Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [OH:1][C:2]1([CH3:9])[CH:6]=[CH:5][C:4](=[O:7])[CH:3]1[CH3:8].[C:10](OC(=O)C)(=[O:12])[CH3:11]>>[C:10]([O:1][C:2]1([CH3:9])[CH:6]=[CH:5][C:4](=[O:7])[CH:3]1[CH3:8])(=[O:12])[CH3:11]
Reactant: CC(=O)OC(C)=O
Reactant: CC1C(=O)C=CC1(C)O
Product: CC(=O)OC1(C)C=CC(=O)C1C

Procedure:
Into the same flask as used in Example 1, dl-3-hydroxy-2,3-dimethyl-4-cyclopentenone (12.6 g) and acetic anhydride (30 g) were charged, and the resultant mixture was stirred at 80°-100° C. for 3 hours. After completion of the reaction, the reaction mixture was subjected to the same work-up as in Example 11, followed by purification to give 16.2 g of dl-3-acetoxy-2,3-dimethyl-cyclopentenone. Yield, 96.5%. B.P., 52°-55° C./0.4-0.5 mmHg.
Reaction SMILES: [CH3:1][C:2]1([CH3:9])[CH2:7][CH2:6][C:5](=[O:8])[CH2:4][CH2:3]1.F[B-](F)(F)F.[CH2:15]([O:17][CH+:18][O:19][CH2:20][CH3:21])[CH3:16].C(N(CC)C(C)C)(C)C>>[CH2:15]([O:17][CH:18]([O:19][CH2:20][CH3:21])[CH:4]1[CH2:3][C:2]([CH3:9])([CH3:1])[CH2:7][CH2:6][C:5]1=[O:8])[CH3:16]
Reactant: CC1(C)CCC(=O)CC1
Reactant: CCO[CH+]OCC
Agent: F[B-](F)(F)F
Solvent: CCN(C(C)C)C(C)C
Product: CCOC(OCC)C1CC(C)(C)CCC1=O

Procedure:
reacting 4,4-dimethylcyclohexanone, diethoxycarbenium fluoroborate and N,N-diisopropylethylamine at about −60° C. to −90° C. to provide (2-(diethoxymethyl)-4,4-dimethylcyclohexanone and isolating or not isolating the 2-(diethoxymethyl)-4,4-dimethylcyclohexanone;
Reaction SMILES: [CH2:1]([Li])[CH2:2][CH2:3][CH3:4].O1CCCC1.[CH2:11]([O:13][C:14](=[O:36])[CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][C@@H:21]1[C:25](=[CH:26][CH2:27][C:28](=[O:34])[CH2:29][CH2:30][CH2:31][CH2:32][CH3:33])[CH2:24][CH2:23][C@H:22]1[OH:35])[CH3:12].[NH4+].[Cl-]>C(OCC)C>[CH2:11]([O:13][C:14](=[O:36])[CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][C@@H:21]1[C:25](=[CH:26][CH2:27][C:28]([OH:34])([CH2:1][CH2:2][CH2:3][CH3:4])[CH2:29][CH2:30][CH2:31][CH2:32][CH3:33])[CH2:24][CH2:23][C@H:22]1[OH:35])[CH3:12]
Reactant: CCCCCC(=O)CC=C1CC[C@@H](O)[C@@H]1CCCCCCC(=O)OCC
Reactant: [Li]CCCC
Agent: [Cl-]
Agent: [NH4+]
Solvent: CCOCC
Solvent: C1CCOC1
Product: CCCCCC(O)(CC=C1CC[C@@H](O)[C@@H]1CCCCCCC(=O)OCC)CCCC

Procedure:
1.6 g. Butyl lithium, dissolved in 60 ml. tetrahydrofuran, is added dropwise to 3.7 g. 9β-hydroxy-15-oxo-12-prostenoic acid ethyl ester, dissolved in 150 ml. dry diethyl ether, with the exclusion of moisture, under argon and with stirring at -15°. The mixture is stirred for another hour, allowed to warm to 0° and mixed dropwise, with ice cooling, with 300 ml. saturated aqueous NH4Cl solution. The organic phase is separated, washed with water and dried over Na2SO4. The solvent is removed to obtain as residue 9β,15-dihydroxy-15-butyl-12-prostenoic acid ethyl ester.
Reaction SMILES: [Br:1][C:2]1[CH:7]=[CH:6][C:5]([C@H:8]([NH:13][C@@H:14]([CH2:18][CH:19]([CH3:21])[CH3:20])[C:15]([OH:17])=[O:16])[C:9]([F:12])([F:11])[F:10])=[CH:4][CH:3]=1.S(=O)(=O)(O)O.[CH:27](O)([CH3:29])[CH3:28]>>[CH:27]([O:16][C:15](=[O:17])[C@@H:14]([NH:13][C@@H:8]([C:5]1[CH:4]=[CH:3][C:2]([Br:1])=[CH:7][CH:6]=1)[C:9]([F:12])([F:11])[F:10])[CH2:18][CH:19]([CH3:21])[CH3:20])([CH3:29])[CH3:28]
Reactant: CC(C)O
Reactant: CC(C)C[C@H](N[C@@H](c1ccc(Br)cc1)C(F)(F)F)C(=O)O
Agent: O=S(=O)(O)O
Product: CC(C)C[C@H](N[C@@H](c1ccc(Br)cc1)C(F)(F)F)C(=O)OC(C)C
Temperature: 80 °C
Yield: 88 %

