Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: Cl.[CH2:2]([N:9]([CH2:13][CH2:14]Cl)[CH2:10][CH2:11]Cl)[C:3]1[CH:8]=[CH:7][CH:6]=[CH:5][CH:4]=1.[C:16]([N:23]1[CH2:27][CH2:26][C@H:25]([NH2:28])[CH2:24]1)([O:18][C:19]([CH3:22])([CH3:21])[CH3:20])=[O:17].C(=O)(O)[O-].[Na+]>C(O)C>[CH2:2]([N:9]1[CH2:13][CH2:14][N:28]([C@H:25]2[CH2:26][CH2:27][N:23]([C:16]([O:18][C:19]([CH3:22])([CH3:21])[CH3:20])=[O:17])[CH2:24]2)[CH2:11][CH2:10]1)[C:3]1[CH:8]=[CH:7][CH:6]=[CH:5][CH:4]=1
Reactant: ClCCN(CCCl)Cc1ccccc1
Reactant: CC(C)(C)OC(=O)N1CC[C@H](N)C1
Agent: Cl
Agent: O=C([O-])O
Agent: [Na+]
Solvent: CCO
Product: CC(C)(C)OC(=O)N1CC[C@H](N2CCN(Cc3ccccc3)CC2)C1

Procedure:
6.23 g (26.8 mmol) of benzylbis(2-chloroethyl)amine hydrochloride were dissolved in ethanol (100 ml) and, while stirring, 5.00 g (26.8 mmol) of (S)-(−)-N-Boc-3-aminopyrrolidine and 9.02 g (107 mmol) of sodium bicarbonate were added. The resulting reaction solution was heated under reflux for 4 h. The cooled reaction mixture was concentrated in vacuo, 100 ml of water were added, and the aqueous phase was extracted with ethyl acetate (4×60 ml). The combined organic phases were washed with saturated aqueous NaHCO3 solution, dried over magnesium sulfate and concentrated in vacuo. The residue was purified by chromatography on silica gel (mobile phase gradient 0-5% methanol in dichloromethane). Yield: 6.99 g (75%) of yellow solid
Reaction SMILES: [CH3:1][O:2][C:3]([C@H:6]1[CH2:11][CH2:10][C@H:9]([O:12]C2CCCCO2)[CH2:8][CH2:7]1)([CH3:5])[CH3:4].CC1C=CC(S(O)(=O)=O)=CC=1>CO>[CH3:1][O:2][C:3]([C@H:6]1[CH2:7][CH2:8][C@H:9]([OH:12])[CH2:10][CH2:11]1)([CH3:5])[CH3:4]
Reactant: COC(C)(C)[C@H]1CC[C@H](OC2CCCCO2)CC1
Agent: Cc1ccc(S(=O)(=O)O)cc1
Solvent: CO
Product: COC(C)(C)[C@H]1CC[C@H](O)CC1
Temperature: 25 °C
Reaction time: 2 h

Procedure:
To a solution of 2-((trans)-4-(2-methoxypropan-2-yl)cyclohexyloxy)tetrahydro-2H-pyran (1.2 g, 4.7 mmol) in MeOH (10 mL) was added p-TsOH (8.9 g, 4.7 mmol, 1.0 eq) slowly at rt. Then the mixture was stirred at rt for 2 h, and the solvent was removed in vacuo. The residue was purified on silica gel (EA/PE=1:3) to give the title compound as a colorless oil (660 mg, yield: 82%). 1H NMR (400 MHz, CDCl3) δ: 4.07-4.05 (m, 1H), 3.17 (s, 3H), 1.87-1.82 (m, 2H), 1.55-1.38 (m, 7H), 1.10 (s, 6H).
Reaction SMILES: [C:1]([NH:5][C:6](=[O:27])[CH2:7][N:8]1[C:14]2[CH:15]=[CH:16][CH:17]=[CH:18][C:13]=2[CH:12]([C:19]2[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=2)[CH2:11][CH:10]([NH2:25])[C:9]1=[O:26])([CH3:4])([CH3:3])[CH3:2].[C:28]1([CH3:37])[CH:33]=[CH:32][CH:31]=[C:30]([N:34]=[C:35]=[O:36])[CH:29]=1>C(Cl)Cl>[C:1]([NH:5][C:6](=[O:27])[CH2:7][N:8]1[C:14]2[CH:15]=[CH:16][CH:17]=[CH:18][C:13]=2[CH:12]([C:19]2[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=2)[CH2:11][CH:10]([NH:25][C:35]([NH:34][C:30]2[CH:29]=[C:28]([CH3:37])[CH:33]=[CH:32][CH:31]=2)=[O:36])[C:9]1=[O:26])([CH3:4])([CH3:2])[CH3:3]
Reactant: CC(C)(C)NC(=O)CN1C(=O)C(N)CC(c2ccccc2)c2ccccc21
Reactant: Cc1cccc(N=C=O)c1
Solvent: ClCCl
Product: Cc1cccc(NC(=O)NC2CC(c3ccccc3)c3ccccc3N(CC(=O)NC(C)(C)C)C2=O)c1
Reaction time: 0.25 h
Yield: 88 %

