25 °C
Reaction time: 72 h
Yield: 85.7 %

Procedure:
5-{3-[(1S)-2-Methoxy-1-methylethoxy]-5-[(triisopropylsilyl)oxy]phenyl}-1H-pyrrole-2-carboxylic acid (2.05 g, 4.58 mmol) synthesized in Example (106c) was dissolved in methanol (20 mL), and commercially available L-threoninol (1.50 g, 14.27 mmol) and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride n hydrate (2.85 g, 10.30 mmol) were added, followed by stirring at room temperature for 3 days under nitrogen atmosphere. After the solvent was distilled off under reduced pressure, a saturated aqueous ammonium chloride solution (50 mL) was added, and extraction was carried out with methylene chloride (80 mL). The organic layer was washed with saturated brine, and subsequently dried over anhydrous magnesium sulfate. The resulting residue was purified using silica gel column chromatography (elution solvent: methanol/methylene chloride=3%-7%) to afford the desired compound (2.10 g, yield 86%) as a white foam.
Reaction SMILES: [C:1]1([C:7]2[C:16]3[C:11](=[CH:12][CH:13]=[CH:14][CH:15]=3)[CH:10]=[C:9]([C:17](O)=[O:18])[N:8]=2)[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.C(N(CC)CC)C.ClC(OCC)=O.[CH2:33]([NH:37][CH2:38][CH2:39][CH2:40][CH3:41])[CH2:34][CH2:35][CH3:36]>C1(C)C=CC=CC=1>[CH2:33]([N:37]([CH2:38][CH2:39][CH2:40][CH3:41])[C:17]([C:9]1[N:8]=[C:7]([C:1]2[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=2)[C:16]2[C:11]([CH:10]=1)=[CH:12][CH:13]=[CH:14][CH:15]=2)=[O:18])[CH2:34][CH2:35][CH3:36]
Reactant: O=C(O)c1cc2ccccc2c(-c2ccccc2)n1
Reactant: CCCCNCCCC
Agent: CCOC(=O)Cl
Solvent: Cc1ccccc1
Solvent: CCN(CC)CC
Product: CCCCN(CCCC)C(=O)c1cc2ccccc2c(-c2ccccc2)n1
Yield: 41.5 %

Procedure:
Operations are carried out as for Example 7, starting from 2.5 g of 1-phenyl isoquinoline 3-carboxylic acid, 1.15 g of triethylamine, 1.24 g of ethyl chloroformate and 1.66 g of dibutylamine in 100 ml of toluene. After chromatography and recrystallization in petroleum ether, 1.5 g of N,N-dibutyl 1-phenyl isoquinoline 3-carboxamide melting at 62° C. is obtained.
Reaction SMILES: [NH2:1][C:2]1[CH:17]=[CH:16][C:5]([C:6]([O:8][CH2:9][C:10]2[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=2)=[O:7])=[CH:4][C:3]=1[O:18][CH3:19].C([O-])([O-])=O.[K+].[K+].Cl[C:27]1[N:32]=[C:31]([Cl:33])[C:30]([C:34]([F:37])([F:36])[F:35])=[CH:29][N:28]=1>O1CCOCC1>[Cl:33][C:31]1[C:30]([C:34]([F:36])([F:35])[F:37])=[CH:29][N:28]=[C:27]([NH:1][C:2]2[CH:17]=[CH:16][C:5]([C:6]([O:8][CH2:9][C:10]3[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=3)=[O:7])=[CH:4][C:3]=2[O:18][CH3:19])[N:32]=1
Reactant: FC(F)(F)c1cnc(Cl)nc1Cl
Reactant: COc1cc(C(=O)OCc2ccccc2)ccc1N
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: C1COCCO1
Product: COc1cc(C(=O)OCc2ccccc2)ccc1Nc1ncc(C(F)(F)F)c(Cl)n1
Temperature: 130 °C

