Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [S:1]1[CH:5]=[CH:4][CH:3]=[C:2]1[NH:6][CH2:7][C:8]#[N:9].[ClH:10].[NH2:11][OH:12]>CO>[ClH:10].[S:1]1[CH:5]=[CH:4][CH:3]=[C:2]1[NH:6][CH2:7][C:8](=[N:11][OH:12])[NH2:9]
Reactant: NO
Reactant: N#CCNc1cccs1
Agent: Cl
Solvent: CO
Product: NC(CNc1cccs1)=NO
Yield: 90.8 %

Procedure:
5.6 g of the α-(2-thienyl)aminoacetonitrile thus obtained was dissolved in 30 ml of methanol and 2.8 g of hydroxylamine hydrochloride was added thereto in a water bath. After stirring for a while, the mixture began to crystallize while showing slight heat generation. The mixture was stirred at room temperature for several hours thereafter. After the completion of the reaction, the reaction mixture was concentrated and the solvent was distilled off. After recrystallizing from ethanol, 7.6 g of the aimed α-(2-thienyl)aminoacetamidoxime hydrochloride was obtained.
Reaction SMILES: Cl[C:2]1[CH:7]=[C:6]([C:8]([F:11])([F:10])[F:9])[CH:5]=[CH:4][C:3]=1[C:12]1[CH:21]=[CH:20][CH:19]=[C:18]2[C:13]=1[CH:14]=[CH:15][C:16]([S:22]([NH:25][C:26]1[CH:31]=[CH:30][N:29]=[CH:28][N:27]=1)(=[O:24])=[O:23])=[CH:17]2.CC1(C)C(C)(C)OB([C:40]2[CH2:45][CH2:44][N:43]([C:46]([O:48][C:49]([CH3:52])([CH3:51])[CH3:50])=[O:47])[CH2:42][CH:41]=2)O1.P([O-])([O-])([O-])=O.[K+].[K+].[K+]>C(C1C(C(C)(C)C)=C([Pd]Cl)C=CC=1NC)(C)(C)C.CCOC(C)=O>[N:29]1[CH:30]=[CH:31][C:26]([NH:25][S:22]([C:16]2[CH:17]=[C:18]3[C:13](=[CH:14][CH:15]=2)[C:12]([C:3]2[CH:4]=[CH:5][C:6]([C:8]([F:9])([F:10])[F:11])=[CH:7][C:2]=2[C:40]2[CH2:45][CH2:44][N:43]([C:46]([O:48][C:49]([CH3:52])([CH3:51])[CH3:50])=[O:47])[CH2:42][CH:41]=2)=[CH:21][CH:20]=[CH:19]3)(=[O:24])=[O:23])=[N:27][CH:28]=1
Reactant: O=S(=O)(Nc1ccncn1)c1ccc2c(-c3ccc(C(F)(F)F)cc3Cl)cccc2c1
Reactant: CC(C)(C)OC(=O)N1CC=C(B2OC(C)(C)C(C)(C)O2)CC1
Agent: CNc1ccc([Pd]Cl)c(C(C)(C)C)c1C(C)(C)C
Agent: O=P([O-])([O-])[O-]
Agent: [K+]
Solvent: CCOC(C)=O
Product: CC(C)(C)OC(=O)N1CC=C(c2cc(C(F)(F)F)ccc2-c2cccc3cc(S(=O)(=O)Nc4ccncn4)ccc23)CC1
Temperature: 110 °C
Yield: 46.1 %

