Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [CH3:1]/[C:2](/[CH2:7][CH2:8]/[CH:9]=[C:10](\[CH3:18])/[CH2:11][CH2:12][C:13](=[O:17])[C:14]([CH3:16])=[CH2:15])=[CH:3]\[C:4]([NH2:6])=[O:5].[C:19]([O:23][CH3:24])(=[O:22])[CH2:20][SH:21].C(N(CC)CC)C>CO>[C:4](/[CH:3]=[C:2](\[CH3:1])/[CH2:7][CH2:8]/[CH:9]=[C:10](\[CH3:18])/[CH2:11][CH2:12][C:13](=[O:17])[CH:14]([CH3:16])[CH2:15][S:21][CH2:20][C:19]([O:23][CH3:24])=[O:22])(=[O:5])[NH2:6]
Reactant: COC(=O)CS
Reactant: C=C(C)C(=O)CC/C(C)=C/CC/C(C)=C/C(N)=O
Solvent: CO
Solvent: CCN(CC)CC
Product: COC(=O)CSCC(C)C(=O)CC/C(C)=C/CC/C(C)=C/C(N)=O
Temperature: 25 °C
Reaction time: 8 h

Procedure:
A solution of 2.0 g (0.008 mol) of (E,E)-3,7,11-trimethyl-10-oxo-2,6,11-dodecatrienamide in 60 ml of methanol is treated with 2.3 ml of methyl thioglycolate and 3.4 ml of triethylamine. The solution is stirred at room temperature for 8 hours under argon. After removing the solvent the residue is taken up in water and methylene chloride. After extraction the organic phase is dried and freed from solvent. The residue is chromatographed on silica gel with ether-methanol 20:1. There is obtained methyl [[(6E,10E)-11-carbamoyl-2,6,10-trimethyl-3-oxo-6,10-undecadienyl]thio]acetate which exhibits the following absorption bands in the IR spectrum: 3447 cm-1, 3352 cm-1, 3195 cm-1, 1735 cm-1, 1712 cm-1, 1669 cm-1, 1638 cm-1 1609 cm-1, 1436 cm-1, 1300 cm-1, 1137 cm-1, 1008 cm-1.
Reaction SMILES: I[C:2]1[N:7]=[C:6]([CH3:8])[CH:5]=[CH:4][C:3]=1[OH:9].C(N(CC)CC)C.[C:17]([N:24]1[CH2:28][CH2:27][CH2:26][C@H:25]1[C:29]#[CH:30])([O:19][C:20]([CH3:23])([CH3:22])[CH3:21])=[O:18]>CN(C=O)C.Cl.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.[Cu]I>[C:17]([N:24]1[CH2:28][CH2:27][CH2:26][C@H:25]1[C:29]1[O:9][C:3]2[C:2](=[N:7][C:6]([CH3:8])=[CH:5][CH:4]=2)[CH:30]=1)([O:19][C:20]([CH3:23])([CH3:22])[CH3:21])=[O:18]
Reactant: Cc1ccc(O)c(I)n1
Reactant: C#C[C@@H]1CCCN1C(=O)OC(C)(C)C
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: [Cu]I
Agent: Cl
Solvent: CN(C)C=O
Solvent: CCN(CC)CC
Product: Cc1ccc2oc([C@@H]3CCCN3C(=O)OC(C)(C)C)cc2n1
Temperature: 25 °C
Reaction time: 1 h

Procedure:
A 3.10 g (13.2 mmol) sample of 6-iodo-2-picoline-5-ol (Aldrich Chem. Co.) was dissolved in 5 mL of DMF, and (Ph3P)2PdCl2 (0.38 g, 0.50 mmol), CuI (0.377 g, 1.98 mmol) and triethylamine (1.80 mL, 13.2 mmol) were added. The mixture was stirred under N2 at room temperature for 1 hour, then 2.15 g (11 mmol) of 1-BOC-2-(S)-ethynylpyrrolidine, from Example 1c above, dissolved in 1 mL of DMF, was added carefully. The reaction was stirred at 60° C. for 16 hours, then cooled to room temperature. The reaction mixture was diluted with 2 N HCl and extracted with ether. The aqueous layer was adjusted to pH 10 with K2CO3, then extracted with CH2Cl2. The extract was washed with 20% NaOH, brine, dried over MgSO4, and the solvent was removed. The residue was repeatedly dissolved in toluene and distilled to azeotropically remove the DMF. The residue was chromatographed on silica gel, eluting with 100:0 to 50:50 hexane:EtOAc to give 521 mg of title compound: 1H NMR (CDCl3, 300 MHz) δ 1.33 and 1.47 (2 s, 9H), 1.90-2.30 (m, 4H), 2.63 (s, 3H), 3.45-3.65 (m, 2H), 4.95 and 5.10 (2 s, 1H), 5.58 (s, 1H), 7.02 (d, 1H), 7.55 (d, 1H); MS m/z: 303 (M+H)+.
Reaction SMILES: [NH:1]([C:3]1[C:8]([C:9]2[CH:10]=[N:11][CH:12]=[CH:13][CH:14]=2)=[CH:7][CH:6]=[CH:5][N:4]=1)[NH2:2].[CH:15](OCC)(OCC)OCC>>[N:11]1[CH:12]=[CH:13][CH:14]=[C:9]([C:8]2[C:3]3[N:4]([CH:15]=[N:2][N:1]=3)[CH:5]=[CH:6][CH:7]=2)[CH:10]=1
Reactant: NNc1ncccc1-c1cccnc1
Reactant: CCOC(OCC)OCC
Product: c1cncc(-c2cccn3cnnc23)c1
Temperature: 100 °C