Procedure:
To a 25 ml round-bottomed flask equipped with N2 inlet were added N-tert-butyl-2-[3-amino-2-oxo-5-phenyl-2,3,4,5-tetrahydro-1H-(1)benzazepin-1-yl] ethanoic acid amide (0.50 g, 1.368 mmoles)and 10 ml methylene chloride under nitrogen, and the reaction cooled in an ice bath. A solution of m-tolyl isocyanate (0.194 ml, 1.5 mmol) in 5 ml methylene chloride was then added dropwise. A solid formed immediately. Stirring was continued for 15 minutes and then the ice bath removed, allowing the reaction to come to room temperature for several hours. The solid was filtered and washed with methylene chloride/hexane (1:1), yielding 600 mg (87.9%) of product, mp 263°-266° C.
Reaction SMILES: [CH2:1]([O:8][C:9]([NH:11][C:12]1[C:17](=[O:18])[N:16]([CH2:19][C:20](O)=[O:21])[C:15]([C:23]2[CH:28]=[CH:27][CH:26]=[CH:25][CH:24]=2)=[N:14][CH:13]=1)=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[NH2:29][CH:30]([CH2:37][C:38]1[CH:43]=[CH:42][CH:41]=[CH:40][CH:39]=1)[CH:31]([OH:36])[C:32]([F:35])([F:34])[F:33].CCN=C=NCCCN(C)C.Cl.C1C=CC2N(O)N=NC=2C=1>CN(C=O)C>[CH2:1]([O:8][C:9]([NH:11][C:12]1[C:17](=[O:18])[N:16]([CH2:19][C:20]([NH:29][CH:30]([CH2:37][C:38]2[CH:43]=[CH:42][CH:41]=[CH:40][CH:39]=2)[C:31](=[O:36])[C:32]([F:33])([F:34])[F:35])=[O:21])[C:15]([C:23]2[CH:28]=[CH:27][CH:26]=[CH:25][CH:24]=2)=[N:14][CH:13]=1)=[O:10])[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: O=C(O)Cn1c(-c2ccccc2)ncc(NC(=O)OCc2ccccc2)c1=O
Reactant: NC(Cc1ccccc1)C(O)C(F)(F)F
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: CN(C)C=O
Product: O=C(Cn1c(-c2ccccc2)ncc(NC(=O)OCc2ccccc2)c1=O)NC(Cc1ccccc1)C(=O)C(F)(F)F

Procedure:
To a solution of (5-benzyloxycarbonylamino-6-oxo-2-phenyl-1,6-dihydro-1-pyrimidinyl)acetic acid (title compound in Reference Example 2, 8.57 g, 22.6 mmol) and 3-amino-1,1,1-trifluoro-4-phenyl-2-butanol (title compound in Reference Example 1, 5.91 g, 27.2 mmol) in DMF (75 mL) were added WSCI hydrochloride (5.20 g, 27.2 mmol) and HOBT (6.10 g, 45.1 mmol). The resulting mixture was stirred at room temperature for 16 h, poured into 0.5N hydrochloric acid (500 mL), and then extracted with ethyl acetate. The extract was washed with saturated aqueous sodium hydrogencarbonate solution and saturated brine, and dried over anhydrous magnesium sulfate. The residue obtained by concentration of the extract was separated and purified by silica gel column chromatography (chloroform-ethyl acetate, 83:17) to give 11.4 g (87%) of 2-(5-benzyloxycarbonylamino-6-oxo-2-phenyl-1,6-dihydro-1-pyrimidyl)-N-(1-benzyl-3,3,3-trifluoro-2-hydroxypropyl)-acetamide as colorless crystals.
Reaction SMILES: [NH2:1][C@H:2]([C:8]([NH:10][C@H:11]([C:18]([OH:20])=[O:19])[CH2:12][C:13]1[N:17]=[CH:16][NH:15][CH:14]=1)=[O:9])[CH2:3][CH2:4][C:5](=[O:7])[OH:6].C([O-])(O)=O.[Na+].[CH3:26][C:27]1[CH:32]=[CH:31][C:30]([S:33](Cl)(=[O:35])=[O:34])=[CH:29][CH:28]=1>O.O1CCOCC1>[NH2:1][C@H:2]([C:8]([NH:10][C@H:11]([C:18]([OH:20])=[O:19])[CH2:12][C:13]1[N:17]=[CH:16][N:15]([S:33]([C:30]2[CH:31]=[CH:32][C:27]([CH3:26])=[CH:28][CH:29]=2)(=[O:35])=[O:34])[CH:14]=1)=[O:9])[CH2:3][CH2:4][C:5](=[O:6])[OH:7]
Reactant: Cc1ccc(S(=O)(=O)Cl)cc1
Reactant: N[C@@H](CCC(=O)O)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O
Agent: O=C([O-])O
Agent: [Na+]
Solvent: O
Solvent: C1COCCO1
Product: Cc1ccc(S(=O)(=O)n2cnc(C[C@H](NC(=O)[C@@H](N)CCC(=O)O)C(=O)O)c2)cc1
Temperature: 25 °C