Procedure:
A microwave vial was charged with 5-(2-chloro-4-(trifluoromethyl)phenyl)-N-(pyrimidin-4-yl)naphthalene-2-sulfonamide (Intermediate X) (82.5 mg, 0.178 mmol), tert-butyl 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-5,6-dihydropyridine-1(2H)-carboxylate (110 mg, 0.356 mmol), potassium phosphate (113 mg, 0.534 mmol), and 1,1-bis[(di-t-butyl-p-methylaminophenyl]palladium(II) chloride (12.59 mg, 0.018 mmol). The vial was sealed, flushed with N2 and dioxane (1334 μl) and water (445 μl) was added. The mixture was sparged for 5 min with N2. The mixture was heated in a microwave at 110° C. for 4 h. The mixture was concentrated for purification by MPLC. The residue was taken up in minimal CH2Cl2 and absorbed onto a 5 g loading cartridge and passed through a silica gel column (12 g) using a 98:2 Heptane:EtOAc to 100% EtOAc (with 1% constant EtOH additive) gradient to afford tert-butyl 4-(2-(6-(N-(pyrimidin-4-yl)sulfamoyl)naphthalen-1-yl)-5-(trifluoromethyl)phenyl)-5,6-dihydropyridine-1(2H)-carboxylate (50.0 mg, 0.082 mmol) as a light-yellow amorphous solid.
Reaction SMILES: [NH2:1][C:2]1[N:6]([CH3:7])[N:5]=[CH:4][C:3]=1[C:8]#[N:9].C[Si](C)(C)[N-][Si](C)(C)C.[Na+].[N+](C1C=CC([O:29][C:30]([C:32]2[C:40]3[S:39][C:38]([C:41]([F:44])([F:43])[F:42])=[N:37][C:36]=3[C:35]([O:45][CH3:46])=[CH:34][CH:33]=2)=O)=CC=1)([O-])=O>CN(C)C=O.O1CCCC1>[C:8]([C:3]1[CH:4]=[N:5][N:6]([CH3:7])[C:2]=1[NH:1][C:30]([C:32]1[C:40]2[S:39][C:38]([C:41]([F:44])([F:43])[F:42])=[N:37][C:36]=2[C:35]([O:45][CH3:46])=[CH:34][CH:33]=1)=[O:29])#[N:9]
Reactant: Cn1ncc(C#N)c1N
Reactant: COc1ccc(C(=O)Oc2ccc([N+](=O)[O-])cc2)c2sc(C(F)(F)F)nc12
Agent: C[Si](C)(C)[N-][Si](C)(C)C
Agent: [Na+]
Solvent: C1CCOC1
Solvent: CN(C)C=O
Product: COc1ccc(C(=O)Nc2c(C#N)cnn2C)c2sc(C(F)(F)F)nc12
Temperature: 25 °C
Reaction time: 2 h
Yield: 34.8 %

Procedure:
A solution of 5-amino-1-methyl-1H-pyrazole-4-carbonitrile (93 mg) in dimethyl formamide (10 ml) was treated with a solution of sodium hexamethyldisilazide in tetrahydrofuran (0.76 ml, 1.0M). After three minutes the mixture was treated with 4-methoxy-2-trifluoromethylbenzothiazole-7-carboxylic acid 4-nitrophenyl ester (150 mg) and the reaction stirred at room temperature for 2 hours. The solvent was removed in vacuo. Purification by flash chromatography (eluent ethyl acetate) to yield the title compound as an off-white solid (50 mg). TLC Rf 0.48 (ethyl acetate); MS found M+1 382.
Reaction SMILES: [C:1]([CH:3]1[CH2:8][CH2:7][N:6]([C:9]([N:11]2[CH2:16][CH:15]([C:17]3[CH:22]=[CH:21][C:20]([C:23]([F:26])([F:25])[F:24])=[CH:19][CH:18]=3)[CH2:14][CH:13]([C:27]([OH:29])=O)[CH2:12]2)=[O:10])[CH2:5][CH2:4]1)#[N:2].O[N:31]=[C:32]([C:34]1[CH:35]=[N:36][CH:37]=[CH:38][CH:39]=1)[NH2:33]>>[N:36]1[CH:37]=[CH:38][CH:39]=[C:34]([C:32]2[N:33]=[C:27]([CH:13]3[CH2:14][CH:15]([C:17]4[CH:22]=[CH:21][C:20]([C:23]([F:25])([F:24])[F:26])=[CH:19][CH:18]=4)[CH2:16][N:11]([C:9]([N:6]4[CH2:7][CH2:8][CH:3]([C:1]#[N:2])[CH2:4][CH2:5]4)=[O:10])[CH2:12]3)[O:29][N:31]=2)[CH:35]=1
Reactant: NC(=NO)c1cccnc1
Reactant: N#CC1CCN(C(=O)N2CC(C(=O)O)CC(c3ccc(C(F)(F)F)cc3)C2)CC1
Product: N#CC1CCN(C(=O)N2CC(c3ccc(C(F)(F)F)cc3)CC(c3nc(-c4cccnc4)no3)C2)CC1