Procedure:
A 4.15 g portion of 2-hydrazino-3,3'-bipyridine was dissolved in 30 ml of triethyl orthoformate and heated at 100° C. for 2 hours. The volatiles were removed at reduced pressure and the residue purified by chromatography on hydrous magnesium silicate, eluting with ethyl acetate. The solid was recrystallized from methylene chloride-hexane, giving 2.67 g of the desired product, mp 186°-189° C.
Reaction SMILES: [C:1]1([CH:7]([O:14][C:15]([C:17]2[N:22]3[C:23](=[O:26])[C@@H:24]([NH2:25])[C@H:21]3[S:20][CH2:19][C:18]=2[S:27][CH:28]([C:35]([C:48]2[CH:53]=[CH:52][CH:51]=[CH:50][CH:49]=2)([C:42]2[CH:47]=[CH:46][CH:45]=[CH:44][CH:43]=2)[C:36]2[CH:41]=[CH:40][CH:39]=[CH:38][CH:37]=2)[S:29][C:30]2[N:31]=[N:32][NH:33][CH:34]=2)=[O:16])[C:8]2[CH:13]=[CH:12][CH:11]=[CH:10][CH:9]=2)[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.[C:54](O)(=[O:63])[C@@H:55]([C:57]1[CH:62]=[CH:61][CH:60]=[CH:59][CH:58]=1)[OH:56].C1(N=C=NC2CCCCC2)CCCCC1>ClCCl>[C:1]1([CH:7]([O:14][C:15]([C:17]2[N:22]3[C:23](=[O:26])[C@@H:24]([NH:25][C:54](=[O:63])[C@@H:55]([C:57]4[CH:62]=[CH:61][CH:60]=[CH:59][CH:58]=4)[OH:56])[C@H:21]3[S:20][CH2:19][C:18]=2[S:27][CH:28]([C:35]([C:48]2[CH:53]=[CH:52][CH:51]=[CH:50][CH:49]=2)([C:42]2[CH:43]=[CH:44][CH:45]=[CH:46][CH:47]=2)[C:36]2[CH:37]=[CH:38][CH:39]=[CH:40][CH:41]=2)[S:29][C:30]2[N:31]=[N:32][NH:33][CH:34]=2)=[O:16])[C:8]2[CH:13]=[CH:12][CH:11]=[CH:10][CH:9]=2)[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1
Reactant: O=C(O)[C@H](O)c1ccccc1
Reactant: N[C@@H]1C(=O)N2C(C(=O)OC(c3ccccc3)c3ccccc3)=C(SC(Sc3c[nH]nn3)C(c3ccccc3)(c3ccccc3)c3ccccc3)CS[C@H]12
Agent: C(=NC1CCCCC1)=NC1CCCCC1
Solvent: ClCCl
Product: O=C(OC(c1ccccc1)c1ccccc1)C1=C(SC(Sc2c[nH]nn2)C(c2ccccc2)(c2ccccc2)c2ccccc2)CS[C@@H]2[C@H](NC(=O)[C@H](O)c3ccccc3)C(=O)N12
Reaction time: 1 h
Yield: 49.5 %