Procedure:
To a stirred solution of (S)-2-[(S)-1-(4-bromo-phenyl)-2,2,2-trifluoro-ethylamino]-4-methyl-pentanoic acid, prepared as shown in Li, C. S. et al Bioorg. Med. Chem. Lett. 2006, 16, 1985, (1.80 g, 4.9 mmol) in isopropyl alcohol (100 mL) was added concentrated sulphuric acid (2 mL). The resulting solution was heated at 80° C. for 4 hours. The reaction mixture was allowed to cool and was then concentrated in vacuo. The resulting oil was dispersed in CH2Cl2 (100 mL), washed with saturated NaHCO3 (2×50 mL), dried (MgSO4) and concentrated in vacuo to yield the title compound as a brown oil (1.77 g, 88%). MS [M+H] 412.
Reaction SMILES: [Cl:1][C:2]1[CH:17]=[CH:16][C:5]([C:6]([C:8]2[CH:13]=[CH:12][C:11]([Cl:14])=[CH:10][C:9]=2[Cl:15])=O)=[CH:4][CH:3]=1.Cl.[NH2:19][OH:20].[OH-].[K+].Cl>O.C(O)C>[Cl:1][C:2]1[CH:17]=[CH:16][C:5]([C:6](=[N:19][OH:20])[C:8]2[CH:13]=[CH:12][C:11]([Cl:14])=[CH:10][C:9]=2[Cl:15])=[CH:4][CH:3]=1
Reactant: NO
Reactant: O=C(c1ccc(Cl)cc1)c1ccc(Cl)cc1Cl
Agent: Cl
Agent: [K+]
Agent: [OH-]
Solvent: CCO
Solvent: O
Product: ON=C(c1ccc(Cl)cc1)c1ccc(Cl)cc1Cl
Yield: 83.1 %

Procedure:
A mixture of 4-chloro 2',4'-dichlorobenzophenone (8 g.), hydroxylamine hydrochloride (2.9 g.), powdered potassium hydroxide (7.7 g.), ethanol (10 ml.) and water (2 ml.) was heated under reflux for 15 minutes. The mixture was poured into water (300 ml.) containing concentrated hydrochloric acid (30 ml.), and the precipitated oil was left to crystallise. The mixture was then filtered, and the solid residue (7.0 g., 83% yield) of 4-chloro-2',4'-dichlorobenzophenone oxime (m.p. 98°-100° C.) was used in the above process without further purification. A sample recrystallised from petrol also had m.p. 98°-100° C.
Reaction SMILES: Br[C:2]1[N:7]=[CH:6][C:5]([C@@H:8]2[CH2:10][C@H:9]2[NH:11][C:12](=[O:18])[O:13][C:14]([CH3:17])([CH3:16])[CH3:15])=[CH:4][CH:3]=1.C(=O)([O-])[O-].[K+].[K+].[F:25][C:26]([F:37])([F:36])[C:27]1[CH:28]=[C:29](B(O)O)[CH:30]=[CH:31][CH:32]=1>CC#N.O>[F:25][C:26]([F:37])([F:36])[C:27]1[CH:32]=[C:31]([C:2]2[N:7]=[CH:6][C:5]([C@@H:8]3[CH2:10][C@H:9]3[NH:11][C:12](=[O:18])[O:13][C:14]([CH3:17])([CH3:16])[CH3:15])=[CH:4][CH:3]=2)[CH:30]=[CH:29][CH:28]=1
Reactant: OB(O)c1cccc(C(F)(F)F)c1
Reactant: CC(C)(C)OC(=O)N[C@@H]1C[C@H]1c1ccc(Br)nc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC#N
Solvent: O
Product: CC(C)(C)OC(=O)N[C@@H]1C[C@H]1c1ccc(-c2cccc(C(F)(F)F)c2)nc1
Yield: 57.8 %