Procedure:
Benzyl 4-amino-3-methoxybenzoate (1.92 g, 6.8 mmol) and K2CO3 (2.38 g, 17 mmol) are suspended in 4 mL dioxane and then mixed with 2,4-dichloro-5-trifluoromethylpyrimidine (1.48 mL, 6.8 mmol). The suspension is then refluxed for 100 min with stirring in the oil bath (approx. 130° C.). Once the reaction has ended the reaction mixture is filtered, the filtrate is concentrated by rotary evaporation and purified by normal-phase column chromatography. The product-containing fractions of A-3a (HPLC-MS: tRet.=1.94 min; MS (m-H)−=436) are combined and concentrated by rotary evaporation.
Reaction SMILES: [CH2:1]([O:8][C:9](=[O:47])[CH:10]([NH:12][C:13](=[O:46])[CH:14]([CH2:33][C:34]1[CH:39]=[CH:38][C:37]([C:40]2[CH:45]=[CH:44][CH:43]=[CH:42][CH:41]=2)=[CH:36][CH:35]=1)[CH:15]=[P:16]([CH:18]([NH:21][C:22]([O:24][CH:25]([O:27][C:28](=[O:32])[CH:29]([CH3:31])[CH3:30])[CH3:26])=[O:23])[CH2:19]O)=[O:17])[CH3:11])[C:2]1C=CC=CC=1.Cl.C([O:51]C(=O)[C@H](C)N)C>>[CH2:1]([O:8][C:9](=[O:47])[CH:10]([NH:12][C:13](=[O:46])[CH:14]([CH2:33][C:34]1[CH:39]=[CH:38][C:37]([C:40]2[CH:41]=[CH:42][CH:43]=[CH:44][CH:45]=2)=[CH:36][CH:35]=1)[CH2:15][P:16]([OH:51])([CH:18]([NH:21][C:22]([O:24][CH:25]([O:27][C:28](=[O:32])[CH:29]([CH3:31])[CH3:30])[CH3:26])=[O:23])[CH3:19])=[O:17])[CH3:11])[CH3:2]
Reactant: CC(OC(=O)NC(CO)[P+]([O-])=CC(Cc1ccc(-c2ccccc2)cc1)C(=O)NC(C)C(=O)OCc1ccccc1)OC(=O)C(C)C
Reactant: CCOC(=O)[C@H](C)N
Agent: Cl
Product: CCOC(=O)C(C)NC(=O)C(Cc1ccc(-c2ccccc2)cc1)CP(=O)(O)C(C)NC(=O)OC(C)OC(=O)C(C)C

Procedure:
The compound from example 3 (500 mg) is coupled under the conditions in step 4 of example 3 with alanine ethyl ester hydrochloride (152 mg). The crude product obtained is chromatographed on silica gel using the 7:3:0.2 CH2Cl2/MeOH/AcOH mixture. White solid, 530 mg (88%).
Reaction SMILES: Br[C:2]1[CH:7]=[CH:6][C:5]([C:8]2[C:9]3[N:10]([N:14]=[C:15]([Cl:17])[N:16]=3)[CH:11]=[CH:12][CH:13]=2)=[CH:4][CH:3]=1.[CH3:18][N:19]1[CH2:24][CH2:23][N:22]([CH:25]2[CH2:30][CH2:29][NH:28][CH2:27][CH2:26]2)[CH2:21][CH2:20]1>>[Cl:17][C:15]1[N:16]=[C:9]2[C:8]([C:5]3[CH:6]=[CH:7][C:2]([N:28]4[CH2:27][CH2:26][CH:25]([N:22]5[CH2:21][CH2:20][N:19]([CH3:18])[CH2:24][CH2:23]5)[CH2:30][CH2:29]4)=[CH:3][CH:4]=3)=[CH:13][CH:12]=[CH:11][N:10]2[N:14]=1
Reactant: CN1CCN(C2CCNCC2)CC1
Reactant: Clc1nc2c(-c3ccc(Br)cc3)cccn2n1
Product: CN1CCN(C2CCN(c3ccc(-c4cccn5nc(Cl)nc45)cc3)CC2)CC1