Procedure:
To a solution of 7β-amino-3-(trityl-1,2,3-triazol-4-ylthiomethylthio)-3-cephem-4-carboxylic acid diphenylmethyl ester (800 mg: 1.06 mMol.) and D-(-)-mandelic acid (242 mg: 1.59 mMol.) in dichloromethane (4 ml) is added dicyclohexylcarbodiimide (328 mg: 1.59 mMol.), and the mixture is stirred under ice cooling for 1 hour. The reaction mixture is concentrated, diluted with ethyl acetate, and filtered to remove solid. The filtrate is washed with brine, dried over sodium sulfate, and concentrated under reduced pressure. The residue is purified by Lobar column chromatography (toluene: ethyl acetate=2:1) to give 7β-D-mandelamido-3-(trityl-1,2,3-triazol-4-ylthiomethylthio)-3-cephem-4-carboxylic acid diphenylmethyl ester (466 mg) as yellow foam. Yield: 50%.
Reaction SMILES: [NH:1]([CH2:3][C:4](O)=O)[CH3:2].[CH3:7][O:8][C:9](=[O:12])[CH:10]=[CH2:11].C=O>C1(C)C=CC=CC=1>[CH3:2][N:1]1[CH2:3][CH2:4][CH:10]([C:9]([O:8][CH3:7])=[O:12])[CH2:11]1
Reactant: C=CC(=O)OC
Reactant: CNCC(=O)O
Agent: C=O
Solvent: Cc1ccccc1
Product: COC(=O)C1CCN(C)C1
Temperature: 25 °C
Reaction time: 16 h
Yield: 43.1 %

Procedure:
A solution of sarcosine (30 g, 0.34 mol), methylacrylate (29 g, 0.34 mol) and paraformaldehyde (20.2 g, 0.67 mol) in toluene (3 l) was refluxed in a Dean-Stark trap apparatus for 0.5 h. The reaction mixture was cooled to room temperature and stirred for 16 h. Filtration through cotton wool and concentration under vacuum gave the title ester as a pale yellow liquid (21 g) m/e 143 (M+); δ(250 MHz, CDCl3) 2.05-2.16 (2H, m, CH2); 2.36 (3H, s, N--Me); 2.48-2.84 (4H, m, 2 of CH2 --N); 2.98-3.10 (1H, m, CH--CO2Me); 3.70 (3H, s, CO2Me).
Reaction SMILES: [OH:1][C:2]1[CH:3]=[C:4]([CH:9]=[CH:10][CH:11]=1)[C:5]([O:7][CH3:8])=[O:6].C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.CC(OC(/N=N/C(OC(C)C)=O)=O)C.[C:45]1([C:51]#[C:52][C:53]2[N:57]3[CH:58]=[CH:59][CH:60]=[CH:61][C:56]3=[N:55][C:54]=2[CH2:62]O)[CH:50]=[CH:49][CH:48]=[CH:47][CH:46]=1>O1CCCC1>[C:45]1([C:51]#[C:52][C:53]2[N:57]3[CH:58]=[CH:59][CH:60]=[CH:61][C:56]3=[N:55][C:54]=2[CH2:62][O:1][C:2]2[CH:3]=[C:4]([CH:9]=[CH:10][CH:11]=2)[C:5]([O:7][CH3:8])=[O:6])[CH:46]=[CH:47][CH:48]=[CH:49][CH:50]=1
Reactant: OCc1nc2ccccn2c1C#Cc1ccccc1
Reactant: COC(=O)c1cccc(O)c1
Agent: CC(C)OC(=O)/N=N/C(=O)OC(C)C
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: C1CCOC1
Product: COC(=O)c1cccc(OCc2nc3ccccn3c2C#Cc2ccccc2)c1
Yield: 42.3 %

Procedure:
0.09 g (0.594 mmol) of methyl 3-hydroxybenzoate were dissolved in 1 ml of tetrahydrofurane with magnetic stirring and then 0.312 g (1.188 mmol) of triphenylphosphine and 0.231 ml (1.188 mmol) of DIAD were added. The mixture was stirred at r.t. for 15 min and then a solution of 0.076 g (0.297 mmol) of (3-(phenylethynyl)imidazo[1,2-a]pyridin-2-yl)methanol in 4 ml of tetrahydrofurane was added and the mixture was stirred at r.t. for 16 h. A mixture of 0.09 g (0.594 mmol) of methyl 3-hydroxybenzoate, 0.312 g (1.188 mmol) of triphenylphosphine and 0.231 ml (1.188 mmol) of DIAD dissolved in 1 ml of tetrahydrofurane was added and the reaction medium was stirred at r.t. for a further 2 h. The reaction medium was treated with 10 ml. The aqueous phase was extracted with 3×10 ml of ethyl acetate and then the combined organic phases were washed with 10 ml of a saturated NaCl solution and then dried on Na2SO4 which was then removed by filtration. The obtained filtrate was concentrated in vacuo. The crude residue was purified by flash chromatography on a silica gel cartridge (eluent: heptane/ethyl acetate, from 70% to 40% heptane, v/v). 0.048 g (yield=42%) of methyl 3-((3-(phenylethynyl)imidazo[1,2-a]pyridin-2-yl)methoxy)benzoate were obtained as a pale yellow solid. LC-MS: m/z=383 (MH+); UV purity at 254 nm=99%. 1H NMR (300 MHz, DMSO) δ 8.64 (d, J=6.8 Hz, 1H), 7.68 (dd, J=17.0, 7.2 Hz, 4H), 7.55 (d, J=8.7 Hz, 1H), 7.52-7.34 (m, 6H), 7.15 (t, J=7.3 Hz, 1H), 5.42 (s, 2H), 3.80 (s, 3H).
Reaction SMILES: [NH2:1][C:2]1[N:3]=[C:4]([NH:15][C:16]2[CH:21]=[CH:20][C:19]([N+:22]([O-])=O)=[CH:18][CH:17]=2)[S:5][C:6]=1[C:7]([C:9]1[CH:14]=[CH:13][CH:12]=[CH:11][CH:10]=1)=[O:8]>C(O)C>[NH2:1][C:2]1[N:3]=[C:4]([NH:15][C:16]2[CH:17]=[CH:18][C:19]([NH2:22])=[CH:20][CH:21]=2)[S:5][C:6]=1[C:7]([C:9]1[CH:10]=[CH:11][CH:12]=[CH:13][CH:14]=1)=[O:8]
Reactant: Nc1nc(Nc2ccc([N+](=O)[O-])cc2)sc1C(=O)c1ccccc1
Solvent: CCO
Product: Nc1ccc(Nc2nc(N)c(C(=O)c3ccccc3)s2)cc1