Procedure:
100 mg (0.244 mmol) of 1-[(4-cyanopiperidin-1-yl)carbonyl]-5-[4-(trifluoromethyl)phenyl]piperidine-3-carboxylic acid (Example 100A) and 36.8 mg (0.269 mmol) of N′-hydroxypyridine-3-carboximidamide were reacted according to the General Method 1. Yield: 58.6 mg (46% of theory).
Reaction SMILES: [CH3:1][N:2]1[C:10]2[C:5](=[C:6]([CH3:11])[CH:7]=[CH:8][CH:9]=2)[CH:4]=[CH:3]1.[Li]CCCC.[C:17](=[O:19])=[O:18].O>CCOCC>[CH3:1][N:2]1[C:10]2[C:5](=[C:6]([CH3:11])[CH:7]=[CH:8][CH:9]=2)[CH:4]=[C:3]1[C:17]([OH:19])=[O:18]
Reactant: Cc1cccc2c1ccn2C
Reactant: O=C=O
Agent: [Li]CCCC
Solvent: O
Solvent: CCOCC
Product: Cc1cccc2c1cc(C(=O)O)n2C
Reaction time: 1 h
Yield: 26.4 %

Procedure:
A solution of 1,4-dimethyl-1H-indole (0.9 g, 6.2 mmole) in anhydrous Et2O (20 mL) was treated with 2.5 M n-BuLi in hexanes (5.0 mL, 12 mmole) and the reaction was heated at reflux for 15 hr. The dark reaction mixture was poured into a slurry of excess crushed dry ice in Et2O, and the mixture was allowed to stand for 1 hr. Water (10 mL) was added, the layers separated, and the aqueous layer was filtered through celite®. The clear filtrate was acidified with 2.0 N HCl to pH 2, and the precipitate was collected and dried to afford the title compound (0.29 g, 26.4%) as an off-white solid: MS (ES) m/e 190.2 (M+H)+.
Reaction SMILES: [C:1]([NH:20][C:21]1[S:22][CH:23]=[C:24](/[C:26](=[N:53]/[O:54][C:55]([C:58]([O:60][C:61]([CH3:64])([CH3:63])[CH3:62])=[O:59])([CH3:57])[CH3:56])/[C:27]([NH:29][CH:30]2[C:51](=[O:52])[N:32]3[C:33]([C:39]([O:41][CH2:42][C:43]4[CH:48]=[CH:47][C:46]([O:49][CH3:50])=[CH:45][CH:44]=4)=[O:40])=[C:34]([CH2:37]Cl)[CH2:35][S:36][C@H:31]23)=[O:28])[N:25]=1)([C:14]1[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=1)([C:8]1[CH:13]=[CH:12][CH:11]=[CH:10][CH:9]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[SH:65][C:66]1[S:67][C:68]2[CH:69]=[N:70][CH:71]=[CH:72][C:73]=2[N:74]=1.SC1SC2C=CN=CC=2N=1>>[C:1]([NH:20][C:21]1[S:22][CH:23]=[C:24](/[C:26](=[N:53]/[O:54][C:55]([C:58]([O:60][C:61]([CH3:64])([CH3:63])[CH3:62])=[O:59])([CH3:57])[CH3:56])/[C:27]([NH:29][CH:30]2[C:51](=[O:52])[N:32]3[C:33]([C:39]([O:41][CH2:42][C:43]4[CH:48]=[CH:47][C:46]([O:49][CH3:50])=[CH:45][CH:44]=4)=[O:40])=[C:34]([CH2:37][S:65][C:66]4[S:67][C:68]5[CH:69]=[N:70][CH:71]=[CH:72][C:73]=5[N:74]=4)[CH2:35][S:36][C@H:31]23)=[O:28])[N:25]=1)([C:14]1[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=1)([C:8]1[CH:13]=[CH:12][CH:11]=[CH:10][CH:9]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: Sc1nc2ccncc2s1
Reactant: COc1ccc(COC(=O)C2=C(CCl)CS[C@@H]3C(NC(=O)/C(=N\OC(C)(C)C(=O)OC(C)(C)C)c4csc(NC(c5ccccc5)(c5ccccc5)c5ccccc5)n4)C(=O)N23)cc1
Agent: Sc1nc2cnccc2s1
Product: COc1ccc(COC(=O)C2=C(CSc3nc4ccncc4s3)CS[C@@H]3C(NC(=O)/C(=N\OC(C)(C)C(=O)OC(C)(C)C)c4csc(NC(c5ccccc5)(c5ccccc5)c5ccccc5)n4)C(=O)N23)cc1
Yield: 68.2 %