Procedure:
3 g (10 mmols) of Glu-His-OH and 2.3 g of NaHCO3 are dissolved in 20 ml of water and, while stirring at room temperature, a solution of 2.1 g (10% excess) of p-toluene sulfochloride in about 10 ml of dioxane is slowly added drop by drop. When the addition is terminated, stirring of the mixture is continued for a further hour, whereupon it is extracted twice with ether. The aqueous phase is acidified to pH 2 with 2 N HCl and the precipitate is filtered off with suction. It is washed with water and the filer residue is dried over P2O5 under reduced pressure. Yield 2.2 g.
Reaction SMILES: Cl[C:2]1[C:3]([O:8][CH:9]2[CH2:12][N:11]([C:13]3[CH:22]=[CH:21][C:20]4[C:15](=[CH:16][CH:17]=[CH:18][CH:19]=4)[N:14]=3)[CH2:10]2)=[N:4][CH:5]=[CH:6][N:7]=1.C(N(CC)CC)C.[CH2:30]([OH:33])[C:31]#[CH:32]>[Cu]I>[N:14]1[C:15]2[C:20](=[CH:19][CH:18]=[CH:17][CH:16]=2)[CH:21]=[CH:22][C:13]=1[N:11]1[CH2:12][CH:9]([O:8][C:3]2[C:2]([C:32]#[C:31][CH2:30][OH:33])=[N:7][CH:6]=[CH:5][N:4]=2)[CH2:10]1
Reactant: Clc1nccnc1OC1CN(c2ccc3ccccc3n2)C1
Reactant: C#CCO
Agent: [Cu]I
Solvent: CCN(CC)CC
Product: OCC#Cc1nccnc1OC1CN(c2ccc3ccccc3n2)C1
Temperature: 110 °C
Reaction time: 2 h
Yield: 600 %

Procedure:
A microwave tube was charged with 2-(3-((3-chloropyrazin-2-yl)oxy)azetidin-1-yl)quinoline (see PREPARATION P2.6; 150 mg, 0.5 mmol), triethylamine (100 mg, 1.0 mmol), CuI (10 mg, 0.05 mmol), Pd (PPh3)2Cl2 (35 mg, 0.05 mmol), prop-2-yn-1-ol (28 mg, 0.05 mmol). After several cycles of vacuum/purge with argon, 2 mL of DMF are added. The reaction mixture is then stirred at 110° C. under microwave for 2 hours. The reaction mixture is poured onto a solution of NaHCO3 and diluted with EtOAc and the layers are separated. The organic extracts were washed with water (10 mL) and brine (10 mL), dried over Na2SO4, and filtered. The filtrate was evaporated in vacuo and the residue was purified by flash column chromatography on silica gel (5% to 30% EtOAc in petroleum ether) to give the title product (99 mg, 0.3 mmol, 61% yield) as white solid. ESI-MS (M+1): 333 calc. for C19H16N4O2 332.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([S:9]([NH:12][C:13]2[CH:14]=[C:15]3[C:19](=[CH:20][CH:21]=2)[NH:18][C:17]([C:22]([O:24]CC)=[O:23])=[CH:16]3)(=[O:11])=[O:10])[CH:5]=[C:6]([Cl:8])[CH:7]=1.[OH-].[Na+].Cl>O1CCCC1.O>[Cl:1][C:2]1[CH:3]=[C:4]([S:9]([NH:12][C:13]2[CH:14]=[C:15]3[C:19](=[CH:20][CH:21]=2)[NH:18][C:17]([C:22]([OH:24])=[O:23])=[CH:16]3)(=[O:10])=[O:11])[CH:5]=[C:6]([Cl:8])[CH:7]=1
Reactant: CCOC(=O)c1cc2cc(NS(=O)(=O)c3cc(Cl)cc(Cl)c3)ccc2[nH]1
Agent: Cl
Agent: [Na+]
Agent: [OH-]
Solvent: C1CCOC1
Solvent: O
Product: O=C(O)c1cc2cc(NS(=O)(=O)c3cc(Cl)cc(Cl)c3)ccc2[nH]1
Temperature: 25 °C
Reaction time: 48 h