Procedure:
The title compound was prepared in a manner similar to that described for Example D(1). Catalytic reduction of the title compound from Example A(8) (i.e., [4-amino-2-(4-nitro-phenylamino)-thiazol-5-yl]-phenyl-methanone, 450 mg, 1.32 mmol) gave, after recrystallization from ethanol, 120 mg (29% yield) of orange powder, mp 167-169° C.
Reaction SMILES: CN(C)[CH:3]=[C:4]([C:13]1[CH:14]=[N:15][CH:16]=[CH:17][CH:18]=1)[C:5]([C:7]1[CH:11]=[CH:10][O:9][C:8]=1[CH3:12])=O.Cl.[CH3:21][CH:22]1[CH2:27][CH2:26][CH2:25][N:24]([C:28](=[NH:30])[NH2:29])[CH2:23]1.CC(C)([O-])C.[K+]>C(O)C.O>[CH3:12][C:8]1[O:9][CH:10]=[CH:11][C:7]=1[C:5]1[C:4]([C:13]2[CH:14]=[N:15][CH:16]=[CH:17][CH:18]=2)=[CH:3][N:29]=[C:28]([N:24]2[CH2:25][CH2:26][CH2:27][CH:22]([CH3:21])[CH2:23]2)[N:30]=1
Reactant: CC1CCCN(C(=N)N)C1
Reactant: Cc1occc1C(=O)C(=CN(C)C)c1cccnc1
Agent: CC(C)(C)[O-]
Agent: Cl
Agent: [K+]
Solvent: O
Solvent: CCO
Product: Cc1occc1-c1nc(N2CCCC(C)C2)ncc1-c1cccnc1
Temperature: 25 °C
Yield: 8.4 %

Procedure:
A mixture of 3-(dimethylamino)-1-(2-methyl-3-furanyl)-2-(3-pyridinyl)-2-propen-1-one (256 mg, 1 mmol) and 3-methyl-1-piperidinecarboximidamide hydrochloride (267 mg, 1.5 mmol) in ethanol (5 ml) was stirred at room temperature. Potassium tert-butoxide (224 mg, 2 mmol) was added and the mixture was heated at reflux for 45 minutes. After cooling to room temperature the reaction mixture was diluted with water and extracted with ethyl acetate. The organic extracts were combined, washed with water and brine, dried and evaporated. The residue was purified by silica gel chromatography eluting with 25% ethyl acetate and isohexane to give 4-(2-methyl-3-furanyl)-2-(3-methyl-1-piperidinyl)-5-(3-pyridinyl)pyrimidine (28 mg, 8%). A solution of 4-(2-methyl-3-furanyl)-2-(3-methyl-1-piperidinyl)-5-(3-pyridinyl)pyrimidine (28 mg, 0.084 mmol) in dichloromethane (1 ml) was treated with hydrogen chloride (1M in diethyl ether, 0.1 ml). The solvent was evaporated and the residue co-evaporated with dichloromethane (×2). The resulting solid was dried to give the title compound as a solid (24 mg, 77%). LC/MS [M+H]+=335. 1H NMR (400 MHz, d6-DMSO): δ 8.75-8.73 (2H, m), 8.45 (1H, s), 8.17 (1H, d), 7.86-7.82 (1H, m), 7.45 (1H, d), 5.87 (1H, d), 4.65-4.59 (2H, m), 3.02-2.95 (1H, m), 2.71-2.65 (1H, m), 2.38 (3H, s), 1.91-1.18 (5H, m), 0.92 (3H, d).
Reaction SMILES: Cl[C:2]1[N:7]2[N:8]=[C:9]([NH:11][C:12](=[O:19])[C:13]3[CH:18]=[CH:17][CH:16]=[N:15][CH:14]=3)[N:10]=[C:6]2[CH:5]=[C:4]([Cl:20])[CH:3]=1.[CH:21]1([NH2:25])[CH2:24][CH2:23][CH2:22]1>>[Cl:20][C:4]1[CH:3]=[C:2]([NH:25][CH:21]2[CH2:24][CH2:23][CH2:22]2)[N:7]2[N:8]=[C:9]([NH:11][C:12](=[O:19])[C:13]3[CH:18]=[CH:17][CH:16]=[N:15][CH:14]=3)[N:10]=[C:6]2[CH:5]=1
Reactant: O=C(Nc1nc2cc(Cl)cc(Cl)n2n1)c1cccnc1
Reactant: NC1CCC1
Product: O=C(Nc1nc2cc(Cl)cc(NC3CCC3)n2n1)c1cccnc1
Temperature: 180 °C
Yield: 21 %