Procedure:
A solution of tert-butyl (trans)-2-(6-bromopyridin-3-yl)cyclopropylcarbamate (Intermediate J[a2]) (100 mg, 0.32 mmol), potassium carbonate (132 mg, 0.96 mmol) and 3-trifluoromethylbenzeneboronic acid (72 mg, 0.38 mmol) in CH3CN:H2O (4:1) (10 mL) was degassed for 30 mins, added tetrakis triphenylphosphine palladium (37 mg, 0.032 mmol), degassed for 10 mins and heated the reaction mixture at reflux temperature for 2 h. After completion, the reaction mixture was poured in ice water (100 mL), extracted with ethyl acetate (5×40 mL). The combined extract were washed with water (70 mL), brine (70 mL), dried over anhydrous Na2SO4, filtered and evaporated. The crude residue was purified by column chromatography (SiO2), by using EtOAc:Petroleum ether (1:9) to get tert-butyl (trans)-2-(6-(3-(trifluoromethyl)phenyl)pyridin-3-yl)cyclopropylcarbamate (70 mg, 58.3%) as a white solid.
Reaction SMILES: [C:1]1([C:23]2[CH:28]=[CH:27][CH:26]=[CH:25][CH:24]=2)[CH:6]=[CH:5][C:4]([CH2:7][C@@H:8]([NH:15][C:16]([O:18][C:19]([CH3:22])([CH3:21])[CH3:20])=[O:17])[CH2:9][C:10](=[CH2:14])[C:11]([OH:13])=[O:12])=[CH:3][CH:2]=1.[H][H]>[Rh].C(OC(C)C)(=O)C>[C:1]1([C:23]2[CH:24]=[CH:25][CH:26]=[CH:27][CH:28]=2)[CH:2]=[CH:3][C:4]([CH2:7][C@@H:8]([NH:15][C:16]([O:18][C:19]([CH3:22])([CH3:20])[CH3:21])=[O:17])[CH2:9][C@@H:10]([CH3:14])[C:11]([OH:13])=[O:12])=[CH:5][CH:6]=1
Reactant: C=C(C[C@@H](Cc1ccc(-c2ccccc2)cc1)NC(=O)OC(C)(C)C)C(=O)O
Reactant: [H][H]
Agent: [Rh]
Solvent: CC(=O)OC(C)C
Product: C[C@H](C[C@@H](Cc1ccc(-c2ccccc2)cc1)NC(=O)OC(C)(C)C)C(=O)O
Temperature: 25 °C

Procedure:
20 mg (R)-5-Biphenyl-4-yl-4-tert-butoxycarbonylamino-2-methylenepentanoic acid (2-a, R1=Boc, R2=H, R3=CO2H) is added to isopropyl acetate (400 μl). 5% Rhodium on carbon (2 mg) is then added. Hydrogen gas at ambient pressure is applied to the mixture. The mixture is stirred at ambient temperature and pressure overnight. The mixture is then filtered over Celite and washed with isopropyl acetate (2×0.5 ml). The mixture is then concentrated in vacuo to give (2R,4S)-5-biphenyl-4-yl-4-tert-butoxycarbonylamino-2-methylpentanoic acid (1-a, R1=Boc, R2=H, R3=CO2H) and (2S,4S)-5-biphenyl-4-yl-4-tert-butoxycarbonylamino-2-methylpentanoic acid (1-b, R1=Boc, R2=H, R3=CO2H). Spectroscopic data as in Example 40, Method 1.
Reaction SMILES: [Cl:1][C:2]1[N:7]=[C:6](Cl)[C:5]([O:9][CH3:10])=[CH:4][N:3]=1.Cl.Cl.[NH:13]1[C:17]2[CH2:18][CH2:19][CH2:20][NH:21][C:16]=2[N:15]=[CH:14]1.C(N(C(C)C)C(C)C)C>C(O)CCC>[Cl:1][C:2]1[N:7]=[C:6]([N:21]2[CH2:20][CH2:19][C:18]3[N:15]=[CH:14][NH:13][C:17]=3[CH2:16]2)[C:5]([O:9][CH3:10])=[CH:4][N:3]=1
Reactant: COc1cnc(Cl)nc1Cl
Reactant: c1nc2c([nH]1)CCCN2
Agent: Cl
Solvent: CCN(C(C)C)C(C)C
Solvent: CCCCO
Product: COc1cnc(Cl)nc1N1CCc2nc[nH]c2C1
Temperature: 50 °C
Reaction time: 16 h