Procedure:
Using 276 mg of p-methoxybenzyl 7-{(Z)-2-(2-tritylaminothiazol-4-yl)-2-(1-tert-butoxycarbonyl-1-methylethoxyimino)acetamido}-3-chloromethyl-3-cephem-4-carboxylate and 60 mg of 2-mercaptothiazolo[5,4-c]pyridine in place of p-methoxybenzyl 7-{(Z)-2-(2-tritylaminothiazol-4-yl)-2-methoxyimino-acetamido}-3-chloromethyl-3-cephem-4-carboxylate and 2-mercaptothiazolo[4,5-c]pyridine, respectively, the reaction and purification were carried out in the same manner as in Example 1(a) to obtain 215 mg of the title compound in a yield of 68%.
Reaction SMILES: Cl.[NH2:2][CH2:3][C:4]1[CH:5]=[C:6]2[C:10](=[CH:11][CH:12]=1)[C:9](=[O:13])[N:8]([CH:14]1[CH2:19][CH2:18][C:17](=[O:20])[NH:16][C:15]1=[O:21])[C:7]2=[O:22].[Cl:23][C:24]1[CH:32]=[CH:31][C:27]([C:28](Cl)=[O:29])=[CH:26][CH:25]=1.CCN(C(C)C)C(C)C>C1COCC1>[Cl:23][C:24]1[CH:32]=[CH:31][C:27]([C:28]([NH:2][CH2:3][C:4]2[CH:5]=[C:6]3[C:10](=[CH:11][CH:12]=2)[C:9](=[O:13])[N:8]([CH:14]2[CH2:19][CH2:18][C:17](=[O:20])[NH:16][C:15]2=[O:21])[C:7]3=[O:22])=[O:29])=[CH:26][CH:25]=1
Reactant: O=C(Cl)c1ccc(Cl)cc1
Reactant: NCc1ccc2c(c1)C(=O)N(C1CCC(=O)NC1=O)C2=O
Agent: Cl
Solvent: CCN(C(C)C)C(C)C
Solvent: C1CCOC1
Product: O=C1CCC(N2C(=O)c3ccc(CNC(=O)c4ccc(Cl)cc4)cc3C2=O)C(=O)N1
Temperature: 40 °C
Yield: 62.6 %

Procedure:
To a stirred mixture of 5-aminomethyl-2-(2,6-dioxo-piperidin-3-yl)-isoindole-1,3-dione hydrochloride (0.97 g, 3.00 mmol) and 4-chlorobenzoyl chloride (0.53 g, 3.30 mmol) in THF (20 mL), was added DIPEA (1.05 mL, 6.00 mmol) at room temperature under nitrogen. The mixture was heated to 40° C. for 18 h then cooled to rt. The solvent was removed in vacuo and the residue was dissolved in EtOAc (100 mL). The organic layer was washed with dil. aq. HCl (2×150 mL), water (100 mL), dried (MgSO4) and then concentrated. The crude product was purified by column chromatography (0-5% MeOH CH2Cl2). The product fractions were combined, concentrated and triturated in Et2O (50 mL) for 18 h. The product was isolated by filtration and dried in vacuo to give 4-chloro-N-[2-(2,6-dioxo-piperidin-3-yl)-1,3-dioxo-2,3-dihydro-1H-isoindol-5-ylmethyl]-benzamide as a white solid (0.80 g, 63% yield): HPLC: Waters Symmetry C18, 5 μm, 3.9×150 mm, 1 mL/min, 240 nm, 40/60 CH3CN/0.1% H3PO4, 4.97 min (97.05%); mp: 178-180° C.; 1H NMR (DMSO-d6) δ 1.92-2.15 (m, 1H, CHH), 2.54-2.71 (m, 2H, CHH, CHH), 2.77-3.02 (m, 1H, CHH), 4.65 (d, J=5.9 Hz, 2H, CH2), 5.15 (dd, J=5.5, 12.8 Hz, 1H, CH), 7.53-7.63 (m, 2H, Ar), 7.74-7.87 (m, 2H, Ar), 7.87-8.03 (m, 3H, Ar), 9.31 (t, J=5.9 Hz, 1H, NH), 11.13 (s, 1H, NH); 13C NMR (DMSO-d6) δ 21.99, 30.93, 42.67, 48.99, 122.01, 123.55, 128.50, 129.21, 129.84, 131.62, 132.64, 133.47, 136.30, 147.38, 165.40, 166.96, 167.10, 169.80, 172.72; LCMS: MH=426/428; Anal Calcd for C21H16N3O5Cl: C, 58.98; H, 3.82; N, 9.83. Found: C, 58.67; H, 3.67; N, 9.53.
Reaction SMILES: [CH3:1][C:2]1[CH:7]=[C:6]([NH:8][C:9]([NH:11][CH2:12][CH2:13][N:14]2[CH2:19][CH2:18][CH:17]([NH:20][CH3:21])[CH2:16][CH2:15]2)=[O:10])[CH:5]=[C:4]([CH3:22])[N:3]=1.[Cl:23][C:24]1[CH:25]=[C:26]([CH2:31][C:32](Cl)=[O:33])[CH:27]=[CH:28][C:29]=1[Cl:30]>C(Cl)Cl>[Cl:23][C:24]1[CH:25]=[C:26]([CH2:31][C:32]([N:20]([CH:17]2[CH2:16][CH2:15][N:14]([CH2:13][CH2:12][NH:11][C:9]([NH:8][C:6]3[CH:5]=[C:4]([CH3:22])[N:3]=[C:2]([CH3:1])[CH:7]=3)=[O:10])[CH2:19][CH2:18]2)[CH3:21])=[O:33])[CH:27]=[CH:28][C:29]=1[Cl:30]
Reactant: O=C(Cl)Cc1ccc(Cl)c(Cl)c1
Reactant: CNC1CCN(CCNC(=O)Nc2cc(C)nc(C)c2)CC1
Solvent: ClCCl
Product: Cc1cc(NC(=O)NCCN2CCC(N(C)C(=O)Cc3ccc(Cl)c(Cl)c3)CC2)cc(C)n1
Temperature: 25 °C
Reaction time: 15 h

