Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [OH:1][CH:2]([C:6]1[CH:11]=[CH:10][C:9]([C:12]2[N:16]=[C:15]([C:17]3[O:21][N:20]=[C:19]([C:22]4[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=4)[C:18]=3[C:28]([F:31])([F:30])[F:29])[O:14][N:13]=2)=[CH:8][CH:7]=1)[C:3]([OH:5])=O.CN1CCOCC1.[NH2:39][CH2:40][C:41]([NH2:43])=[O:42].CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F>CN(C=O)C>[NH2:43][C:41](=[O:42])[CH2:40][NH:39][C:3](=[O:5])[CH:2]([OH:1])[C:6]1[CH:7]=[CH:8][C:9]([C:12]2[N:16]=[C:15]([C:17]3[O:21][N:20]=[C:19]([C:22]4[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=4)[C:18]=3[C:28]([F:30])([F:31])[F:29])[O:14][N:13]=2)=[CH:10][CH:11]=1
Reactant: O=C(O)C(O)c1ccc(-c2noc(-c3onc(-c4ccccc4)c3C(F)(F)F)n2)cc1
Reactant: NCC(N)=O
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CN(C)C=O
Solvent: CN1CCOCC1
Product: NC(=O)CNC(=O)C(O)c1ccc(-c2noc(-c3onc(-c4ccccc4)c3C(F)(F)F)n2)cc1
Reaction time: 8 h
Yield: 42.9 %

Procedure:
(R/S)-2-Hydroxy-2-(4-(5-(3-phenyl-4-(trifluoromethyl)isoxazol-5-yl)-1,2,4-oxadiazol-3-yl)phenyl)acetic acid (Int-V, 30 mg, 0.07 mmol) was dissolved in DMF (1 mL) prior to the addition of 4-methylmorpholine (0.061 mL, 0.556 mmol), 2-aminoacetamide (6.70 mg, 0.090 mmol), and HATU (39.7 mg, 0.104 mmol). This was stirred overnight and was then purified by preparative HPLC (PHENOMENEX® Luna 5u C18 21.2×100 mm, gradient elution with Method 1—MeOH/water containing 0.1% trifluoroacetic acid as defined above, 0% B to 100% B over 10 min, 20 mL/min, 220 nM) to give (R/S)-N-(2-amino-2-oxoethyl)-2-hydroxy-2-(4-(5-(3-phenyl-4-(trifluoromethyl)isoxazol-5-yl)-1,2,4-oxadiazol-3-yl)phenyl)acetamide (17.4 mg, 0.030 mmol, 43.2% yield): LCMS=488.2 [M+H]+; 1H NMR (400 MHz, methanol-d4) δ ppm 8.18 (2 H, d, J=8.35 Hz), 7.66-7.80 (4 H, m), 7.51-7.65 (3 H, m), 5.20 (1 H, s), 3.80-4.02 (2 H, m); HPLC Peak RT=8.1 min (Analytical Method D).
Reaction SMILES: [OH:1][N:2]1[C:7]([CH3:9])([CH3:8])[CH2:6][CH:5]([O:10][C:11](=[O:18])[C:12]2[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=2)[CH2:4][C:3]1([CH3:20])[CH3:19].[C:21](Cl)(=[O:39])[CH2:22][CH2:23][CH2:24][CH2:25][CH2:26][CH2:27][CH2:28][CH2:29][CH2:30][CH2:31][CH2:32][CH2:33][CH2:34][CH2:35][CH2:36][CH2:37][CH3:38]>>[C:11]([O:10][CH:5]1[CH2:6][C:7]([CH3:9])([CH3:8])[N:2]([O:1][C:21](=[O:39])[CH2:22][CH2:23][CH2:24][CH2:25][CH2:26][CH2:27][CH2:28][CH2:29][CH2:30][CH2:31][CH2:32][CH2:33][CH2:34][CH2:35][CH2:36][CH2:37][CH3:38])[C:3]([CH3:20])([CH3:19])[CH2:4]1)(=[O:18])[C:12]1[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1
Reactant: CCCCCCCCCCCCCCCCCC(=O)Cl
Reactant: CC1(C)CC(OC(=O)c2ccccc2)CC(C)(C)N1O
Product: CCCCCCCCCCCCCCCCCC(=O)ON1C(C)(C)CC(OC(=O)c2ccccc2)CC1(C)C
Yield: 60 %