Procedure:
The title compound was prepared following procedure described for example 84, but starting from N-(5,7-dichloro[1,2,4]triazolo[1,5-a]pyridin-2-yl)nicotinamide ((B10), 100 mg; 0.32 mmol; 1.0 eq) and cyclobutylamine (139 μL; 1.62 mmol; 5.0 eq) heated at 180° C. for 1800 s after which solvents were evaporated under vacuum, then resuspended in water, filtered and washed with EtOAc to give the title compound as a white solid (23 mg, 21%). HPLC, Rt: 2.95 min. (purity 96.7%). LC/MS, M+(ESI): 342.8, M−(ESI): 340.9.
Reaction SMILES: Br[C:2]1[C:6]2=[N:7][CH:8]=[CH:9][CH:10]=[C:5]2[S:4][C:3]=1[C:11]1[N:15]2[N:16]=[C:17]([CH3:25])[CH:18]=[C:19]([CH:20]([CH2:23][CH3:24])[CH2:21][CH3:22])[C:14]2=[N:13][C:12]=1[CH3:26].[CH3:27][O-:28].[Na+]>[Cu]I.CO>[CH2:21]([CH:20]([C:19]1[C:14]2[N:15]([C:11]([C:3]3[S:4][C:5]4[C:6](=[N:7][CH:8]=[CH:9][CH:10]=4)[C:2]=3[O:28][CH3:27])=[C:12]([CH3:26])[N:13]=2)[N:16]=[C:17]([CH3:25])[CH:18]=1)[CH2:23][CH3:24])[CH3:22]
Reactant: C[O-]
Reactant: CCC(CC)c1cc(C)nn2c(-c3sc4cccnc4c3Br)c(C)nc12
Agent: [Cu]I
Agent: [Na+]
Solvent: CO
Product: CCC(CC)c1cc(C)nn2c(-c3sc4cccnc4c3OC)c(C)nc12
Temperature: 120 °C
Yield: 43.8 %

Procedure:
50 mg of 3-(3-Bromo-thieno[3,2-b]pyridin-2-yl)-8-(1-ethyl-propyl)-2,6-dimethyl-imidazo[1,2-b]pyridazine (0.12 mmol) and 13 mg of sodium methoxide (0.24 mmol) and 22 mg of copper (I) iodide (0.12 mmol) are placed into 4 ml reaction vial with 3.0 ml of dry MeOH. The reaction vial is capped with a Teflon cap and heated at 120° C. overnight. The reaction mixture is filtered, and water and CH2Cl2 are added. The separated CH2Cl2 is dried over Na2SO4 and evaporated. The crude product is applied onto a silica-gel chromatography column (1st column; Hexane:AcOEt:2M NH3 in MeOH=20:4:1, 2nd column; CH2Cl2:Hexane:Acetnitrile=5:4:1) to give the title compound 20 mg (45%). mass spectrum (m/e): 381; 1H-NMR (CDCl3): 8.72 (m, 1H), 8.10 (m, 1H), 7.29 (dd, 1H, J=4.6 Hz, 8.3 Hz), 6.72 (s, 1H), 4.03 (s, 3H), 3.34 (m, 1H), 2.55 (s, 3H), 2.54 (s, 3H), 1.84 (m, 4H), 0.88 (t, 6H, J=7.6 Hz) ppm.
Reaction SMILES: [C:1](Cl)(=O)[C:2]([Cl:4])=[O:3].[F:7][C:8]([F:22])([F:21])[C:9]1[CH:10]=[CH:11][C:12]2[CH:16]=C(C(O)=O)[S:14][C:13]=2[CH:20]=1>CN(C=O)C>[F:22][C:8]([F:7])([F:21])[C:9]1[CH:10]=[CH:11][C:12]2[CH:16]=[C:1]([C:2]([Cl:4])=[O:3])[S:14][C:13]=2[CH:20]=1
Reactant: O=C(O)c1cc2ccc(C(F)(F)F)cc2s1
Reactant: O=C(Cl)C(=O)Cl
Solvent: CN(C)C=O
Product: O=C(Cl)c1cc2ccc(C(F)(F)F)cc2s1
Temperature: 25 °C
Reaction time: 4 h