Procedure:
To a cooled (0° C.) mixture of 1-(2,6-dimethyl-pyridin-4-yl)-3-[2-(4-methylamino-piperidin-1-yl)-ethyl]-urea (Example E1., 0.3 mmol) and TEA (0.5 mL, 0.35 mmol) in CH2Cl2 (2 mL) is added a solution of (3,4-dichloro-phenyl)-acetyl chloride (67.0 mg, 0.3 mmol) in CH2Cl2 (1 mL). The mixture is stirred at r.t. for 15 h and evaporated. the residue is purified by HPLC to provide the title compound.
Reaction SMILES: [Br:1][CH2:2][CH2:3]Br.C(=O)([O-])[O-].[K+].[K+].[N+:11]([C:14]1[CH:19]=[CH:18][C:17]([SH:20])=[CH:16][CH:15]=1)([O-:13])=[O:12]>C(#N)C>[Br:1][CH2:2][CH2:3][S:20][C:17]1[CH:18]=[CH:19][C:14]([N+:11]([O-:13])=[O:12])=[CH:15][CH:16]=1
Reactant: BrCCBr
Reactant: O=[N+]([O-])c1ccc(S)cc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC#N
Product: O=[N+]([O-])c1ccc(SCCBr)cc1
Temperature: 80 °C
Reaction time: 18 h
Yield: 82 %

Procedure:
6.94 ml of 1,2-dibromoethane was diluted with 100 ml of acetonitrile, mixed with 11.2 g of potassium carbonate and 5.0 g of 4-nitro-benzenethiol, and stirred at 80° C. for 18 hours. After washing with 300 ml of distilled water and with 300 ml of aqueous NaCl, the resulting organic layer was dried over magnesium sulfate, filtrated, and distilled under a reduced pressure. The residue obtained thus was subjected to column chromatography to obtain 6.9 g of the title compound (yield 82%).
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([N:8]2[CH2:13][CH2:12][N:11]([CH2:14][C:15]3[CH:20]=[CH:19][C:18]([O:21][CH3:22])=[C:17]([O:23][CH3:24])[CH:16]=3)[CH:10]([C:25]([NH:27][CH:28]([CH3:30])[CH3:29])=O)[CH2:9]2)[CH:5]=[CH:6][CH:7]=1.[H-].[Al+3].[Li+].[H-].[H-].[H-]>>[Cl:1][C:2]1[CH:3]=[C:4]([N:8]2[CH2:13][CH2:12][N:11]([CH2:14][C:15]3[CH:20]=[CH:19][C:18]([O:21][CH3:22])=[C:17]([O:23][CH3:24])[CH:16]=3)[CH:10]([CH2:25][NH:27][CH:28]([CH3:30])[CH3:29])[CH2:9]2)[CH:5]=[CH:6][CH:7]=1
Reactant: COc1ccc(CN2CCN(c3cccc(Cl)c3)CC2C(=O)NC(C)C)cc1OC
Agent: [Al+3]
Agent: [H-]
Agent: [Li+]
Product: COc1ccc(CN2CCN(c3cccc(Cl)c3)CC2CNC(C)C)cc1OC