Procedure:
100 mg ethyl 5-(3,5-dichloro-phenylsulphonylamino)-1H-indole-2-carboxylate are dissolved in 2 ml of tetrahydrofuran, combined with 2 ml 1 N sodium hydroxide solution and stirred for 48 hours at ambient temperature. Then the tetrahydrofuran is eliminated in vacuo, diluted with some water and combined with 2 ml of 2 N hydrochloric acid. The solid is suction filtered, washed with water and dried in vacuo.
Reaction SMILES: [Cl:1][C:2]1[C:7]2[C:8](=[O:24])[N:9]([CH3:23])[CH2:10][C:11]3[N:12]([CH:13]=[N:14][C:15]=3[C:16]([N:18]3C=C[N:20]=[CH:19]3)=[O:17])[C:6]=2[CH:5]=[CH:4][CH:3]=1>CN(C)C=O>[Cl:1][C:2]1[C:7]2[C:8](=[O:24])[N:9]([CH3:23])[CH2:10][C:11]3[N:12]([CH:13]=[N:14][C:15]=3[C:16]3[O:17][N:20]=[C:19]([CH2:8][CH2:7][CH2:2][CH2:3][CH2:4][CH2:5][CH3:6])[N:18]=3)[C:6]=2[CH:5]=[CH:4][CH:3]=1
Reactant: CN1Cc2c(C(=O)n3ccnc3)ncn2-c2cccc(Cl)c2C1=O
Solvent: CN(C)C=O
Product: CCCCCCCc1noc(-c2ncn3c2CN(C)C(=O)c2c(Cl)cccc2-3)n1

Procedure:
6.80 g (20 mmol) of 1-[[7-chloro-5,6-dihydro-5-methyl-6-oxo-4H-imidazo[1,5-a][1,4]benzodiazepin-3-yl]carbonyl]imidazole, 50 ml of N,N-dimethylformamide and 3.2 g (20 mmol) of heptanecarboxamidoxime are stirred at 100° overnight. The solution is then evaporated and the residue is dissolved in methylene chloride. The organic solution is washed with water and the solvent is evaporated. By chromatography of the residue on silica gel while eluting with ethyl acetate and subsequent recrystallization from ethyl acetate there is obtained 7-chloro-3-(3-heptyl-1,2,4-oxadiazol-5-yl)-4,5-dihydro-5-methyl-6H-imidazo[1,5-a][1,4]benzodiazepin-6-one of melting point 108°-110°.
Reaction SMILES: [NH2:1][C:2]1[C:7]([N+:8]([O-])=O)=[CH:6][C:5]([N+:11]([O-:13])=[O:12])=[CH:4][N:3]=1>CO>[NH2:1][C:2]1[C:7]([NH2:8])=[CH:6][C:5]([N+:11]([O-:13])=[O:12])=[CH:4][N:3]=1
Reactant: Nc1ncc([N+](=O)[O-])cc1[N+](=O)[O-]
Solvent: CO
Product: Nc1cc([N+](=O)[O-])cnc1N
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 78.7 %