Procedure:
Using 1-hydroxy-4-benzoyloxy-2,2,6,6-tetramethylpiperidine, prepared as described by Kurumada T. et. al., loc.cit., and stearoyl chloride in a procedure otherwise similar to the preparation of the compound 101 gives a 60% yield of the compound 109 which is obtained in the form of colourless crystals; melting point: 85-89° C. (acetonitrile).
Reaction SMILES: [NH2:1][C:2]1[O:3][CH2:4][C@@:5]2([N:27]=1)[C:18]1[C:17]([Br:19])=[C:16]([OH:20])[CH:15]=[CH:14][C:13]=1[O:12][C:11]1[C:6]2=[CH:7][C:8]([C:21]2[CH:22]=[N:23][CH:24]=[CH:25][CH:26]=2)=[CH:9][CH:10]=1.C(=O)([O-])[O-].[Cs+].[Cs+].I[CH2:35][C:36]([CH3:39])([CH3:38])[CH3:37]>CN(C=O)C>[Br:19][C:17]1[C:18]2[C@:5]3([CH2:4][O:3][C:2]([NH2:1])=[N:27]3)[C:6]3[C:11](=[CH:10][CH:9]=[C:8]([C:21]4[CH:22]=[N:23][CH:24]=[CH:25][CH:26]=4)[CH:7]=3)[O:12][C:13]=2[CH:14]=[CH:15][C:16]=1[O:20][CH2:35][C:36]([CH3:39])([CH3:38])[CH3:37]
Reactant: CC(C)(C)CI
Reactant: NC1=N[C@@]2(CO1)c1cc(-c3cccnc3)ccc1Oc1ccc(O)c(Br)c12
Agent: O=C([O-])[O-]
Agent: [Cs+]
Solvent: CN(C)C=O
Product: CC(C)(C)COc1ccc2c(c1Br)[C@]1(COC(N)=N1)c1cc(-c3cccnc3)ccc1O2
Temperature: 110 °C
Reaction time: 0.17 h

Procedure:
A vial was charged with (S)-2-amino-1′-bromo-7′-(pyridin-3-yl)-5H-spiro[oxazole-4,9′-xanthen]-2′-ol (163 mg, 0.384 mmol), cesium carbonate (375 mg, 1.152 mmol), and DMF (2.0 mL). The mixture was stirred for 10 min, then 1-iodo-2,2-dimethylpropane (102 μL, 0.768 mmol) was added. The vial was sealed and heated in a Biotage Initiator microwave reactor for 2 h at 110° C. LCMS at this time shows no starting material and mainly desired product. The mixture was partitioned between water and EtOAc. Brine was added to break up the emulsioon that formed and this was partially successful. The aqueous layer was extracted with EtOAc (2×), and the combined organic extracts were dried over sodium sulfate, filtered, and evaporated. The residue was chromatographed on a 50-g SNAP column, eluting with 0-70% of a 90:10:1 mix of DCM/MeOH/NH4OH in DCM to give (S)-1′-bromo-2′-(neopentyloxy)-7′-(pyridin-3-yl)-5H-spiro[oxazole-4,9′-xanthen]-2-amine as an off-white solid after evaporation from DCM/hexane.
Reaction SMILES: Cl.[NH2:2][CH2:3][C:4]1[CH:12]=[CH:11][CH:10]=[C:9]2[C:5]=1[C:6](=[O:22])[N:7]([CH:14]1[CH2:19][CH2:18][C:17](=[O:20])[NH:16][C:15]1=[O:21])[C:8]2=[O:13].C(N(CC)CC)C.[CH3:30][O:31][C:32]1[CH:33]=[C:34]([N:38]=[C:39]=[O:40])[CH:35]=[CH:36][CH:37]=1>C1COCC1>[O:21]=[C:15]1[CH:14]([N:7]2[C:6](=[O:22])[C:5]3[C:9](=[CH:10][CH:11]=[CH:12][C:4]=3[CH2:3][NH:2][C:39]([NH:38][C:34]3[CH:35]=[CH:36][CH:37]=[C:32]([O:31][CH3:30])[CH:33]=3)=[O:40])[C:8]2=[O:13])[CH2:19][CH2:18][C:17](=[O:20])[NH:16]1
Reactant: COc1cccc(N=C=O)c1
Reactant: NCc1cccc2c1C(=O)N(C1CCC(=O)NC1=O)C2=O
Agent: Cl
Solvent: CCN(CC)CC
Solvent: C1CCOC1
Product: COc1cccc(NC(=O)NCc2cccc3c2C(=O)N(C2CCC(=O)NC2=O)C3=O)c1
Temperature: 5 °C
Reaction time: 5 h
Yield: 80.2 %