Procedure:
2-Chloro-8-{4-[4-(4-methyl-piperazin-1-yl)-piperidin-1-yl]-phenyl}-[1,2,4]triazolo[1,5-a]pyridine was prepared from 8-(4-bromo-phenyl)-2-chloro-[1,2,4]triazolo[1,5-a]pyridine (100.0 mg, 0.3241 mmol) and 1-methyl-4-piperidin-4-yl-piperazine (66.0 mg, 0.360 mmol) in a manner analogous to Example 2d. Product isolated as a pale yellow solid (0.023 g, 17%). 1H NMR (400 MHz, CDCl3, δ, ppm): 8.40 (d, J=6.7 Hz, 1H), 7.93 (d, J=8.0 Hz, 2H), 7.64 (d, J=7.4 Hz, 1H), 7.10 (t, J=6.8 Hz, 1H), 7.03 (d, J=8.3 Hz, 2H), 3.87 (d, J=12.5 Hz, 2H), 2.82 (t, J=12.6 Hz, 2H), 2.70-2.35 (m, 9H), 2.30 (s, 3H), 1.95 (d, J=11.9 Hz, 2H), 1.75-1.60 (m, 2H). MS=411 (MH)+.
Reaction SMILES: O[CH2:2][CH2:3][CH:4]1[O:9][CH2:8][CH2:7][N:6]([C:10]([O:12][CH2:13][C:14]2[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=2)=[O:11])[CH2:5]1.CN(C)C=O.S(Cl)([Cl:27])=O>C(Cl)(Cl)Cl>[Cl:27][CH2:2][CH2:3][CH:4]1[O:9][CH2:8][CH2:7][N:6]([C:10]([O:12][CH2:13][C:14]2[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=2)=[O:11])[CH2:5]1
Reactant: O=S(Cl)Cl
Reactant: O=C(OCc1ccccc1)N1CCOC(CCO)C1
Solvent: ClC(Cl)Cl
Solvent: CN(C)C=O
Product: O=C(OCc1ccccc1)N1CCOC(CCCl)C1

Procedure:
To a mixture of 2-(2-hydroxyethyl)-4-benzyloxycarbonylmorpholine (15 g), dimethylformamide (1 ml), and chloroform (50 ml) is dropwise added thionyl chloride (16.3 ml). The mixture is refluxed for 2 hours, allowed to cool, and evaporated under reduced pressure to give the title compound (16 g) as an oil.
Reaction SMILES: [Br:1][C:2]1[S:6][C:5]([C:7]([O:9]CC)=[O:8])=[C:4]([C:12]2[CH:17]=[CH:16][C:15]([Cl:18])=[CH:14][C:13]=2[Cl:19])[C:3]=1[C:20]#[N:21].O.[OH-].[Na+]>O1CCCC1>[Br:1][C:2]1[S:6][C:5]([C:7]([OH:9])=[O:8])=[C:4]([C:12]2[CH:17]=[CH:16][C:15]([Cl:18])=[CH:14][C:13]=2[Cl:19])[C:3]=1[C:20]#[N:21]
Reactant: CCOC(=O)c1sc(Br)c(C#N)c1-c1ccc(Cl)cc1Cl
Agent: [Na+]
Agent: [OH-]
Solvent: O
Solvent: C1CCOC1
Product: N#Cc1c(Br)sc(C(=O)O)c1-c1ccc(Cl)cc1Cl
Temperature: 25 °C
Reaction time: 8 h