Procedure:
To a stirred suspension of 2-Amino-3,5-dinitropyridine (2) (2 g, 10.8 mmol) in MeOH (75 mL) was added an aqueous solution of (NH4)2S (20%, 19 mL) dropwise at room temperature over 20 minutes. The mixture was stirred for an additional 30 minutes at room temperature and then heated at reflux for 30 minutes. The solution was cooled to room temperature and the solid collected by filtration, rinsed with cold MeOH (2×20 mL), and dried in vacuo at room temperature to give 3 as a red solid (1.31 g, 8.5 mmol, 79%). 1H NMR (500 MHz, DMSO-d6) δ5.31 (s, 2H), 6.98 (s, 2H), 7.35 (d, J=2.55 Hz, 1H), 8.28 (d, J=2.91 Hz, 1H). EIMS M+1 155.1.
Reaction SMILES: [N:1]1([CH2:6][CH:7]([N:9]2[C:22]3[CH:21]=[C:20]([C:23](=[S:25])[NH2:24])[CH:19]=[CH:18][C:17]=3[S:16][C:15]3[C:10]2=[CH:11][CH:12]=[CH:13][CH:14]=3)[CH3:8])[CH2:5][CH2:4][CH2:3][CH2:2]1.[CH2:26](N)[CH2:27][CH2:28][CH2:29][CH3:30].S>C(O)C>[CH2:26]([NH:24][C:23]([C:20]1[CH:19]=[CH:18][C:17]2[S:16][C:15]3[C:10](=[CH:11][CH:12]=[CH:13][CH:14]=3)[N:9]([CH:7]([CH3:8])[CH2:6][N:1]3[CH2:5][CH2:4][CH2:3][CH2:2]3)[C:22]=2[CH:21]=1)=[S:25])[CH2:27][CH2:28][CH2:29][CH3:30]
Reactant: CC(CN1CCCC1)N1c2ccccc2Sc2ccc(C(N)=S)cc21
Reactant: CCCCCN
Agent: S
Solvent: CCO
Product: CCCCCNC(=S)c1ccc2c(c1)N(C(C)CN1CCCC1)c1ccccc1S2
Temperature: 100 °C

Procedure:
A suspension of 10-[(2RS)-1-(1-pyrrolidinyl)-2-propyl]-2-phenothiazinecarbothioamide (2 g) and pentylamine (3 cc) in absolute ethanol (30 cc) is saturated with hydrogen sulphide and then heated for 2 hours at a temperature in the region of 100° C. After cooling, the mixture is concentrated to dryness under reduced pressure (30 mm Hg; 4 kPa) at 40° C. The pasty residue is taken up with ethyl ether (50 cc) and distilled water (15 cc). The organic phase is separated, dried over potassium carbonate and concentrated to dryness under reduced pressure (30 mm Hg; 4 kPa) at 40° C. The residual viscous yellow oil is purified by chromatography on a column (height: 35 cm; diameter: 2.6 cm) of silica gel (0.2-0.063 mm), eluting with ethyl acetate (300 cc) and collecting 25-cc fractions. Fractions 3 to 9 are combined and concentrated to dryness under reduced pressure (30 mm Hg; 4 kPa) at 40° C. N-Pentyl-10-[(2RS)-1-(1-pyrrolidinyl)-2-propyl]-2-phenothiazinecarbothioamide (2.25 g) is thereby obtained in the form of a yellow oil. 0.55 g of this product is dissolved in isopropyl ether (20 cc), and a 3.3N solution (0.6 cc) of hydrochloric acid in isopropyl ether is introduced dropwise and with stirring. The precipitate formed is drained, washed with isopropyl ether (3×5 cc) and dried under reduced pressure (5 mm Hg; 0.68 kPa) at 40° C. N-Pentyl-10-[(2RS)-1-(1-pyrrolidinyl)-2-propyl]-2-phenothiazinecarbothioamide hydrochloride (0.56 g) is thereby obtained in the form of a pale yellow powder, m.p. 155°-160° C. (melts forming a paste).
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[CH:27]=[CH:26][C:11]([CH2:12][O:13][C:14]([C:22]([F:25])([F:24])[F:23])([C:18]([F:21])([F:20])[F:19])[C:15]([OH:17])=[O:16])=[CH:10][CH:9]=2)=[CH:4][CH:3]=1.[N+](=[CH2:30])=[N-]>>[Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[CH:9]=[CH:10][C:11]([CH2:12][O:13][C:14]([C:18]([F:19])([F:20])[F:21])([C:22]([F:23])([F:24])[F:25])[C:15]([O:17][CH3:30])=[O:16])=[CH:26][CH:27]=2)=[CH:4][CH:3]=1
Reactant: O=C(O)C(OCc1ccc(-c2ccc(Cl)cc2)cc1)(C(F)(F)F)C(F)(F)F
Reactant: C=[N+]=[N-]
Product: COC(=O)C(OCc1ccc(-c2ccc(Cl)cc2)cc1)(C(F)(F)F)C(F)(F)F