Procedure:
A suspension of 4-aminomethyl-2-(2,6-dioxo-piperidin-3-yl)-isoindole-1,3-dione hydrochloride (0.7 g, 2.0 mmol) and triethylamine (0.3 g, 2.6 mmol) in THF (30 mL) was cooled to 5° C. 3-Methoxyphenyl isocyanate (0.4 g, 2.6 mmol) was added, and the mixture was stirred at room temperature 5 hours. The mixture was concentrated, and the residue was dissolved in CH2Cl2 (80 mL). The CH2Cl2 solution was washed with 1N HCl (40 mL), water (40 mL), and brine (40 mL), and dried (MgSO4). Solvent was removed, and the solid was slurried with ethanol (20 mL) to give 1-[2-(2,6-dioxo-piperidin-3-yl)-1,3-dioxo-2,3 dihydro-1H-isoindol-4-ylmethyl]-3-(3-methoxy-phenyl)-urea (0.7 g, 80%) as a white solid: mp 160-162° C.; 1H NMR (DMSO-d6) δ 2.06-2.10 (m, 1H), 2.50-2.65 (m, 2H), 2.85-2.99 (m, 1H), 3.69 (s, 3H, OCH3), 4.69 (d, J=5.2 Hz, 2H, CH2), 5.14-5.20 (dd, J=4.6 and 12.1 Hz, 1H, CH), 6.49 (d, J=7.9 Hz, 1H, Ar), 6.76-6.86 (m, 2H, Ar), 7.08-7.14 (m, 2H), 7.76-7.85 (m, 3H, Ar), 8.81 (s, 1H, NH), 11.16 (s, 1H, NH); 13C NMR (DMSO-d6) δ 21.99, 30.94, 38.72, 48.87, 54.82, 103.44, 106.70, 110.05, 121.86, 127.19, 129.36, 131.61, 133.62, 134.72, 140.23, 141.51, 155.15, 159.62, 167.01, 167.60, 169.82, 172.76; Anal. calcd. for C22H20N4O6: C, 60.55; H, 4.62; N, 12.84. Found: C, 60.18; H, 4.42; N, 12.63.
Reaction SMILES: [CH3:1][O:2][C:3](=[O:15])[CH2:4][C:5]1[N:10]=[C:9](Cl)[C:8]([F:12])=[C:7]([O:13][CH3:14])[N:6]=1.O.C(OCC)(=O)C.[NH:23]1[CH2:28][CH2:27][O:26][CH2:25][CH2:24]1>>[CH3:1][O:2][C:3](=[O:15])[CH2:4][C:5]1[N:6]=[C:7]([O:13][CH3:14])[C:8]([F:12])=[C:9]([N:23]2[CH2:28][CH2:27][O:26][CH2:25][CH2:24]2)[N:10]=1
Reactant: C1COCCN1
Reactant: COC(=O)Cc1nc(Cl)c(F)c(OC)n1
Solvent: O
Solvent: CCOC(C)=O
Product: COC(=O)Cc1nc(OC)c(F)c(N2CCOCC2)n1

Procedure:
A solution of 8.36 g of (4-chloro-5-fluoro-6-methoxypyrimidin-2-yl)acetic acid methyl ester in 76 ml of morpholine is stirred at ambient temperature for one and a half hours. The reaction medium is concentrated under reduced pressure. The residue obtained is taken up with 50 ml of water and 200 ml of ethyl acetate. After settling out, the organic phase is dried over magnesium sulfate, filtered, and then concentrated under reduced pressure, so as to give 8.86 g of (5-fluoro-4-methoxy-6-morpholin-4-ylpyrimidin-2-yl)acetic acid methyl ester in the form of a beige solid, the characteristics of which are the following:
Reaction SMILES: [NH2:1][CH2:2][CH2:3][CH2:4][CH2:5][C@H:6]([NH:14][C:15](=[O:34])[NH:16][C@@H:17]([CH2:25][CH2:26][C:27]([O:29][C:30]([CH3:33])([CH3:32])[CH3:31])=[O:28])[C:18]([O:20][C:21]([CH3:24])([CH3:23])[CH3:22])=[O:19])[C:7]([O:9][C:10]([CH3:13])([CH3:12])[CH3:11])=[O:8].[C:35]([O:39][C:40](=[O:68])[CH2:41][N:42]1[CH:46]=[CH:45][N:44]=[C:43]1[CH2:47][N:48]([CH2:57][C:58]1[CH:63]=[CH:62][C:61]([O:64][CH2:65][C:66]#[CH:67])=[CH:60][CH:59]=1)[CH2:49][CH2:50][CH2:51][CH2:52][CH2:53][C:54](O)=[O:55])([CH3:38])([CH3:37])[CH3:36].CCN=C=NCCCN(C)C.C1C=CC2N(O)N=NC=2C=1.CCN(C(C)C)C(C)C>ClCCCl>[C:35]([O:39][C:40](=[O:68])[CH2:41][N:42]1[CH:46]=[CH:45][N:44]=[C:43]1[CH2:47][N:48]([CH2:57][C:58]1[CH:63]=[CH:62][C:61]([O:64][CH2:65][C:66]#[CH:67])=[CH:60][CH:59]=1)[CH2:49][CH2:50][CH2:51][CH2:52][CH2:53][C:54](=[O:55])[NH:1][CH2:2][CH2:3][CH2:4][CH2:5][C@@H:6]([C:7]([O:9][C:10]([CH3:13])([CH3:12])[CH3:11])=[O:8])[NH:14][C:15](=[O:34])[NH:16][C@H:17]([C:18]([O:20][C:21]([CH3:22])([CH3:23])[CH3:24])=[O:19])[CH2:25][CH2:26][C:27]([O:29][C:30]([CH3:33])([CH3:32])[CH3:31])=[O:28])([CH3:36])([CH3:38])[CH3:37]
Reactant: C#CCOc1ccc(CN(CCCCCC(=O)O)Cc2nccn2CC(=O)OC(C)(C)C)cc1
Reactant: CC(C)(C)OC(=O)CC[C@H](NC(=O)N[C@@H](CCCCN)C(=O)OC(C)(C)C)C(=O)OC(C)(C)C
Agent: CCN=C=NCCCN(C)C
Agent: On1nnc2ccccc21
Solvent: ClCCCl
Solvent: CCN(C(C)C)C(C)C
Product: C#CCOc1ccc(CN(CCCCCC(=O)NCCCC[C@H](NC(=O)N[C@@H](CCC(=O)OC(C)(C)C)C(=O)OC(C)(C)C)C(=O)OC(C)(C)C)Cc2nccn2CC(=O)OC(C)(C)C)cc1
Yield: 57.1 %