Procedure:
1 g 2,4-dichloro-5-methoxy-pyrimidine are dissolved in 4 mL butanol and combined with 1.04 g 4,5,6,7-tetrahydroimidazopyridine dihydrochloride and 2.96 mL ethyldiisopropylamine. This mixture is stirred for 16 h at 50° C. and then the solvent is eliminated in vacuo. The crude mixture is purified by column chromatography. The carrier material used is C18-RP-silica gel and a gradient is run through which consists at the starting point of 95% water and 5% acetonitrile and at the finishing point of 70% water and 30% acetonitrile. 0.2% formic acid is added to both eluants. The suitable fractions are freeze-dried.
Reaction SMILES: [C:1]([C:3]1[CH:8]=[CH:7][CH:6]=[CH:5][C:4]=1[CH2:9][C:10]([O:12][CH3:13])=[O:11])#[CH:2].Cl[C:15]1[C:20]([C:21]([F:24])([F:23])[F:22])=[CH:19][N:18]=[C:17]([NH:25][C:26]2[CH:31]=[CH:30][C:29]([CH:32]3[CH2:37][CH2:36][N:35]([C:38]([O:40][C:41]([CH3:44])([CH3:43])[CH3:42])=[O:39])[CH2:34][CH2:33]3)=[CH:28][C:27]=2[O:45][CH3:46])[N:16]=1.C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.C(N(CC)CC)C>[Cu]I.Cl[Pd](Cl)([P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1)[P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1.O.CN(C=O)C>[CH3:46][O:45][C:27]1[CH:28]=[C:29]([CH:32]2[CH2:37][CH2:36][N:35]([C:38]([O:40][C:41]([CH3:44])([CH3:43])[CH3:42])=[O:39])[CH2:34][CH2:33]2)[CH:30]=[CH:31][C:26]=1[NH:25][C:17]1[N:18]=[C:19]([C:2]#[C:1][C:3]2[CH:8]=[CH:7][CH:6]=[CH:5][C:4]=2[CH2:9][C:10]([O:12][CH3:13])=[O:11])[C:20]([C:21]([F:23])([F:24])[F:22])=[CH:15][N:16]=1
Reactant: COc1cc(C2CCN(C(=O)OC(C)(C)C)CC2)ccc1Nc1ncc(C(F)(F)F)c(Cl)n1
Reactant: C#Cc1ccccc1CC(=O)OC
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: [Cu]I
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: CN(C)C=O
Solvent: CCN(CC)CC
Solvent: O
Product: COC(=O)Cc1ccccc1C#Cc1nc(Nc2ccc(C3CCN(C(=O)OC(C)(C)C)CC3)cc2OC)ncc1C(F)(F)F
Temperature: 120 °C
Yield: 98 %

Procedure:
A mixture of methyl 2-(2-ethynylphenyl)acetate (I4) (0.472 g, 2.71 mmol), tert-butyl 4-(4-((4-chloro-5-(trifluoromethyl)pyrimidin-2-yl)amino)-3-methoxyphenyl)piperidine-1-carboxylate (I27) (1.10 g, 2.26 mmol), triphenylphosphine (59 mg, 10 mol %), copper(I) iodide (43 mg, 10 mol %), bis(triphenylphosphine)palladium(II) chloride (79 mg, 5 mol %), DMF (12 mL) and triethylamine (1.26 mL, 9.04 mmol) was degassed with nitrogen in a microwave tube then heated under microwave irradiation at 120° C. for 15 minutes. Three additional tubes were prepared and heated as described above (i.e. a total of 4.40 g of I27). The cooled mixtures were combined, and poured into water (600 mL). The resulting mixture was extracted with dichloromethane (3×250 mL) then the combined organic phases were washed with water (2×300 mL), brine (300 mL), dried over sodium sulfate and evaporated to dryness. The residue was chromatographed (120 g silica cartridge, 0-50% ethyl acetate/petroleum benzine 40-60° C.) to give the title compound (I28) (5.52 g, 98% yield) as a yellow solid; 1H NMR (400 MHz, CDCl3) δ 8.63 (s, 1H), 8.38 (d, J=8.3 Hz, 1H), 8.00 (s, 1H), 7.69 (dd, J=7.7, 0.9 Hz, 1H), 7.43 (td, J=7.6, 1.4 Hz, 1H), 7.36 (d, J=7.9 Hz, 1H), 7.32 (dd, J=7.5, 1.4 Hz, 1H), 6.87 (dd, J=8.4, 1.8 Hz, 1H), 6.76 (d, J=1.8 Hz, 1H), 4.26 (s, 2H), 3.97 (s, 2H), 3.91 (s, 3H), 3.71 (s, 3H), 2.81 (t, J=12.6 Hz, 2H), 2.64 (tt, J=12.2, 3.6 Hz, 1H), 1.84 (d, J=12.6 Hz, 2H), 1.69-1.55 (m, overlaps with water), 1.49 (s, 9H). LCMS Method C: rt 7.05 min; m/z (625.1 [M+H]+, 569.1 [M-tBu+2H]+; m/z 623.2 [M−H]−.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[C:9]([C:16]3[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=3)=[CH:10][N:11]3[C:15]=2[CH2:14][CH2:13][CH2:12]3)=[CH:4][CH:3]=1.C(N(CC)CC)C.[O:29]=[C:30](Cl)OC(Cl)(Cl)Cl.[C:37]([OH:41])([CH3:40])([CH3:39])[CH3:38]>C1COCC1>[Cl:1][C:2]1[CH:3]=[CH:4][C:5]([C:8]2[C:9]([C:16]3[CH:17]=[CH:18][CH:19]=[CH:20][CH:21]=3)=[C:10]([C:30]([O:41][C:37]([CH3:40])([CH3:39])[CH3:38])=[O:29])[N:11]3[C:15]=2[CH2:14][CH2:13][CH2:12]3)=[CH:6][CH:7]=1
Reactant: CC(C)(C)O
Reactant: O=C(Cl)OC(Cl)(Cl)Cl
Reactant: Clc1ccc(-c2c(-c3ccccc3)cn3c2CCC3)cc1
Solvent: C1CCOC1
Solvent: CCN(CC)CC
Product: CC(C)(C)OC(=O)c1c(-c2ccccc2)c(-c2ccc(Cl)cc2)c2n1CCC2
Temperature: 25 °C
Reaction time: 48 h
Yield: 38.6 %