Procedure:
Oxalyl chloride (2.29 mmol, 0.20 mL) was added to a solution of 6-(trifluoromethyl)benzo[b]thiophene-2-carboxylic acid (2.03 mmol, 500 mg) CH2Cl2 (15 mL). DMF (15 μL) was added and the resulting mixture was stirred for 4 h at room temperature. The resulting solution was concentrated to yield 6-(trifluoromethyl)benzo[b]thiophene-2-carbonyl chloride, which was used in the next step without purification.
Reaction SMILES: [CH2:1]([O:8][C:9]1[CH:10]=[C:11]2[C:16](=[CH:17][C:18]=1[O:19][CH3:20])[NH:15][CH:14]=[C:13]([N+:21]([O-:23])=[O:22])[C:12]2=O)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.P(Cl)(Cl)([Cl:27])=O>CN(C)C=O>[CH2:1]([O:8][C:9]1[CH:10]=[C:11]2[C:16](=[CH:17][C:18]=1[O:19][CH3:20])[N:15]=[CH:14][C:13]([N+:21]([O-:23])=[O:22])=[C:12]2[Cl:27])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: COc1cc2[nH]cc([N+](=O)[O-])c(=O)c2cc1OCc1ccccc1
Reactant: O=P(Cl)(Cl)Cl
Solvent: CN(C)C=O
Product: COc1cc2ncc([N+](=O)[O-])c(Cl)c2cc1OCc1ccccc1
Temperature: 100 °C
Yield: 99.5 %

Procedure:
6-Benzyloxy-7-methoxy-3-nitro-1H-quinolin-4-one (9.10 g, 27.89 mmol, see Acta Pharmacologica Sinica 2008, 29(12), 1529-1538) was suspended in dry N,N-dimethylformamide (70 ml). Phosphoryl chloride (2.82 ml, 30.68 mmol) was subsequently added, and the mixture was heated at 100° C. for 30 min. After cooling, the reaction mixture was added to ice-water (500 ml) with stirring and stirred for a further 30 min. The precipitate formed was filtered off with suction, washed with water and dried in vacuo, giving 6-benzyloxy-4-chloro-7-methoxy-3-nitroquinoline (9.57 g, 27.76 mmol) as solid. MS: 345.1 (M+H+), TLC (HPTLC): Rf=0.44 (cyclohexane/ethyl acetate 2:1, parts by volume).
Reaction SMILES: [C:1]12([C:11](Cl)=[O:12])[CH2:10][CH:5]3[CH2:6][CH:7]([CH2:9][CH:3]([CH2:4]3)[CH2:2]1)[CH2:8]2.[CH2:14]([NH2:21])[C:15]1[CH:20]=[CH:19][CH:18]=[CH:17][CH:16]=1>C(OCC)C>[CH2:14]([NH:21][C:11]([C:1]12[CH2:10][CH:5]3[CH2:6][CH:7]([CH2:9][CH:3]([CH2:4]3)[CH2:2]1)[CH2:8]2)=[O:12])[C:15]1[CH:20]=[CH:19][CH:18]=[CH:17][CH:16]=1
Reactant: NCc1ccccc1
Reactant: O=C(Cl)C12CC3CC(CC(C3)C1)C2
Solvent: CCOCC
Product: O=C(NCc1ccccc1)C12CC3CC(CC(C3)C1)C2