Procedure:
Ethyl 5-bromo-4-cyano-3-(2,4-dichlorophenyl)thiophene-2-carboxylate (4.60 g, 0.0114 mol) was dissolved in Tetrahydrofuran (100 mL) and Water (20 mL) and 1.00 M of Sodium hydroxide in Water (34.1 mL, 0.0341 mol) was added The mixture was stirred at room temperature overnight. Reaction was quenched by addition of 1N HCl (36 mL), extracted with EA (3×), dried MgSO4, filtered and evaporated to give the product that was used without further purification (4.28 g, 100%). LCMS: (FA) ES−, 374, 376, 378. 1H NMR (400 MHz, d1-chloroform) δ: 7.52 (d, J=1.99 Hz, 1H), 7.35 (dd, J=8.28, 2.02 Hz, 1H), 7.21 (d, J=8.27 Hz, 1H).
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[C:6]([F:8])[CH:5]=[CH:4][C:3]=1[C:9]1[N:13]([CH3:14])[N:12]=[C:11]([CH3:15])[C:10]=1[N+:16]([O-])=O.[Cl-].[NH4+]>C(O)C.C(OCC)(=O)C.[Fe]>[Cl:1][C:2]1[CH:7]=[C:6]([F:8])[CH:5]=[CH:4][C:3]=1[C:9]1[N:13]([CH3:14])[N:12]=[C:11]([CH3:15])[C:10]=1[NH2:16]
Reactant: Cc1nn(C)c(-c2ccc(F)cc2Cl)c1[N+](=O)[O-]
Agent: [Fe]
Agent: [Cl-]
Agent: [NH4+]
Solvent: CCOC(C)=O
Solvent: CCO
Product: Cc1nn(C)c(-c2ccc(F)cc2Cl)c1N
Temperature: 80 °C

Procedure:
A mixture of 5-(2-chloro-4-fluorophenyl)-1,3-dimethyl-4-nitro-1H-pyrazole (i.e. the product of Step A) (0.2 g, 0.74 mmol), iron powder (0.2 g, 3.6 mmol) and saturated aqueous ammonium chloride solution (1 mL) in ethanol (5 mL) was heated at 80° C. for 4 h. After cooling to room temperature, the reaction mixture was diluted with ethyl acetate and filtered through a pad of Celite® (diatomaceous earth) on a sintered glass frit funnel. The filtrate was concentrated under reduced pressure and the resulting material was purified by silica gel column chromatography (ethyl acetate as eluant) to provide the title compound (0.14 g).
Reaction SMILES: C[O:2][C:3](=[O:41])[C:4]([CH3:40])([CH3:39])[CH2:5][CH2:6][O:7][C:8]1[CH:13]=[CH:12][C:11]([C:14]([N:16]2[C:25]3[C:20](=[CH:21][CH:22]=[CH:23][CH:24]=3)[C@H:19]([N:26]([C:34](=[O:36])[CH3:35])[C:27]3[CH:32]=[CH:31][C:30]([Cl:33])=[CH:29][CH:28]=3)[CH2:18][C@@H:17]2[CH3:37])=[O:15])=[CH:10][C:9]=1[F:38].[OH-].[Li+].Cl>CO.C1COCC1>[C:34]([N:26]([C:27]1[CH:28]=[CH:29][C:30]([Cl:33])=[CH:31][CH:32]=1)[C@H:19]1[C:20]2[C:25](=[CH:24][CH:23]=[CH:22][CH:21]=2)[N:16]([C:14]([C:11]2[CH:12]=[CH:13][C:8]([O:7][CH2:6][CH2:5][C:4]([CH3:40])([CH3:39])[C:3]([OH:41])=[O:2])=[C:9]([F:38])[CH:10]=2)=[O:15])[C@@H:17]([CH3:37])[CH2:18]1)(=[O:36])[CH3:35]
Reactant: COC(=O)C(C)(C)CCOc1ccc(C(=O)N2c3ccccc3[C@H](N(C(C)=O)c3ccc(Cl)cc3)C[C@@H]2C)cc1F
Agent: Cl
Agent: [Li+]
Agent: [OH-]
Solvent: CO
Solvent: C1CCOC1
Product: CC(=O)N(c1ccc(Cl)cc1)[C@@H]1C[C@H](C)N(C(=O)c2ccc(OCCC(C)(C)C(=O)O)c(F)c2)c2ccccc21
Reaction time: 1 h