Procedure:
A solution of 2-[4-(4-chlorophenyl)benzyloxy]-3,3,3-trifluoro-2-trifluoromethylpropionic acid (1.2 g.) in either (20 ml.) is treated at 0° C. with an excess of an ethereal solution of diazomethane. The solution is evaporated, and the residue is recrystallised from light petroleum (b.p. 40°-60° C.) to give methyl 2-[4(4-chlorophenyl)benzyloxy]-3,3,3-trifluoro-2-trifluoromethylpropionate (1.1 g.), m.p. 61.5°-62.5° C.
Reaction SMILES: Cl.[Cl:2][C:3]1[CH:15]=[CH:14][C:13]([C:16]([F:19])([F:18])[F:17])=[CH:12][C:4]=1OCC1CCNC1.[OH:20][CH2:21][CH:22]1[CH2:26][CH2:25][N:24](C(OC(C)(C)C)=O)[CH2:23]1>>[ClH:2].[F:17][C:16]([F:19])([F:18])[C:13]1[CH:14]=[CH:15][CH:3]=[CH:4][C:12]=1[O:20][CH:21]1[CH2:22][CH2:23][NH:24][CH2:25][CH2:26]1
Reactant: FC(F)(F)c1ccc(Cl)c(OCC2CCNC2)c1
Reactant: CC(C)(C)OC(=O)N1CCC(CO)C1
Agent: Cl
Product: FC(F)(F)c1ccccc1OC1CCNCC1
Yield: 72 %

Procedure:
The synthesis of intermediate 1n is performed starting with 3-hydroxymethyl-1-BOC-pyrrolidine following the operating mode described for the synthesis of 1a (white solid, total yield 72%). TLC silica gel 60 F 254 Merck, CH2Cl2-MeOH—AcOH: 90:9:1, Rf=0.10
Reaction SMILES: Cl[C:2]1[N:7]=[C:6]([O:8][CH3:9])[N:5]=[C:4]([NH:10][CH2:11][CH2:12][C:13]2[CH:18]=[CH:17][C:16]([Cl:19])=[CH:15][C:14]=2[Cl:20])[CH:3]=1.[NH:21]1[CH2:29][CH2:28][CH2:27][CH:23]([C:24]([OH:26])=[O:25])[CH2:22]1.C([O-])([O-])=O.[K+].[K+].Cl>O.CN1CCCC1=O>[Cl:20][C:14]1[CH:15]=[C:16]([Cl:19])[CH:17]=[CH:18][C:13]=1[CH2:12][CH2:11][NH:10][C:4]1[N:5]=[C:6]([O:8][CH3:9])[N:7]=[C:2]([N:21]2[CH2:29][CH2:28][CH2:27][CH:23]([C:24]([OH:26])=[O:25])[CH2:22]2)[CH:3]=1
Reactant: COc1nc(Cl)cc(NCCc2ccc(Cl)cc2Cl)n1
Reactant: O=C(O)C1CCCNC1
Agent: Cl
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: O
Solvent: CN1CCCC1=O
Product: COc1nc(NCCc2ccc(Cl)cc2Cl)cc(N2CCCC(C(=O)O)C2)n1
Temperature: 140 °C
Reaction time: 5 h
Yield: 47.4 %

Procedure:
In a tube is combined (6-chloro-2-methoxy-pyrimidin-4-yl)-[2-(2,4-dichloro-phenyl)-ethyl]-amine [200 mg, 0.6 mmol, Intermediate (44)], nipecotic acid (194 mg, 1.5 mmol), K2CO3 (249 mg, 1.8 mmol) and 1-methyl-2-pyrrolidinone (2.5 mL). The tube is sealed and heated to 140° C. and stirred for 5 hours. The mixture is allowed to cool to ambient temperature, stand for 12 hours, diluted with water (20 mL) and acidified using 3M HCl. A precipitate forms and is collected by filtration and dried under high vacuum to afford 1-{6-[2-(2,4-dichloro-phenyl)-ethylamino]-2-methoxy-pyrimidin-4-yl}-piperidine-3-carboxylic acid [121 mg, 47%, Example 73] as a solid. LCMS RT=2.15 minutes, MS: 425 (M+H). IC50=0.8 nM
Reaction SMILES: [CH3:1][C:2]1[C:3](=[O:9])[NH:4][C:5](=[O:8])[NH:6][CH:7]=1.C([O-])([O-])=O.[K+].[K+].Br[CH2:17][CH2:18][CH2:19][CH2:20][Cl:21].O>CS(C)=O>[Cl:21][CH2:20][CH2:19][CH2:18][CH2:17][N:6]1[CH:7]=[C:2]([CH3:1])[C:3](=[O:9])[NH:4][C:5]1=[O:8]
Reactant: Cc1c[nH]c(=O)[nH]c1=O
Reactant: ClCCCCBr
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CS(C)=O
Solvent: O
Product: Cc1cn(CCCCCl)c(=O)[nH]c1=O
Temperature: 25 °C
Reaction time: 20 h