Procedure:
Dissolve 2.0 g. of (10 mmoles) of 1-adamantane carboxylic acid chloride in 20 ml. of ethyl ether and add to 3.0 ml. (28.0 mmoles) of benzylamine and repeat the process of Example 11 to obtain the product of this example, m.p. 170°-172° C.
Reaction SMILES: CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.[S:25]1[CH:29]=[CH:28][C:27]2[CH:30]=[C:31]([C:34]([OH:36])=O)[CH:32]=[CH:33][C:26]1=2.[O:37]1[C:42]2([CH2:47][CH2:46][N:45]([CH2:48][C:49]3[C:50]([F:58])=[C:51]([CH2:55][CH2:56][OH:57])[CH:52]=[CH:53][CH:54]=3)[CH2:44][CH2:43]2)[CH2:41][NH:40][CH2:39][CH2:38]1.C(N(CC)CC)C>CN(C=O)C>[S:25]1[CH:29]=[CH:28][C:27]2[CH:30]=[C:31]([C:34]([N:40]3[CH2:41][C:42]4([CH2:47][CH2:46][N:45]([CH2:48][C:49]5[CH:54]=[CH:53][CH:52]=[C:51]([CH2:55][CH2:56][OH:57])[C:50]=5[F:58])[CH2:44][CH2:43]4)[O:37][CH2:38][CH2:39]3)=[O:36])[CH:32]=[CH:33][C:26]1=2
Reactant: O=C(O)c1ccc2sccc2c1
Reactant: OCCc1cccc(CN2CCC3(CC2)CNCCO3)c1F
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CN(C)C=O
Solvent: CCN(CC)CC
Product: O=C(c1ccc2sccc2c1)N1CCOC2(CCN(Cc3cccc(CCO)c3F)CC2)C1
Temperature: 25 °C
Reaction time: 2 h

Procedure:
HATU (0.181 g) was added in one portion to a stirred solution at 0° C. of benzo[b]thiophene-5-carboxylic acid (0.065 g) and 2-(3-(1-oxa-4,9-diazaspiro[5.5]undecan-9-ylmethyl)-2-fluorophenyl)ethanol (example 67, step f) (0.113 g) and triethylamine (0.153 mL) in DMF (5 mL). The reaction mixture was stirred at room temperature for 2 hours. The mixture was partitioned between ethyl acetate and brine, the organic layer was washed twice with brine, dried over sodium sulphate, filtered and the solvent evaporated under reduced pressure to afford the subtitled compound. Yield 0.160 g.
Reaction SMILES: [CH2:1]([O:3][C:4](=[O:21])[CH2:5][CH:6]1[O:10][B:9]([OH:11])[C:8]2[CH:12]=[C:13]([OH:20])[CH:14]=[C:15]([CH2:16][N:17]=[N+:18]=[N-:19])[C:7]1=2)[CH3:2].Cl[C:23]1[CH:28]=[N:27][CH:26]=[CH:25][N:24]=1.C([O-])([O-])=O.[Cs+].[Cs+].Cl>CN(C=O)C>[CH2:1]([O:3][C:4](=[O:21])[CH2:5][CH:6]1[O:10][B:9]([OH:11])[C:8]2[CH:12]=[C:13]([O:20][C:23]3[CH:28]=[N:27][CH:26]=[CH:25][N:24]=3)[CH:14]=[C:15]([CH2:16][N:17]=[N+:18]=[N-:19])[C:7]1=2)[CH3:2]
Reactant: Clc1cnccn1
Reactant: CCOC(=O)CC1OB(O)c2cc(O)cc(CN=[N+]=[N-])c21
Agent: Cl
Agent: O=C([O-])[O-]
Agent: [Cs+]
Solvent: CN(C)C=O
Product: CCOC(=O)CC1OB(O)c2cc(Oc3cnccn3)cc(CN=[N+]=[N-])c21
Temperature: 80 °C
Yield: 28.7 %

Procedure:
To a mixture of (4-azidomethyl-1,6-dihydroxy-1,3-dihydro-benzo[c][1,2]oxaborol-3-yl)-acetic acid ethyl ester (550 mg, 1.89 mmol), 2-chloropyrazine (350 mg, 3.05 mmol), Cs2CO3 (1.34 g, 4.11 mmol) in 5 mL of DMF was heated to 80° C. for 3.5 h. The reaction mixture was adjusted to pH 3 by 1N HCl. The crude product was purified by HPLC to yield 200 mg of the title compound.
Reaction SMILES: Cl.[F:2][C:3]1([F:19])[C@H:7]([OH:8])[C@@H:6]([CH2:9][OH:10])[O:5][C@H:4]1[N:11]1[CH:18]=[CH:17][C:15]([NH2:16])=[N:14][C:12]1=[O:13].[C:20]1(=[O:26])[O:25][C:23](=[O:24])[CH2:22][CH2:21]1>N1C=CC=CC=1>[C:23]([CH2:22][CH2:21][C:20]([O:10][CH2:9][C@H:6]1[O:5][C@@H:4]([N:11]2[CH:18]=[CH:17][C:15]([NH2:16])=[N:14][C:12]2=[O:13])[C:3]([F:2])([F:19])[C@@H:7]1[OH:8])=[O:26])([OH:25])=[O:24]
Reactant: Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)C2(F)F)c(=O)n1
Reactant: O=C1CCC(=O)O1
Agent: Cl
Solvent: c1ccncc1
Product: Nc1ccn([C@@H]2O[C@H](COC(=O)CCC(=O)O)[C@@H](O)C2(F)F)c(=O)n1
Temperature: 25 °C
Reaction time: 1.5 h