Procedure:
7-(4-Chlorophenyl)-6-phenyl-2,3-dihydro-1H-pyrrolizine (Example 21 b, 0.75 g, 2.5 mmol), dissolved in THF (10 ml), is treated with triethylamine (0.3 ml, 0.25 g, 2.5 mmol). A solution of diphosgene (0.25 g, 1.25 mmol), dissolved in THF (5 ml), is added dropwise to this solution at RT, and it is stirred for 18 h. tert-Butyl alcohol (abs., 1.0 ml, 0.786 g, 10 mmol) and triethylamine (0.7 ml, 0.51 g, 5 mmol) are then added, and the mixture is stirred at RT for a further 48 h. The reaction mixture is partitioned between water (30 ml) and CHCl3 (60 ml), and the ether phase is washed with Na2CO3 solution (5%, 20 ml). After removal of the solvent in vacuo, an oily residue (0.7 g), which by TLC (SiO2, hexane/CH2Cl2 1:1) still contains starting material (Rf 0.75) in addition to product (Rf 0.3), is obtained from the THF/CHCl3 phase dried using Na2SO4 sicc. The residue is purified by CC (SiO2, hexane/CH2Cl2 1:1); 190 mg of the pure ester are obtained.
Reaction SMILES: Br[C:2]1[CH:3]=[C:4]([CH:8]=[CH:9][C:10]=1[CH3:11])[C:5]([OH:7])=[O:6].[Li]CCCC.[B:17](OC)([O:20]C)[O:18]C>C1COCC1>[B:17]([C:2]1[CH:3]=[C:4]([CH:8]=[CH:9][C:10]=1[CH3:11])[C:5]([OH:7])=[O:6])([OH:20])[OH:18]
Reactant: Cc1ccc(C(=O)O)cc1Br
Reactant: COB(OC)OC
Agent: [Li]CCCC
Solvent: C1CCOC1
Product: Cc1ccc(C(=O)O)cc1B(O)O
Temperature: -78 °C
Reaction time: 1 h
Yield: 33 %

Procedure:
3-Bromo-4-methylbenzoic acid (11.00 g, 51.2 mmol) was dissolved in anhydrous THF (150 ml) under argon in a 500 ml 3-necked round bottom flask fitted with two dropping funnels and argon inlet. The stirred solution was cooled to −78° C. and n-BuLi (1.6M in hexane, 60.7 ml, 97.0 mmol) was added drop wise from a dropping funnel (during 1 h). After completion of the addition, the solution was stirred at −78° C. for another 1 h. To this, B(OMe)3 (17.7 ml, 159.0 mmol) was added slowly from a second dropping funnel. The mixture was stirred 1 h at −78° C. and then warmed up to room temperature overnight. The solvent was evaporated under reduced pressure. The crude product was dissolved in ether and poured into aqueous HCl (1N). The mixture was extracted with ether (3×150 ml), and the combined organic layers were washed with brine, dried over anhydrous MgSO4, filtered, and evaporated to dryness. The crude product was purified using an ISCO system (220 g silica column, hexane/EtOAc gradient and later DCM/MeOH gradient). The impurities washed off in hexane/EtOAc and the pure product eluted in MeOH/DCM (5:95) solvent mixture to give 3.3 g (33% yield) of pure SKC-01-126. 1H NMR (400 MHz, Acetone-d6) δ 12.10 (br s, 1H), 8.16 (s, 1H), 7.90-7.63 (m, 1H), 7.11 (d, J=7.9 Hz, 1H), 2.42 (s, 3H).
Reaction SMILES: Cl[C:2]1[N:10]=[CH:9][N:8]=[C:7]2[C:3]=1[NH:4][CH:5]=[N:6]2.[CH3:11][C:12]1[S:29][C:15]2=[N:16][C:17]([C:23]3[CH:28]=[CH:27][CH:26]=[CH:25][N:24]=3)=[C:18]([C@@H:20]([NH2:22])[CH3:21])[CH:19]=[C:14]2[CH:13]=1.CCN(C(C)C)C(C)C>C(O)CCC>[CH3:11][C:12]1[S:29][C:15]2=[N:16][C:17]([C:23]3[CH:28]=[CH:27][CH:26]=[CH:25][N:24]=3)=[C:18]([C@@H:20]([NH:22][C:2]3[N:10]=[CH:9][N:8]=[C:7]4[C:3]=3[N:4]=[CH:5][NH:6]4)[CH3:21])[CH:19]=[C:14]2[CH:13]=1
Reactant: Clc1ncnc2nc[nH]c12
Reactant: Cc1cc2cc([C@H](C)N)c(-c3ccccn3)nc2s1
Solvent: CCCCO
Solvent: CCN(C(C)C)C(C)C
Product: Cc1cc2cc([C@H](C)Nc3ncnc4[nH]cnc34)c(-c3ccccn3)nc2s1
Temperature: 120 °C