Procedure:
A mixture of 5-methyl-2,4(1H,3H)-pyrimidinedione (thimine, 500 mg, commercially available from Aldrich) and K2CO3 (546 mg) in dry DMSO (15 mL) was stirred for 1 hour at room temperature. 1-bromo-4-chlorobutane (0.46 mL) was then added and the mixture was stirred at room temperature for 20 hours. Water was then added and the resulting mixture was extracted with EtAcO. The aqueous phase was acidified to pH 7 with aqueous 2% HCl solution and extracted with DCM. The organic phases were washed with brine, dried over Na2SO4 and concentrated in vacuo. The crude product was purified by a silica SPE cartridge (25 g) eluting with toluene/acetone from 95/5 to 75/25 to give the title compound as a colourless oil (250 mg).
Reaction SMILES: [CH2:1]([C:8]1[CH:20]=[CH:19][C:11]([O:12][CH2:13][C@@H:14]2[CH2:18][CH2:17][CH2:16][NH:15]2)=[CH:10][CH:9]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.CN(C=O)C.[C:26]([O:30][C:31](=[O:34])[CH2:32]Br)([CH3:29])([CH3:28])[CH3:27].C(=O)([O-])[O-].[K+].[K+]>O>[C:26]([O:30][C:31](=[O:34])[CH2:32][N:15]1[CH2:16][CH2:17][CH2:18][C@H:14]1[CH2:13][O:12][C:11]1[CH:19]=[CH:20][C:8]([CH2:1][C:2]2[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=2)=[CH:9][CH:10]=1)([CH3:29])([CH3:28])[CH3:27]
Reactant: CC(C)(C)OC(=O)CBr
Reactant: c1ccc(Cc2ccc(OC[C@@H]3CCCN3)cc2)cc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Solvent: O
Product: CC(C)(C)OC(=O)CN1CCC[C@H]1COc1ccc(Cc2ccccc2)cc1
Temperature: 60 °C
Yield: 64.3 %

Procedure:
(S)-2-(4-Benzyl-phenoxymethyl)-pyrrolidine (200 mg, 0.658 mmol) was taken into DMF (2 mL), and t-butylbromoacetate (141 mg, 0.724 mmol) was added, followed by potassium carbonate (182 mg, 1.317 mmol). The mixture was heated to 60° C. and left to react overnight. The mixture was diluted with water, and extracted with ethyl acetate (3×). The combined ethyl acetate layers were washed with brine, dried over sodium sulfate, and concentrated to dryness. The compound was then purified by flash chromatography (eluted with 0.5% methanol in dichloromethane with a 40:1 silica ratio) to obtain the title product (161 mg, 0.423 mmol, 64% yield); LCMS; m/z 381.52, found 381 (M); 1H NMR (400 MHz, CDCl3) δ 1.45 (s, 9H), 1.66-1.73 (m, 2H), 1.79-1.85 (m, 2H), 1.99-2.06 (m, 1H), 2.63-2.69 (m, 1H), 3.18-3.22 (m, 2H), 3.40 (d, J=17.2, 1H), 3.59 (d, J 16.8, 1H), 3.79-3.83 (m, 1H), 3.91-3.95 (m, 2H), 6.82 (d, J 8.88, 2H), 7.08 (d, J8.8, 2H), 7.15-7.27 (m, 5H).
Reaction SMILES: [Br:1][C:2]1[CH:6]=[CH:5][S:4][C:3]=1[CH2:7]Br.[C-:9]#[N:10].[K+]>C(O)C.O>[Br:1][C:2]1[CH:6]=[CH:5][S:4][C:3]=1[CH2:7][C:9]#[N:10]
Reactant: [C-]#N
Reactant: BrCc1sccc1Br
Agent: [K+]
Solvent: O
Solvent: CCO
Product: N#CCc1sccc1Br
Yield: 71.4 %