Procedure:
A solution of (S)-di-tert-butyl 2-(3-((S)-6-amino-1-(tert-butoxy)-1-oxohexan-2-yl)ureido)pentanedioate (0.480 g, 1.0 mmol), 6-(((1-(2-(tert-butoxy)-2-oxoethyl)-1H-imidazol-2-yl)methyl)(4-(prop-2-yn-1-yloxy)benzyl)amino)hexanoic acid (0.220 g, 0.468 mmol), EDCI (0.191 g, 1.0 mmol), HOBt (0.135 g, 1.0 mmol) and DIPEA (0.40 mL) in DCE (10.0 mL) was stirred at room temperature for 3 h. The solvent was evaporated to give a residue, which was purified by Biotage eluting with DCM/MeOH to give (14S,18S)-tri-tert-butyl 1-(1-(2-(tert-butoxy)-2-oxoethyl)-1H-imidazol-2-yl)-8,16-dioxo-2-(4-(prop-2-yn-1-yloxy)benzyl)-2,9,15,17-tetraazaicosane-14,18,20-tricarboxylate (0.251 g, 57%). MS (ESI), 939.5 (M+H)+.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]2[C:12](=[O:13])[C:11]3[CH:14]=[C:15]([CH:18]=[CH2:19])[CH:16]=[CH:17][C:10]=3[CH:9]=[CH:8][C:5]2=[N:6][CH:7]=1.BrN1C(=[O:26])CCC1=O.CC([O-])(C)C.[K+]>CS(C)=O.O>[Cl:1][C:2]1[CH:3]=[C:4]2[C:12](=[O:13])[C:11]3[CH:14]=[C:15]([CH:18]4[CH2:19][O:26]4)[CH:16]=[CH:17][C:10]=3[CH:9]=[CH:8][C:5]2=[N:6][CH:7]=1
Reactant: O=C1CCC(=O)N1Br
Reactant: C=Cc1ccc2ccc3ncc(Cl)cc3c(=O)c2c1
Agent: CC(C)(C)[O-]
Agent: [K+]
Solvent: CS(C)=O
Solvent: O
Product: O=c1c2cc(C3CO3)ccc2ccc2ncc(Cl)cc12
Temperature: 60 °C
Reaction time: 0.75 h