Procedure:
In a manner similar to Preparation 2, react 4-(3-chlorophenyl)-1-[(3,4-dimethoxyphenyl)methyl]-N-(1-methylethyl)-2-piperazinecarboxamide with lithium aluminum hydride to obtain the title compound.
Reaction SMILES: [C:1]([C:5]1[CH:6]=[C:7]([CH:16]=[C:17]([C:20]([CH3:23])([CH3:22])[CH3:21])[C:18]=1[OH:19])[C:8]([C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=1)=O)([CH3:4])([CH3:3])[CH3:2].Cl.[NH2:25][OH:26].[OH-].[K+].ClCCl>C(O)C>[C:1]([C:5]1[CH:6]=[C:7]([CH:16]=[C:17]([C:20]([CH3:23])([CH3:22])[CH3:21])[C:18]=1[OH:19])[C:8](=[N:25][OH:26])[C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=1)([CH3:4])([CH3:3])[CH3:2]
Reactant: CC(C)(C)c1cc(C(=O)c2ccccc2)cc(C(C)(C)C)c1O
Reactant: NO
Agent: Cl
Agent: [K+]
Agent: [OH-]
Solvent: CCO
Solvent: ClCCl
Product: CC(C)(C)c1cc(C(=NO)c2ccccc2)cc(C(C)(C)C)c1O

Procedure:
12.4 g of 3,5-di-t-butyl-4-hydroxybenzophenone and 3.15 g of hydroxylamine hydrochloride were dissolved in 100 ml of ethanol, and with stirring, a solution of 2.77 g of potassium hydroxide in 20 ml of ethanol was added dropwise at room temperature. The mixture was then refluxed for 24 hours with stirring. After cooling, dichloromethane was added to the reaction mixture. The dichloromethane layer was separated, washed with water, and dried. The solvent was distilled off, and n-hexane was added to the residue. The precipitated crystals were collected by filtration, and recrystallized from ether/n-hexane to give 3,5-di-t-butyl-4-hydroxybenzophenone oxime.
Reaction SMILES: [CH2:1]([C@H:8]1[CH2:12][O:11][C:10](=[O:13])[NH:9]1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.C([Li])CCC.[S:19]1[CH:23]=[CH:22][CH:21]=[C:20]1[CH2:24][C:25](Cl)=[O:26]>C1COCC1>[CH2:1]([C@H:8]1[CH2:12][O:11][C:10](=[O:13])[N:9]1[C:25](=[O:26])[CH2:24][C:20]1[S:19][CH:23]=[CH:22][CH:21]=1)[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: O=C(Cl)Cc1cccs1
Reactant: O=C1N[C@@H](Cc2ccccc2)CO1
Agent: [Li]CCCC
Solvent: C1CCOC1
Product: O=C(Cc1cccs1)N1C(=O)OC[C@@H]1Cc1ccccc1
Temperature: -78 °C
Reaction time: 0.75 h
Yield: 52.9 %