Procedure:
6-Chloropurine (26.4 mg, 0.171 mmol), (S)-1-(2-methyl-6-(pyridin-2-yl)thieno[2,3-b]pyridin-5-yl)ethanamine (40 mg, 0.148 mmol) and hunig's base (38.9 μL, 0.223 mmol) was dissolved in 2 mL of n-butanol and heated to 120° C. overnight. The reaction was cooled to rt and purified by reverse phase chromatography to afford (S)—N-(1-(2-methyl-6-(pyridin-2-yl)thieno[2,3-b]pyridin-5-yl)ethyl)-9H-purin-6-amine. 1H NMR (400 MHz, CDCl3) δ 12.5 (br s, 1H), 8.78 (br m, 1H), 8.55-7.80 (series of m, 6H), 7.60-7.30 (br m, 1H), 7.26 (m, 1H), 6.89 (br s, 1H), 6.40-6.00 (br m, 1H), 2.60 (br s, 3H), 1.60-1.25 (series of M, 3H). LC/MS (M+1, found=388.1).
Reaction SMILES: [NH2:1][C:2]1[S:3][C:4]([C:8]2[CH:13]=[CH:12][N:11]=[C:10]([NH:14][C:15]3[CH:20]=[CH:19][CH:18]=[C:17]([N+:21]([O-:23])=[O:22])[CH:16]=3)[N:9]=2)=[C:5]([CH3:7])[N:6]=1.[CH3:24][S:25](Cl)(=[O:27])=[O:26].CCN(CC)CC>CN(C=O)C.CCOC(C)=O>[CH3:7][C:5]1[N:6]=[C:2]([NH:1][S:25]([CH3:24])(=[O:27])=[O:26])[S:3][C:4]=1[C:8]1[CH:13]=[CH:12][N:11]=[C:10]([NH:14][C:15]2[CH:20]=[CH:19][CH:18]=[C:17]([N+:21]([O-:23])=[O:22])[CH:16]=2)[N:9]=1
Reactant: CS(=O)(=O)Cl
Reactant: Cc1nc(N)sc1-c1ccnc(Nc2cccc([N+](=O)[O-])c2)n1
Solvent: CCN(CC)CC
Solvent: CN(C)C=O
Solvent: CCOC(C)=O
Product: Cc1nc(NS(C)(=O)=O)sc1-c1ccnc(Nc2cccc([N+](=O)[O-])c2)n1
Temperature: 25 °C
Reaction time: 20 h