Procedure:
3-chloro-7-vinyl-5H-benzo[4,5]cyclohepta[1,2-b]pyridin-5-one (0.30 g, 1.12 mmol) was dissolved in 17 mL DMSO and 3.0 mL water. N-Bromosuccinimide (0.20 g, 1.12 mmol) was added and the reaction was heated in an oil bath at 60° C. for 1 hour at which time an additional 0.1 g N-Bromosuccinimide (0.56 mmol) was added and the mixture was stirred an additional 45 min at 60° C. The resulting mixture was diluted with water and extracted with ethyl acetate three times. The combined organics were washed with brine, dried over sodium sulfate, filtered, and concentrated in vacuo. The resulting crude residue was dissolved in 30 mL tetrahydrofuran and 6 mL t-BuOH. t-BuOK (2.24 mL of 1.0 M in THF, 2.24 mmol) was added dropwise and the resulting orange slurry was stirred at room temperature for 45 min. The reaction was diluted with water and extracted with ethyl acetate three times. The combined organics were washed with brine, dried over magnesium sulfate, concentrated in vacuo, and purified via flash chromatography (silica, 0-25% ethyl acetate/hexanes) to afford the title compound. 1H NMR (600 MHz, CDCl3) δ 8.79 (d, 1H); 8.49 (d, 1H); 8.20 (d, 1H); 7.57 (d, 1H); 7.55 (dd, 1H); 7.27 (d, 1H); 7.23 (d, 1H); 3.99 (dd, 1H); 3.21 (dd, 1H); 2.84 (dd, 1H).
Reaction SMILES: C(N(C(C)C)CC)(C)C.O=[C:11]1[CH2:17][C@H:16]2[N:13]([C:14](=[O:35])[C@H:15]2[C:18]([CH3:34])([O:20][C:21]([O:23][CH2:24][C:25]2[CH:30]=[CH:29][C:28]([N+:31]([O-:33])=[O:32])=[CH:27][CH:26]=2)=[O:22])[CH3:19])[C@H:12]1[C:36]([O:38][CH2:39][C:40]1[CH:45]=[CH:44][C:43]([N+:46]([O-:48])=[O:47])=[CH:42][CH:41]=1)=[O:37].FC(F)(F)S(OS(C(F)(F)F)(=O)=O)(=O)=O.[CH3:64][C:65]1[O:69][C:68]([SH:70])=[N:67][N:66]=1>C(Cl)Cl.CN(C1C=CN=CC=1)C>[CH3:19][C:18]([C@@H:15]1[C:14](=[O:35])[N:13]2[C@@H:16]1[CH2:17][C:11]([S:70][C:68]1[O:69][C:65]([CH3:64])=[N:66][N:67]=1)=[C:12]2[C:36]([O:38][CH2:39][C:40]1[CH:41]=[CH:42][C:43]([N+:46]([O-:48])=[O:47])=[CH:44][CH:45]=1)=[O:37])([O:20][C:21]([O:23][CH2:24][C:25]1[CH:30]=[CH:29][C:28]([N+:31]([O-:33])=[O:32])=[CH:27][CH:26]=1)=[O:22])[CH3:34]
Reactant: CC(C)(OC(=O)OCc1ccc([N+](=O)[O-])cc1)[C@@H]1C(=O)N2[C@@H](C(=O)OCc3ccc([N+](=O)[O-])cc3)C(=O)C[C@H]12
Reactant: Cc1nnc(S)o1
Agent: CN(C)c1ccncc1
Agent: O=S(=O)(OS(=O)(=O)C(F)(F)F)C(F)(F)F
Solvent: ClCCl
Solvent: CCN(C(C)C)C(C)C
Product: Cc1nnc(SC2=C(C(=O)OCc3ccc([N+](=O)[O-])cc3)N3C(=O)[C@@H](C(C)(C)OC(=O)OCc4ccc([N+](=O)[O-])cc4)[C@H]3C2)o1
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 70.1 %

Procedure:
A solution of N,N-diisopropyl-N-ethylamine (0.135 ml) in methylene chloride (1.21 ml) was added to a solution of 4-nitrobenzyl (2R, 5R, 6R)-3,7-dioxo-6-[1-methyl-1-(4-nitrobenzyloxycarbonyloxy)ethyl]-1-azabicyclo[3.2.0]heptane-2-carboxylate (350 mg) and 4-(N,N-dimethylamino)pyridine (7.9 mg) in methylene chloride (17.5 ml) at -30° C. A solution of trifluoromethanesulfonic anhydride (0.114 ml) in methylene chloride (1.02 ml) was added to the mixture and stirring was continued at the same temperature for 30 minutes. A solution of N,N-diisopropyl-N-ethylamine (0.563 ml) in methylene chloride (5.06 ml) and 5-methyl-1,3,4-oxadiazole-2-thiol (225 mg) were then added thereto, and the reaction mixture was stirred at -30° C. for 30 minutes and allowed to warm to ambient temperature over a period of an hour. After stirring at ambient temperature for 4 hours, the mixture was allowed to stand at 5° C. for 14 hours. After the solvent was removed by evaporation, the residue was dissolved in ethyl acetate (20 ml). The organic solution was washed in turn with water and a saturated aqueous sodium chloride, dried over magnesium sulfate and evaporated in vacuo. The residue was chromatographed on deactivated silica gel with 10% water (7 g), eluting with a mixture of benzene and acetone (20:1 to 10:1) to give 4-nitrobenzyl (5R, 6R)-6-[1-methyl-1-(4-nitrobenzyloxycarbonyloxy)ethyl]-3-(5-methyl-1,3,4-oxadiazol-2-ylthio)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylate (290 mg) as an oil.
Reaction SMILES: [NH:1]1[CH:5]=[CH:4][CH:3]=[N:2]1.Cl[C:7]1[N:8]=[C:9]([NH:17][CH2:18][C:19]2[CH:24]=[CH:23][C:22]([O:25][CH3:26])=[C:21]([O:27][CH3:28])[CH:20]=2)[C:10]2[CH:15]=[C:14]([CH3:16])[S:13][C:11]=2[N:12]=1>>[N:1]1([C:7]2[N:8]=[C:9]([NH:17][CH2:18][C:19]3[CH:24]=[CH:23][C:22]([O:25][CH3:26])=[C:21]([O:27][CH3:28])[CH:20]=3)[C:10]3[CH:15]=[C:14]([CH3:16])[S:13][C:11]=3[N:12]=2)[CH:5]=[CH:4][CH:3]=[N:2]1
Reactant: c1cn[nH]c1
Reactant: COc1ccc(CNc2nc(Cl)nc3sc(C)cc23)cc1OC
Product: COc1ccc(CNc2nc(-n3cccn3)nc3sc(C)cc23)cc1OC