Procedure:
To a solution of (S)-(−)-4-benzyl-2-oxazolidinone (350 mg, 2.00 mmol) in dry THF (10 mL) at −30° C. was added dropwise n-butyllithium (2.59 M in hexanes, 0.8 mL). The mixture was cooled to −78° C. and treated with 2-thiopheneacetyl chloride (0.25 mL, 2 mmol). After stirring at −78° C. for 45 minutes, the mixture was allowed to warm to ambient temperature and stir for 1 hour. The mixture was diluted with hexanes (10 mL), quenched with 1M pH7 phosphate buffer, and stirred for 45 minutes. The layers of the resultant biphasic mixture were separated and the aqueousueous phase extracted with EtOAc. The combined organic layers were washed with 0.5N aqueous HCl two times, saturated aqueous NaHCO3 two times, and brine, dried over Na2SO4, and concentrated to provide a crude residue which was purified via flash column chromatography with 20% EtOAc/hex as eluant to yield 319 mg(53%) of 4(S)-benzyl-3-(2-thien-2-yl-acetyl)-2-oxazolidinone as a tan solid, mp 56-9° C. 1H NMR: δ 7.34-7.26 (m, 5H), 7.17-7.14 (m, 2H), 7.02-6.98 (m, 1H), 4.72-4.67 (m, 1H), 4.57, 4.48 (AB quartet, 2H, J=16.8 Hz), 4.26-4.17 (m, 2H), 3.29 (dd, 1H, J=3.2, 13.4 Hz), 2.78 (dd, 1H, J=9.5, 13.4 Hz). Anal. Calculated for C16H15NO3S: C, 63.77; H, 5.02; N, 4.65; S, 10.64. Found: C, 63.87; H, 5.04; N, 4.71; S, 10.74.
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[CH2:13][CH2:12][NH:11][C@@H:10]([CH3:14])[CH2:9]1)=[O:7])([CH3:4])([CH3:3])[CH3:2].[CH2:15]([O:22][C:23]([N:25]1[CH2:30][CH2:29][C:28](=O)[CH2:27][CH2:26]1)=[O:24])[C:16]1[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=1.C([BH3-])#N.[Na+].[OH-].[Na+]>CO.C(O)(=O)C>[C:1]([O:5][C:6]([N:8]1[CH2:13][CH2:12][N:11]([CH:28]2[CH2:29][CH2:30][N:25]([C:23]([O:22][CH2:15][C:16]3[CH:17]=[CH:18][CH:19]=[CH:20][CH:21]=3)=[O:24])[CH2:26][CH2:27]2)[C@@H:10]([CH3:14])[CH2:9]1)=[O:7])([CH3:4])([CH3:2])[CH3:3]
Reactant: O=C1CCN(C(=O)OCc2ccccc2)CC1
Reactant: C[C@H]1CN(C(=O)OC(C)(C)C)CCN1
Agent: [BH3-]C#N
Agent: [Na+]
Agent: [OH-]
Solvent: CO
Solvent: CC(=O)O
Product: C[C@H]1CN(C(=O)OC(C)(C)C)CCN1C1CCN(C(=O)OCc2ccccc2)CC1
Temperature: 25 °C
Reaction time: 1 h
Yield: 34.1 %

Procedure:
To a solution of (S)-3-methyl-piperazine-1-carboxylic acid tert-butyl ester (1.0 g, mmol) and N-benzyloxycarbonyl-4-piperidone (1.2 g, 5 mmol) in methanol (8 mL) was added acetic acid (0.28 mL) and the solution was stirred at RT for 1 h. Sodium cyanoborohydride (310 mg, 5 mmol) was added and the reaction mixture was stirred at 45° C. overnight and then 1 N NaOH (5 mL) was added. The aqueous phase was extracted with EtOAc (3×15 mL). The combined organic extracts were washed with brine, dried over MgSO4, filtered, concentrated under vacuum, and purified by silica gel chromatography (0-5% MeOH/DCM). Pure fractions were combined and concentrated under vacuum to provide the title intermediate (0.71 g, 30% yield) as a clear oil. (m/z): [M+H]+ calcd for C23H35N3O4 418.26 found 418.1.
Reaction SMILES: [NH:1]1[CH2:6][CH2:5][CH:4]([N:7]2[CH:11]=[C:10]([NH:12][C:13]3[N:18]=[C:17]([CH2:19][CH2:20][C:21]4[CH:26]=[CH:25][CH:24]=[CH:23][C:22]=4[CH:27]([CH3:31])[C:28]([NH2:30])=[O:29])[C:16]([C:32]([F:35])([F:34])[F:33])=[CH:15][N:14]=3)[CH:9]=[N:8]2)[CH2:3][CH2:2]1.I[CH:37]([CH3:39])[CH3:38].C([O-])([O-])=O.[K+].[K+]>CC#N>[CH:37]([N:1]1[CH2:2][CH2:3][CH:4]([N:7]2[CH:11]=[C:10]([NH:12][C:13]3[N:18]=[C:17]([CH2:19][CH2:20][C:21]4[CH:26]=[CH:25][CH:24]=[CH:23][C:22]=4[CH:27]([CH3:31])[C:28]([NH2:30])=[O:29])[C:16]([C:32]([F:34])([F:33])[F:35])=[CH:15][N:14]=3)[CH:9]=[N:8]2)[CH2:5][CH2:6]1)([CH3:39])[CH3:38]
Reactant: CC(C)I
Reactant: CC(C(N)=O)c1ccccc1CCc1nc(Nc2cnn(C3CCNCC3)c2)ncc1C(F)(F)F
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC#N
Product: CC(C(N)=O)c1ccccc1CCc1nc(Nc2cnn(C3CCN(C(C)C)CC3)c2)ncc1C(F)(F)F
Yield: 70 %