Procedure:
(2S,4R)-4-(4-{4-[Acetyl-(4-chloro-phenyl)-amino]-2-methyl-3,4-dihydro-2H-quinoline-1-carbonyl}-2-fluoro-phenoxy)-2,2-dimethyl-butyric acid methyl ester (100 mg) was dissolved in methanol/THF (1:1, 5 mL), and lithium hydroxide (1.0N, 1 mL) was added. After 1 hour, the reaction was acidified (HCl) and extracted from with methylene chloride. The organic layer was dried, filtered, and concentrated. The crude residue was purified by silica gel chromatography ethyl acetate-5% MeOH/ethylacetate gradient) to afford the product.
Reaction SMILES: [CH2:1]([O:8][C:9]([NH:11][C@H:12]([C:16]([O:18][CH:19]1[CH2:24][CH2:23][CH:22]([C:25]([O:27][CH2:28]Cl)=[O:26])[CH2:21][CH2:20]1)=[O:17])[CH:13]([CH3:15])[CH3:14])=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[I-:30].[Na+]>CC(C)=O>[CH2:1]([O:8][C:9]([NH:11][C@H:12]([C:16]([O:18][CH:19]1[CH2:24][CH2:23][CH:22]([C:25]([O:27][CH2:28][I:30])=[O:26])[CH2:21][CH2:20]1)=[O:17])[CH:13]([CH3:15])[CH3:14])=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: [I-]
Reactant: CC(C)[C@H](NC(=O)OCc1ccccc1)C(=O)OC1CCC(C(=O)OCCl)CC1
Agent: [Na+]
Solvent: CC(C)=O
Product: CC(C)[C@H](NC(=O)OCc1ccccc1)C(=O)OC1CCC(C(=O)OCI)CC1
Temperature: 25 °C
Reaction time: 8 h

Procedure:
To a solution of chloromethyl 4-(N-benzyloxycarbonyl-L-valyloxy)-cyclohexanoate (4.0 g, 9.4 mmole) in dry acetone (50 ml) was added sodium iodide (6.3 g, 42 mmole) and the mixture was stirred overnight at room temperature. The mixture was evaporated under reduced pressure and extracted with ethyl actate water. The organic phase was washed with a 5% sodium thiosulfate solution, dried with sodium sulfate and evaporated under reduced pressure. Yield 4.5 g=93%.
Reaction SMILES: [N+:1]([C:4]1[CH:9]=[CH:8][C:7]([N:10]2[CH2:15][CH2:14][NH:13][CH2:12][CH2:11]2)=[CH:6][CH:5]=1)([O-:3])=[O:2].[Na].[CH3:17][C:18]([CH3:20])=O.O>ClCCCl>[CH:18]([N:13]1[CH2:14][CH2:15][N:10]([C:7]2[CH:6]=[CH:5][C:4]([N+:1]([O-:3])=[O:2])=[CH:9][CH:8]=2)[CH2:11][CH2:12]1)([CH3:20])[CH3:17]
Reactant: CC(C)=O
Reactant: O=[N+]([O-])c1ccc(N2CCNCC2)cc1
Agent: [Na]
Solvent: O
Solvent: ClCCCl
Product: CC(C)N1CCN(c2ccc([N+](=O)[O-])cc2)CC1
Temperature: 25 °C
Reaction time: 32 h