Procedure:
Following the procedure of Example 97, the reaction of pyrazole with 2-chloro-6-methyl-4-(3,4-dimethoxybenzylamino)-thieno-[2,3-d]-pyrimidine gives 2-(pyrazol-1-yl)-6-methyl-4-(3,4-dimethoxybenzylamino)-thieno-[2,3-d]-pyrimidine.
Reaction SMILES: [F:1][C:2]1[CH:7]=[CH:6][CH:5]=[C:4]([F:8])[C:3]=1[CH2:9][CH2:10][NH2:11].[N:12]1[CH:17]=[CH:16][CH:15]=[CH:14][C:13]=1[NH:18][C:19](N1C=CN=C1)=[S:20].C(OCC)(=O)C>CN(C)C=O>[F:1][C:2]1[CH:7]=[CH:6][CH:5]=[C:4]([F:8])[C:3]=1[CH2:9][CH2:10][NH:11][C:19]([NH:18][C:13]1[CH:14]=[CH:15][CH:16]=[CH:17][N:12]=1)=[S:20]
Reactant: S=C(Nc1ccccn1)n1ccnc1
Reactant: NCCc1c(F)cccc1F
Solvent: CCOC(C)=O
Solvent: CN(C)C=O
Product: Fc1cccc(F)c1CCNC(=S)Nc1ccccn1
Temperature: 25 °C
Yield: 10.1 %

Procedure:
A solution of 2-(2,6-difluorophenyl)ethylamine (0.43 g, 2.7 mmol) and 1-[(2-pyridyl)thiocarbamoyl]imidazole (0.55 g, 2.7 mmol) in N,N-dimethylformamide (20 mL) was stirred at 90° C. for 27 h. The reaction was cooled to room temperature, poured into ethyl acetate, washed with water, 1N aqueous HCl, water, saturated sodium bicarbonate, and brine. The organic layer was concentrated and the resultant oil was purified by chromatography on silica gel to provide 0.08 g (10%) of the titled product as a pale yellow solid:
Reaction SMILES: [CH:1]1([CH2:4][O:5][C:6]2[CH:14]=[CH:13][C:12]([S:15]([CH3:18])(=[O:17])=[O:16])=[CH:11][C:7]=2[C:8]([OH:10])=O)[CH2:3][CH2:2]1.Cl.[N:20]1([C:26]2[C:30]3[CH:31]=[CH:32][CH:33]=[CH:34][C:29]=3[S:28][N:27]=2)[CH2:25][CH2:24][NH:23][CH2:22][CH2:21]1.C(OCC)(=O)C>C(#N)C>[S:28]1[C:29]2[CH:34]=[CH:33][CH:32]=[CH:31][C:30]=2[C:26]([N:20]2[CH2:21][CH2:22][N:23]([C:8]([C:7]3[CH:11]=[C:12]([S:15]([CH3:18])(=[O:17])=[O:16])[CH:13]=[CH:14][C:6]=3[O:5][CH2:4][CH:1]3[CH2:2][CH2:3]3)=[O:10])[CH2:24][CH2:25]2)=[N:27]1
Reactant: c1ccc2c(N3CCNCC3)nsc2c1
Reactant: CS(=O)(=O)c1ccc(OCC2CC2)c(C(=O)O)c1
Agent: Cl
Solvent: CC#N
Solvent: CCOC(C)=O
Product: CS(=O)(=O)c1ccc(OCC2CC2)c(C(=O)N2CCN(c3nsc4ccccc34)CC2)c1

Procedure:
Prepared in analogy to example 1.1 b) from 2-cyclopropylmethoxy-5-methanesulfonyl-benzoic acid (Example 2.6) and 3-piperazin-1-yl-benzo[d]isothiazole hydrochloride (CA=87691-88-1) in acetonitrile. Chromatography (SiO2; ethyl acetate) yields the title compound as a colorless solid.
Reaction SMILES: [CH2:1]([O:5][C:6](=[O:33])[NH:7][C:8]1([C:19]([NH:21][C:22]2[CH:27]=[CH:26][C:25]([N:28]([CH2:31][CH3:32])[CH2:29][CH3:30])=[CH:24][CH:23]=2)=[O:20])[CH2:17][CH2:16][C:15]2[C:10](=[CH:11][CH:12]=[C:13](Br)[CH:14]=2)[CH2:9]1)[CH:2]([CH3:4])[CH3:3].C1(C)C=CC=CC=1P(C1C=CC=CC=1C)C1C=CC=CC=1C.[C:56]([NH2:60])(=[O:59])[CH:57]=[CH2:58].C(N(CC)CC)C>C([O-])(=O)C.[Pd+2].C([O-])(=O)C.CN(C=O)C>[CH2:1]([O:5][C:6](=[O:33])[NH:7][C:8]1([C:19]([NH:21][C:22]2[CH:27]=[CH:26][C:25]([N:28]([CH2:31][CH3:32])[CH2:29][CH3:30])=[CH:24][CH:23]=2)=[O:20])[CH2:17][CH2:16][C:15]2[C:10](=[CH:11][CH:12]=[C:13](/[CH:58]=[CH:57]/[C:56]([NH2:60])=[O:59])[CH:14]=2)[CH2:9]1)[CH:2]([CH3:4])[CH3:3]
Reactant: C=CC(N)=O
Reactant: CCN(CC)c1ccc(NC(=O)C2(NC(=O)OCC(C)C)CCc3cc(Br)ccc3C2)cc1
Agent: [Pd+2]
Agent: CC(=O)[O-]
Agent: Cc1ccccc1P(c1ccccc1C)c1ccccc1C
Solvent: CCN(CC)CC
Solvent: CN(C)C=O
Product: CCN(CC)c1ccc(NC(=O)C2(NC(=O)OCC(C)C)CCc3cc(/C=C/C(N)=O)ccc3C2)cc1
Temperature: 110 °C
Yield: 94.6 %