Procedure:
A mixture of [4-(2-amino-4-methyl-thiazol-5-yl)-pyrimidin-2-yl]-(3-nitro-phenyl)-amine (1.0 mmol, 0.33 g) and methylsulfonyl chloride (2.0 mmol, 0.22 g) in dry DMF (2 mL) was added Et3N (0.28 mL). The reaction mixture was stirred at room temperature for 20 h. After cooling, the mixture was diluted with EtOAc, washed with brine, and dried over MgSO4. The solvent was evaporated and the residue was purified by preparative RP-HPLC using a gradient from 10-70% MeCN in 0.1% aq CF3COOH over 40 min. The title compound was obtained as an orange solid. Anal. RP-HPLC: tR=17.4 min (0-60% MeCN in 0.1% aq CF3COOH over 20 min, 1 mL/min, purity>97%). 1H-NMR (DMSO-d6) δ: 3.10 (s, 3H, CH3), 3.25 (s, 3H, CH3), 7.05 (d, 1H, J=5.2 Hz, pyrimidinyl-H), 7.42 (m, 1H, Ph-H), 7.63 (m, 1H, Ph-H), 7.98 (m, 1H, Ph-H), 8.21(d, 1H, J=5.2 Hz, pyrimidinyl-H), 8.42 (s, 1H, Ph-H), 9.18 (s, 1H, NH).
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:25]=[C:24]([O:26][CH3:27])[CH:23]=[CH:22][C:4]=1[CH2:5][N:6]1[S:10](=[O:12])(=[O:11])[N:9]([CH2:13][C:14]2[S:18][C:17]([CH:19]=[O:20])=[CH:16][CH:15]=2)[CH2:8][C:7]1=[O:21].[CH2:28]([Mg]Br)[CH2:29][CH:30]([CH3:32])[CH3:31]>C1COCC1>[CH3:1][O:2][C:3]1[CH:25]=[C:24]([O:26][CH3:27])[CH:23]=[CH:22][C:4]=1[CH2:5][N:6]1[C:7](=[O:21])[CH2:8][N:9]([CH2:13][C:14]2[S:18][C:17]([CH:19]([OH:20])[CH2:28][CH2:29][CH:30]([CH3:32])[CH3:31])=[CH:16][CH:15]=2)[S:10]1(=[O:12])=[O:11]
Reactant: COc1ccc(CN2C(=O)CN(Cc3ccc(C=O)s3)S2(=O)=O)c(OC)c1
Reactant: CC(C)CC[Mg]Br
Solvent: C1CCOC1
Product: COc1ccc(CN2C(=O)CN(Cc3ccc(C(O)CCC(C)C)s3)S2(=O)=O)c(OC)c1
Temperature: -70 °C
Reaction time: 0.75 h

Procedure:
A solution of the title B compound, 5-[5-(2,4-dimethoxy-benzyl)-1,1,4-trioxo-1,2,5-thiadiazolidin-2-ylmethyl]-thiophene-2-carbaldehyde (545 mg, 1.33 mmol) in dry THF (8 mL) is added dropwise to a cold (−70° C.) solution of isopentylmagnesium bromide (2.22 mmol) in dry THF (10 mL) keeping the temperature below −65° C. The mixture is stirred at −70° C. for 45 min and the reaction is quenched with saturated aqueous NH4Cl solution. The mixture is diluted with EtOAc and the layers are separated. The organic layer is dried over anhydrous MgSO4 and the solvent is evaporated. The residue is chromatographed on silica gel using 0→100% EtOAc in hexane as the eluent to afford 2-(2,4-dimethoxy-benzyl)-5-(5-(1-hydroxy-4-methyl-pentyl)-thiophen-2-ylmethyl]-1,1-dioxo-1,2,5-thiadiazolidin-3-one a yellow oil: [M+NH4]+=500.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]2[N:10]=[C:9]([CH2:11][OH:12])[N:8]([CH3:13])[C:5]2=[N:6][CH:7]=1.O[C:15]1[CH:47]=[CH:46][C:18]([CH2:19][CH:20]2[S:24][C:23](=[O:25])[N:22]([C:26]([C:39]3[CH:44]=[CH:43][CH:42]=[CH:41][CH:40]=3)([C:33]3[CH:38]=[CH:37][CH:36]=[CH:35][CH:34]=3)[C:27]3[CH:32]=[CH:31][CH:30]=[CH:29][CH:28]=3)[C:21]2=[O:45])=[CH:17][CH:16]=1.C(P(CCCC)CCCC)CCC.N(C(N1CCCCC1)=O)=NC(N1CCCCC1)=O>C1(C)C=CC=CC=1>[Cl:1][C:2]1[CH:3]=[C:4]2[N:10]=[C:9]([CH2:11][O:12][C:15]3[CH:47]=[CH:46][C:18]([CH2:19][CH:20]4[S:24][C:23](=[O:25])[N:22]([C:26]([C:39]5[CH:44]=[CH:43][CH:42]=[CH:41][CH:40]=5)([C:33]5[CH:34]=[CH:35][CH:36]=[CH:37][CH:38]=5)[C:27]5[CH:32]=[CH:31][CH:30]=[CH:29][CH:28]=5)[C:21]4=[O:45])=[CH:17][CH:16]=3)[N:8]([CH3:13])[C:5]2=[N:6][CH:7]=1
Reactant: Cn1c(CO)nc2cc(Cl)cnc21
Reactant: O=C1SC(Cc2ccc(O)cc2)C(=O)N1C(c1ccccc1)(c1ccccc1)c1ccccc1
Agent: CCCCP(CCCC)CCCC
Agent: O=C(N=NC(=O)N1CCCCC1)N1CCCCC1
Solvent: Cc1ccccc1
Product: Cn1c(COc2ccc(CC3SC(=O)N(C(c4ccccc4)(c4ccccc4)c4ccccc4)C3=O)cc2)nc2cc(Cl)cnc21