Procedure:
A suspension of 1-(4-nitrophenyl)piperazine (20 g, 190 mmol, 2 eq), sodium triaectoxyborohydride (41 g, 97 mmol, 2 eq), and acetone (18.8 g, 21.3 mL, 290 mmol, 3 eq) in DCE (400 mL) is stirred in a water bath at rt for 32 h. Water (100 mL) is slowly added (gas evolution) and resulting biphasic solution is stirred for 1 h. The phases are separated and the DCE extract is washed with water (2×100 mL). The combined aqueous extracts are extracted with DCE (2×50 mL), and the combined DCE extracts are filtered through a phase separation tube. The filtrate is concentrated on a rotary evaporator and the yellow oil obtained dried under vacuum for a further 2 h. The oily product obtained solidified on standing to provide 1-isopropyl-4-(4-nitrophenyl)piperazine as a yellow solid (16.5 g, 66% recovery). The product is used in the next step without further purification. LCMS Purity: 80% by ELS detection; LCMS-ESI (m/z): calcd for C13H19N3O2 249.1; [M+H]+ found, 250.3.
Reaction SMILES: [CH2:1]([N:3]([CH2:27][CH3:28])[CH2:4][CH2:5][O:6][C:7]1[CH:26]=[CH:25][C:10]([O:11][CH:12]2[CH2:17][CH2:16][N:15](C(OC(C)(C)C)=O)[CH2:14][CH2:13]2)=[CH:9][CH:8]=1)[CH3:2].FC(F)(F)C(O)=O>ClCCl>[CH2:27]([N:3]([CH2:1][CH3:2])[CH2:4][CH2:5][O:6][C:7]1[CH:26]=[CH:25][C:10]([O:11][CH:12]2[CH2:17][CH2:16][NH:15][CH2:14][CH2:13]2)=[CH:9][CH:8]=1)[CH3:28]
Reactant: CCN(CC)CCOc1ccc(OC2CCN(C(=O)OC(C)(C)C)CC2)cc1
Solvent: O=C(O)C(F)(F)F
Solvent: ClCCl
Product: CCN(CC)CCOc1ccc(OC2CCNCC2)cc1
Temperature: 25 °C

Procedure:
10.1 g tert-butyl 4-[4-(2-diethylaminoethoxy)-phenoxy]-piperidine-1-carboxylate are placed in 20 ml dichloromethane and combined with 30 ml trifluoroacetic acid while being cooled. The reaction mixture is stirred at ambient temperature. After 2 hours the reaction mixture is evaporated to dryness. The residue is combined with an NaOH solution (1M) and the product is extracted with dichloromethane. 5.6 g (V-3) are obtained.
Reaction SMILES: O1CCCC1.[NH2:6][C:7]1[S:11][N:10]=[C:9]([C:12](=[N:16][O:17][CH3:18])[C:13](Cl)=[O:14])[N:8]=1.Cl.[NH2:20][CH:21]1[C:46](=[O:47])[N:23]2[C:24]([C:30]([O:32][CH:33]([C:40]3[CH:45]=[CH:44][CH:43]=[CH:42][CH:41]=3)[C:34]3[CH:39]=[CH:38][CH:37]=[CH:36][CH:35]=3)=[O:31])=[C:25]([CH2:28][Cl:29])[CH2:26][S:27][C@H:22]12.C(=O)([O-])O.[Na+]>O>[NH2:6][C:7]1[S:11][N:10]=[C:9]([C:12](=[N:16][O:17][CH3:18])[C:13]([NH:20][CH:21]2[C:46](=[O:47])[N:23]3[C:24]([C:30]([O:32][CH:33]([C:34]4[CH:35]=[CH:36][CH:37]=[CH:38][CH:39]=4)[C:40]4[CH:45]=[CH:44][CH:43]=[CH:42][CH:41]=4)=[O:31])=[C:25]([CH2:28][Cl:29])[CH2:26][S:27][C@H:22]23)=[O:14])[N:8]=1
Reactant: CON=C(C(=O)Cl)c1nsc(N)n1
Reactant: NC1C(=O)N2C(C(=O)OC(c3ccccc3)c3ccccc3)=C(CCl)CS[C@H]12
Agent: Cl
Agent: O=C([O-])O
Agent: [Na+]
Solvent: O
Solvent: C1CCOC1
Product: CON=C(C(=O)NC1C(=O)N2C(C(=O)OC(c3ccccc3)c3ccccc3)=C(CCl)CS[C@H]12)c1nsc(N)n1
Temperature: -15 °C
Reaction time: 1 h
Yield: 98.3 %