Procedure:
A 600 mg portion of dry 2'-deoxy-2',2'-difluorocytidine, hydrochloride, was added to 6 ml of dry pyridine, and 804 mg of succinic anhydride was added. The reaction mixture was stirred at ambient temperature for 1.5 hours. The mixture was then concentrated to an oil under vacuum, and the oil was stored overnight in the freezer. It was then allowed to stand at ambient temperature for 4 hours, and was chromatographed over a 500 ml Q-Sepharose column (Pharmacia Inc.). The oil was dissolved in 6 ml of 0.lM ammonium acetate buffer, and was passed over the column, eluting with a gradient buffer which changed from 0.lM to 1.0M ammonium acetate, at pH 8.0 at all times. Analytical chromatography of the mixture on a small mono-Q column showed that bisacylated and tris-acylated products were present, as well as mono-acylated product and a small amount of starting material. The product-containing fractions, amounting to about 200 ml, were placed in a 37° C. bath, for 68 hours. At the end of that time, the tris-acylated product had been decomposed and both mono- and bisacylated products were still present.
Reaction SMILES: [S:1]([N:11]1[C:15]2[N:16]=[CH:17][N:18]=[C:19]([NH:20][C@@H:21]3[CH2:26][CH2:25][CH2:24][N:23]([C:27]([O:29][C:30]([CH3:33])([CH3:32])[CH3:31])=[O:28])[CH2:22]3)[C:14]=2[CH:13]=[CH:12]1)([C:4]1[CH:10]=[CH:9][C:7]([CH3:8])=[CH:6][CH:5]=1)(=[O:3])=[O:2].[H-].[Na+].[CH2:36](Br)[CH:37]=[CH2:38].O>CN(C=O)C>[CH2:38]([N:20]([C:19]1[C:14]2[CH:13]=[CH:12][N:11]([S:1]([C:4]3[CH:5]=[CH:6][C:7]([CH3:8])=[CH:9][CH:10]=3)(=[O:3])=[O:2])[C:15]=2[N:16]=[CH:17][N:18]=1)[C@@H:21]1[CH2:26][CH2:25][CH2:24][N:23]([C:27]([O:29][C:30]([CH3:33])([CH3:32])[CH3:31])=[O:28])[CH2:22]1)[CH:37]=[CH2:36]
Reactant: Cc1ccc(S(=O)(=O)n2ccc3c(N[C@@H]4CCCN(C(=O)OC(C)(C)C)C4)ncnc32)cc1
Reactant: C=CCBr
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: O
Product: C=CCN(c1ncnc2c1ccn2S(=O)(=O)c1ccc(C)cc1)[C@@H]1CCCN(C(=O)OC(C)(C)C)C1
Reaction time: 1 h
Yield: 83.8 %

Procedure:
To a solution of (R)-tert-butyl 3-(7-tosyl-7H-pyrrolo[2,3-d]pyrimidin-4-ylamino)piperidine-1-carboxylate (1.0 g, 2.1 mmol) in DMF (5 mL), NaH (60% suspension in mineral oil, 100 mg, 2.5 mmol) was added at 0° C. and the reaction mixture was stirred for 1 h. To the reaction mixture was added allyl bromide (308 mg, 2.12 mmol) and the reaction mixture was stirred for 6 h. The solution was diluted with ice-cooled water and stirred for 15 min, the solution was then extracted with EtOAc, dried over Na2SO4 and concentrated in vacuo to give the crude product that was purified by column chromatography (silica gel, gradient, EtOAc in hexanes) to give (0.9 g, 83%) of the titled compound. 1H NMR (400 MHz, CDCl3): δ 8.42 (s, 1H), 8.06 (d, J=8.0 Hz, 2H), 7.43 (d, J=3.2 Hz, 1H), 7.31 (d, J=8.0 Hz, 2H), 6.57 (d, J=3.2 Hz, 1H), 5.98-5.90 (m, 1H), 5.26-5.19 (m, 2H), 4.62-4.51 (m, 1H), 4.29-4.09 (m, 4H), 2.85 (t, J=11.6 Hz, 1H), 2.68-2.60 (m, 1H), 2.41 (s, 3H), 1.97-1.93 (m, 1H), 1.83-1.72 (m, 2H), 1.65-1.58 (m, 1H), 1.42 (s, 9H). LCMS [M+1]: 512.