Procedure:
To a 10 ml pressure tube, the bromide from Example 42B (125 mg, 0.24 mmol), palladium(II)acetate (2.7 mg, 0.012 mmol), tri-o-tolylphosphine (110 mg, 0.36 mmol), acrylamide (34 mg, 048 mmol), triethylamine (0.12 ml, 0.8 mmol) and DMF (2 ml) were added. After purging with nitrogen, the reaction mixture was heated at 110° C. for overnight. The reaction mixture was partitioned between methylene chloride and water. The organic layer was washed with brine and concentrated under reduced pressure. The residue was purified on column of silica gel to provide the titled compound (115 mg, 95%) as a white solid. 1HNNMR (DMSO-d6, 300 MHz), δ 9.13 (b, 1H, NH), 7.45 and 7.30 (b, 2H, NH2), 7.01 (b, 1H, NH), 7.36, 7.32, 6.56 and 6.52 (AB, J=12 Hz, 2H, CH═CH), 7.32, 7.30, 6.61 and 6.58 (AB, 4H, J=9 Hz, Ar—H), 3.76–3.66 (m, 2H, OCH2), 3.27 (q, J=3.0 Hz, 4H, 2NCH2), 3.33, 3.29, 3.07 and 3.03 (AB, J=12 Hz, 2H, CH2), 2.80–2.71 (m, 2H, CH2), 2.35 and 2.09 (m, 2H, CH2), 1.79 (m, H, CH), 1.04 (t, J=3.0 Hz, 6H, 2CH3), 0.84 (d, J=6.0 Hz, 6H, 2 CH3). MS (ESI) (M+1)+ 507, (M−1)+ 505.
Reaction SMILES: [OH:1][CH2:2][C@H:3]1[CH2:7][CH2:6][CH2:5][NH:4]1.[C:8](#[N:11])[CH:9]=[CH2:10]>C(Cl)Cl>[OH:1][CH2:2][C@H:3]1[CH2:7][CH2:6][CH2:5][N:4]1[CH2:10][CH2:9][C:8]#[N:11]
Reactant: C=CC#N
Reactant: OC[C@H]1CCCN1
Solvent: ClCCl
Product: N#CCCN1CCC[C@@H]1CO
Temperature: 25 °C

Procedure:
(R)-2-hydroxymethylpyrrolidine (Tokyo Kasei Kogyo Co., Ltd.) (50 g) was dissolved in methylene chloride (500 mL), and acrylonitrile (36 mL) was added dropwise to the solution with stirring at room temperature. Subsequently, the mixture was stirred overnight at room temperature. After the completion of the reaction, the solvent was concentrated to give (R)-3-(2-hydroxymethylpyrrolidin-1-yl)propionitrile (76 g).
Reaction SMILES: [CH2:1]([N:8]1[CH2:14][C@@H:13]2[C@H:9]1[CH2:10][CH2:11][NH:12]2)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[Cl:15][C:16]1[CH:21]=[CH:20][C:19](I)=[CH:18][N:17]=1.CC(C)([O-])C.[Na+]>>[CH2:1]([N:8]1[CH2:14][C@@H:13]2[C@H:9]1[CH2:10][CH2:11][N:12]2[C:19]1[CH:18]=[N:17][C:16]([Cl:15])=[CH:21][CH:20]=1)[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: c1ccc(CN2C[C@H]3NCC[C@H]32)cc1
Reactant: Clc1ccc(I)cn1
Agent: CC(C)(C)[O-]
Agent: [Na+]
Product: Clc1ccc(N2CC[C@@H]3[C@H]2CN3Cc2ccccc2)cn1
Yield: 84 %