Procedure:
To a mixed solution of dichlorometahne (1000 ml) and tetrahydrofuran (200 ml) were added 2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(methoxyimino)acetyl chloride (syn isomer) (64 g) and benzhydryl 7-amino-3-chloromethyl-3-cephem-4-carboxylate hydrochloride (100 g) at -15° C. The mixture was stirred at -15° C. for one hour. The reaction mixture was poured into ice-cooled water, and neutralized with sodium hydrogencarbonate. The organic layer was separated, dried over magnesium sulfate and evaporated in vacuo. The residue was triturated with diisopropyl ether to give benzhydryl 7-[2-(5-amino-1,2,4-thiadiazol-3-yl)-2-methoxyiminoacetamido]-3-chloromethyl-3-cephem-4-carboxylate (syn isomer) (130.5 g)
Reaction SMILES: [CH3:1][C:2]1[N:6]=[C:5]([C:7]2[S:11][C:10]([NH2:12])=[N:9][C:8]=2[C:13]2[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=2)[O:4][N:3]=1.[C:19]1([CH2:25][C:26](Cl)=[O:27])[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=1>>[CH3:1][C:2]1[N:6]=[C:5]([C:7]2[S:11][C:10]([NH:12][C:26](=[O:27])[CH2:25][C:19]3[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=3)=[N:9][C:8]=2[C:13]2[CH:14]=[CH:15][CH:16]=[CH:17][CH:18]=2)[O:4][N:3]=1
Reactant: Cc1noc(-c2sc(N)nc2-c2ccccc2)n1
Reactant: O=C(Cl)Cc1ccccc1
Product: Cc1noc(-c2sc(NC(=O)Cc3ccccc3)nc2-c2ccccc2)n1

Procedure:
Prepared from 5-(3-methyl-[1,2,4]oxadiazol-5-yl)-4-phenyl-thiazol-2-ylamine and phenyl-acetyl chloride.
Reaction SMILES: Br[CH2:2][CH:3]1[O:8][C:7]2[CH:9]=[CH:10][CH:11]=[CH:12][C:6]=2[O:5][CH2:4]1.[NH:13]1[CH2:18][CH2:17][CH2:16][CH:15]([C:19]2[CH:24]=[CH:23][C:22]([OH:25])=[CH:21][CH:20]=2)[CH2:14]1.Br>C(#N)C>[O:8]1[C:7]2[CH:9]=[CH:10][CH:11]=[CH:12][C:6]=2[O:5][CH2:4][CH:3]1[CH2:2][N:13]1[CH2:18][CH2:17][CH2:16][CH:15]([C:19]2[CH:20]=[CH:21][C:22]([OH:25])=[CH:23][CH:24]=2)[CH2:14]1
Reactant: Oc1ccc(C2CCCNC2)cc1
Reactant: BrCC1COc2ccccc2O1
Agent: Br
Solvent: CC#N
Product: Oc1ccc(C2CCCN(CC3COc4ccccc4O3)C2)cc1

Procedure:
A mixture of 2-bromomethyl-2,3-dihydrobenzo[1,4]dioxine (47 mg, 0.20 mmol), 4-(piperidin-3-yl)phenol.HBr (53 mg, 0.20 mmol) and KHCO3 (84 mg, 0.84 mmol) in acetonitrile (2 mL) was heated in a microwave reactor at 160° C. for 6.5 h. The mixture was absorbed on silica and purified by flash chromatography using a gradient of DCM and MeOH as eluent to give 6 mg of the title compound.