Procedure:
A procedure similar to that described in Preparation 4 was repeated, except that 0.52 9 of 6-chloro-2-hydroxymethyl-3-methylimidazo[5,4-b]pyridine (prepared as described in Preparation 64), 1.23 g of 5-(4-hydroxybenzyl)-3-triphenylmethylthiazolidine-2,4-dione, 0.66 ml of tributylphosphine, 0.67 g of 1,1'-(azodicarbonyl)dipiperidine and 20 ml of toluene were used, to give the title compound as a crude product. This crude product was purified by column chromatography through silica gel, using a 1:1 by volume mixture of hexane and ethyl acetate as the eluent, to give 1.51 g of the title compound, melting at 82°-84° C. (softening).
Reaction SMILES: [F:1][C:2]([F:32])([F:31])[C:3]1[CH:8]=[CH:7][C:6]([C:9]2[C:10]([C:15]([NH:17][C:18]3[CH:27]=[C:26]4[C:21]([CH:22]=[C:23]([C:28]([OH:30])=O)[CH:24]=[N:25]4)=[CH:20][CH:19]=3)=[O:16])=[CH:11][CH:12]=[CH:13][CH:14]=2)=[CH:5][CH:4]=1.[F:33][C:34]1[CH:39]=[CH:38][C:37]([CH:40]([NH2:42])[CH3:41])=[CH:36][CH:35]=1.Cl.CN(C)CCCN=C=NCC.ON1C2C=CC=CC=2N=N1.C(N(CC)CC)C>ClCCl.C(OCC)(=O)C>[F:33][C:34]1[CH:39]=[CH:38][C:37]([CH:40]([NH:42][C:28]([C:23]2[CH:24]=[N:25][C:26]3[C:21]([CH:22]=2)=[CH:20][CH:19]=[C:18]([NH:17][C:15]([C:10]2[C:9]([C:6]4[CH:7]=[CH:8][C:3]([C:2]([F:31])([F:32])[F:1])=[CH:4][CH:5]=4)=[CH:14][CH:13]=[CH:12][CH:11]=2)=[O:16])[CH:27]=3)=[O:30])[CH3:41])=[CH:36][CH:35]=1
Reactant: O=C(O)c1cnc2cc(NC(=O)c3ccccc3-c3ccc(C(F)(F)F)cc3)ccc2c1
Reactant: CC(N)c1ccc(F)cc1
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: ClCCl
Solvent: CCOC(C)=O
Solvent: CCN(CC)CC
Product: CC(NC(=O)c1cnc2cc(NC(=O)c3ccccc3-c3ccc(C(F)(F)F)cc3)ccc2c1)c1ccc(F)cc1
Temperature: 25 °C
Reaction time: 8 h
Yield: 93.6 %

Procedure:
7-[(4′-Trifluoromethyl-biphenyl-2-carbonyl)-amino]-quinoline-3-carboxylic acid (100 mg, 0.23 mmol) was combined with 1-(4-fluorophenyl)-ethylamine (32 mg, 0.23 mmol), 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (53 mg, 0.27 mmol), 1-hydroxybenzotriazole (34 mg, 0.25 mmol), and triethylamine (0.13 ml, 0.92 mmol) in 1.5 ml of dichloromethane. After stirring overnight at ambient temperature, the reaction mixture was diluted with 50 ml of ethyl acetate, and the organic phase washed sequentially with water, and brine, and then dried over anhydrous magnesium sulfate, filtered and concentrated under vacuum to afford 120 mg of the title compound as a yellow solid.
Reaction SMILES: [O:1]=[C:2]([CH2:6][CH3:7])[CH2:3][C:4]#[N:5].[CH2:8](O)[CH2:9][OH:10].C1(C)C=CC(S(O)(=O)=O)=CC=1>C1(C)C=CC=CC=1.C(OCC)(=O)C>[CH2:6]([C:2]1([CH2:3][C:4]#[N:5])[O:10][CH2:9][CH2:8][O:1]1)[CH3:7]
Reactant: CCC(=O)CC#N
Reactant: OCCO
Agent: Cc1ccc(S(=O)(=O)O)cc1
Solvent: Cc1ccccc1
Solvent: CCOC(C)=O
Product: CCC1(CC#N)OCCO1

Procedure:
A solution of 3-oxo-pentanenitrile (1.582 g, 16.49 mmol), ethylene glycol (1.026 ml, 84.59 mmol) and a catalytic amount of p-Toluene Sulphonic acid (8 mg) in Toluene (10 ml) is refluxed at 150° C. for 2 days using Dean-Stark apparatus. The reaction mixture is diluted with ethyl acetate and washed with saturated sodium bicarbonate solution. The organic phase is dried over MgSO4, filtered, and the solvent evaporated to yield (2-ethyl-[1,3]dioxolan-2-yl)-acetonitrile. 1H NMR (400 MHz, CDCl3) d 4.15(2H,m), 4.05 (2H, m), 2.65 (2H, s), 1.80 (2H, q), 0.95 (3H, t)