Procedure:
The product from Example 51E (0.26 g, 1.0 mmol) and 2-chloro-5-iodopyridine were processed according to the procedure described in Example 1A, except that a larger amount of sodium tert-butoxide (0.384 g, 4.0 mmol) was used. The crude product was purified by chromatography on SiO2 (dichloromethane:methanol, 95:5) to provide the title compound (0.25 g, 84%). MS (DCI/NH3) m/z 300/302 (M+H)+.
Reaction SMILES: [H-].[Na+].[Si:3]([O:10][CH2:11][C@H:12]1[O:16][C@@H:15]([N:17]2[CH:24]=[C:23]([I:25])[C:21]([NH2:22])=[N:20][C:18]2=[O:19])[CH2:14][C@@H:13]1[OH:26])([C:6]([CH3:9])([CH3:8])[CH3:7])([CH3:5])[CH3:4].[CH2:27](Br)[CH:28]=[CH2:29]>C1COCC1>[CH2:29]([O:26][C@@H:13]1[C@@H:12]([CH2:11][O:10][Si:3]([C:6]([CH3:9])([CH3:7])[CH3:8])([CH3:4])[CH3:5])[O:16][C@@H:15]([N:17]2[CH:24]=[C:23]([I:25])[C:21]([NH2:22])=[N:20][C:18]2=[O:19])[CH2:14]1)[CH:28]=[CH2:27]
Reactant: CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](n2cc(I)c(N)nc2=O)C[C@@H]1O
Reactant: C=CCBr
Agent: [H-]
Agent: [Na+]
Solvent: C1CCOC1
Product: C=CCO[C@H]1C[C@H](n2cc(I)c(N)nc2=O)O[C@@H]1CO[Si](C)(C)C(C)(C)C
Temperature: 25 °C
Reaction time: 0.75 h

Procedure:
To a solution of NaH (60%, 113 mg, 2.84 mmol) in THF (26 ml) under N2 atmosphere, was slowly added a solution of the starting nucleoside (39) (669 mg, 1.43 mmol) in THF (6 ml). The mixture was stirred at room temperature for 45 minutes, cooled at 0° C. and allyl bromide (134 μL, 1.58 mmol) was slowly added. After 15 h at room temperature, the solution was cooled to 0° C. and quenched by addition of H2O (5 ml). THF evaporated under reduced pressure and the product extracted into EtOAc (3×25 ml). Combined organic extracts were dried (MgSO4) filtered and the volatiles evaporated under reduced pressure to give a residue that was purified by flash chromatography on silica gel with EtOAc affording the expected 3′-O-allyl product (40) (323 mg, 44%) as a colourless oil, together with some unreacted starting material (170 mg); 1H NMR (d6 DMSO) δ 0.00 (s, 3H, CH3), 0.01 (s, 3H, CH3), 0.79 (s, 9H, 3CH3), 1.84 (ddd, J=13.3, 8.2 and 5.5 Hz, 1H, H-2′), 2.20-2.25 (m, 1H, H-2′), 3.62-3.72 (m, 2H, H-5′), 3.88-3.93 (m, 4H, H-3′,4′, HHC—CH═), 5.1 (dd, J=8.5, 1.7 Hz, 1H, CH═CHH), 5.16 (dd, J=17.2, 1.7 Hz, 1H, CH═CHH), 5.75-5.83 (m, 1H, CH═CHH), 5.94 (dd, J=8.4, 5.6 Hz, 1H, H-1′), 6.53 (br s, 1H, NHH), 7.74 (br s, 1H, NHH), 7.83 (s, 1H, H-6); MS (ES): m/z (%) (M−H) 506 (100%).
Reaction SMILES: [CH2:1]([C:4]1[CH:5]=[N:6][C:7]([N:10]2[CH2:15][CH2:14][CH:13]([OH:16])[CH2:12][CH2:11]2)=[N:8][CH:9]=1)[CH2:2][CH3:3].CCN(CC)CC.[CH3:24][S:25](Cl)(=[O:27])=[O:26]>C(Cl)Cl>[CH3:24][S:25]([O:16][CH:13]1[CH2:14][CH2:15][N:10]([C:7]2[N:8]=[CH:9][C:4]([CH2:1][CH2:2][CH3:3])=[CH:5][N:6]=2)[CH2:11][CH2:12]1)(=[O:27])=[O:26]
Reactant: CCCc1cnc(N2CCC(O)CC2)nc1
Reactant: CS(=O)(=O)Cl
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CCCc1cnc(N2CCC(OS(C)(=O)=O)CC2)nc1
Temperature: 25 °C
Reaction time: 1 h
Yield: 558.3 %

Procedure:
To a stirring solution of 1-(5-propylpyrimidin-2-yl)piperidin-4-ol (9.2 g, 41.6 mmol), Et3N (12.85 mL, 91 mmol, Aldrich) in CH2Cl2 (80 mL) at 0° C. was added a solution of Methanesulfonyl chloride (3.54 mL, 45 7 mmol, Acros) in CH2Cl2 (20 mL) dropwise. The reaction mixture was stirred at room temperature for 1 h and washed with 1N HCl in H2O, saturated NaHCO3 in H2O and brine. The organic layer was dried over Na2SO4 and concentrated in vacuo to yield 11.7 g of the desired product as an off-white solid. MS (ESI) 300 (M+H).