Procedure:
3-Bromo-2-(bromomethyl)thiophene (7.1 g) and potassium cyanide (2.7 g) were dissolved in ethanol (93 mL) and water (17 mL), and the mixture was stirred at 50° C. for 2 hours. The reaction solution was concentrated under reduced pressure, and to the residue was added water. The resulting mixture was extracted with ethyl acetate. The organic layer was washed with brine, dried over anhydrous magnesium sulfate, and concentrated under reduced pressure. The obtained residue was purified by column chromatography on silica gel (eluent: n-hexane/ethyl acetate=100/0−80/20) to give the title compound (4.0 g).
Reaction SMILES: [N:1]1([C:8]([NH:10][C@H:11]([CH2:15][CH:16]([CH3:18])[CH3:17])[C:12]([OH:14])=O)=[O:9])[CH2:7][CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1.C(N(CC)CC)C.CN(C(ON1N=NC2C=CC=CC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.[C:50]([O:54][C:55](=[O:73])[C@@H:56]([NH2:72])[CH2:57][C:58]1[CH:63]=[CH:62][C:61]([O:64][CH2:65][C:66]2[CH:71]=[CH:70][CH:69]=[CH:68][CH:67]=2)=[CH:60][CH:59]=1)([CH3:53])([CH3:52])[CH3:51]>C(#N)C>[C:50]([O:54][C:55](=[O:73])[C@@H:56]([NH:72][C:12](=[O:14])[C@H:11]([NH:10][C:8]([N:1]1[CH2:2][CH2:3][CH2:4][CH2:5][CH2:6][CH2:7]1)=[O:9])[CH2:15][CH:16]([CH3:18])[CH3:17])[CH2:57][C:58]1[CH:63]=[CH:62][C:61]([O:64][CH2:65][C:66]2[CH:71]=[CH:70][CH:69]=[CH:68][CH:67]=2)=[CH:60][CH:59]=1)([CH3:53])([CH3:51])[CH3:52]
Reactant: CC(C)C[C@@H](NC(=O)N1CCCCCC1)C(=O)O
Reactant: CC(C)(C)OC(=O)[C@@H](N)Cc1ccc(OCc2ccccc2)cc1
Agent: CN(C)C(On1nnc2ccccc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CC#N
Solvent: CCN(CC)CC
Product: CC(C)C[C@@H](NC(=O)N1CCCCCC1)C(=O)N[C@@H](Cc1ccc(OCc2ccccc2)cc1)C(=O)OC(C)(C)C
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 86.1 %

Procedure:
A solution of the product from Example AA ((R)-2-[(azepane-1-carbonyl)-amino]-4-methyl-pentanoic acid) (1.0 g, 3.9 mmol) and triethylamine (1.1 mL, 7.8 mmol) in acetonitrile (15 mL) was treated with HBTU (1.54 g, 4.06 mmol). The resulting solution was treated with the product from Example A ((S)-2-amino-3-(4-benzyloxy-phenyl)-propionic acid tert-butyl ester) (1.33 g, 4.06 mmol), and the resulting solution was stirred at room temperature for 30 minutes and allowed to stand overnight. The reaction mixture was concentrated and the residue dissolved in ethyl acetate (100 mL) and washed sequentially with 0.6 M aqueous NaHCO3 solution, saturated aqueous NaCl solution, and water. The organic phase was dried over MgSO4 and activated charcoal, filtered, and concentrated. The residue was purified by chromatography (silica gel, 25% ethyl acetate/hexane) to give the title compound as a white solid (1.9 g, 86%), mp=64-66° C.
Reaction SMILES: [C:1]([C:4]1[CH2:9][CH2:8][CH2:7][NH:6][CH:5]=1)(=[O:3])[CH3:2].[H-].[Na+].CN(C)C=O.Br[CH:18]([CH3:20])[CH3:19]>O>[CH3:19][CH:18]([N:6]1[CH2:7][CH2:8][CH2:9][C:4]([C:1]([CH3:2])=[O:3])=[CH:5]1)[CH3:20]
Reactant: CC(C)Br
Reactant: CC(=O)C1=CNCCC1
Agent: [H-]
Agent: [Na+]
Solvent: O
Solvent: CN(C)C=O
Product: CC(=O)C1=CN(C(C)C)CCC1
Temperature: 0 °C
Reaction time: 0.25 h

Procedure:
3-acetyl-1,4,5,6-tetrahydropyridine (20.0 g, 0.16 mole) was added under nitrogen to a mixture of sodium hydride (5.76 g, 0.24 mole) and dry dimethylformamide (50 ml) stirring at 0° C. and stirring was continued for 15 minutes. 2-Bromopropane (21.5 g, 0.175 mole) was then added dropwise over 15 min, stirring continued for a further hour at 0° C. then overnight at room temperature. The reaction mixture was cautiously added to iced water (100 g) under nitrogen and extracted with diethyl ether (3×100 ml). The combined organic phase was extracted with water (150 ml), dried over magnesium sulphate, concentrated under reduced pressure to give methyl 1-(1-methylethyl)-1,4,5,6-tetrahydro-3-pyridyl ketone (1). The product was distilled as a pale yellow oil (b.pt 97°-98° C./0.5 mm Hg).