Procedure:
A suspension of 2-(2-(2-(2-((1-(piperidin-4-yl)-1H-pyrazol-4-yl)amino)-5-(trifluoromethyl)pyrimidin-4-yl)ethyl)phenyl)propanamide A67 (80 mg, 0.16 mmol), 2-iodopropane (25 μL, 0.25 mmol) and K2CO3 (68 mg, 0.49 mmol) in MeCN (5 mL) was irradiated in the microwave at 120° C. for 40 minutes. Additional 2-iodopropane (25 μL, 0.25 mmol) was added and the reaction mixture was irradiated in the microwave at 120° C. for another 40 minutes. Upon cooling, the liquid was decanted from the solid and the volatiles were removed in vacuo. The resultant solid was suspended in water (50 mL) and sonicated for 10 minutes before being filtered. The solid was dissolved in acetone (3 mL) and precipitated by the addition of petroleum benzine 40-60° C. before being collected by filtration and dried under high vacuum to give the title compound 60 as a tan solid (61 mg, 70%). LCMS-D: rt 3.060 min; m/z 530.4 [M+H]+.
Reaction SMILES: C(N1[CH2:13][C@@H:12]([O:14][C:15]([CH3:18])([CH3:17])[CH3:16])[CH2:11][C@H](C(OC)=O)[C@H]1C(OCC1C=CC=CC=1)=O)C1C=CC=CC=1.[CH3:33]C(=C)C.C(N1C[C@@H](O)C[C@H](C(OC)=O)[C@H]1C(OCC1C=CC=CC=1)=O)C1C=CC=CC=1.S(=O)(=O)(O)O>>[C:15]([O:14][C:12]([CH3:11])([CH3:13])[CH3:33])([CH3:16])([CH3:17])[CH3:18]
Reactant: C=C(C)C
Reactant: COC(=O)[C@H]1C[C@H](OC(C)(C)C)CN(Cc2ccccc2)[C@@H]1C(=O)OCc1ccccc1
Agent: COC(=O)[C@H]1C[C@H](O)CN(Cc2ccccc2)[C@@H]1C(=O)OCc1ccccc1
Agent: O=S(=O)(O)O
Product: CC(C)(C)OC(C)(C)C
Temperature: 25 °C
Reaction time: 8 h
Yield: 51 %

Procedure:
Part 1. 2-benzyl 3-methyl(2S, 3S, 5S)-1-benzyl-5-tert-butoxypiperidine-2,3-dicarboxylate: Isobutylene (2.96 mL, 0.0313 mol) was collected at −78 Celsius. To the cold isobutylene was added 2-benzyl 3-methyl(2S,3S,5S)-1-benzyl-5-hydroxypiperidine-2,3-dicarboxylate (0.60 g, 0.0016 mol) tetrahydrofuran (3.00 mL, 0.0370 mol), sulfuric acid (0.021 mL, 0.00039 mol). The reaction was sealed and allowed to warm up to rt and stirred at rt overnight. The mixture was cooled to −78 Celsius again. The seal was replaced with a septa connecting with a balloon. The reaction was then allowed to warm up to rt gradually to allow the evaporating of excess isobutylene. The residue was diluted with EtOAc, neutralized with aq. sodium hydroxide. The organic layers were washed with brine, dried. The residue was purified on silica gel, eluting with 0 to 30% EtOAc in hexane, to afford the tert-butyl ether (0.35 g, 51%). MS (ESI): (M+H)+=440.25.
Reaction SMILES: [Br:1][C:2]1[CH:7]=[CH:6][C:5]([F:8])=[C:4](I)[C:3]=1[Br:10].C1COCC1.[C:16]([Si:18]([CH3:21])([CH3:20])[CH3:19])#[CH:17]>CCOC(C)=O.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>[Br:10][C:3]1[C:2]([Br:1])=[CH:7][CH:6]=[C:5]([F:8])[C:4]=1[C:17]#[C:16][Si:18]([CH3:21])([CH3:20])[CH3:19]
Reactant: C#C[Si](C)(C)C
Reactant: Fc1ccc(Br)c(Br)c1I
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: [Cu]I
Solvent: CCOC(C)=O
Solvent: C1CCOC1
Product: C[Si](C)(C)C#Cc1c(F)ccc(Br)c1Br
Temperature: 40 °C
Reaction time: 40 h
Yield: 79.4 %

Procedure:
A thick-walled glass vessel was charged with 1,2-dibromo-4-fluoro-3-iodobenzene (8.31 g, 21.88 mmol), Pd(PPh3)2Cl2 (0.768 g, 1.094 mmol), and CuI (0.292 g, 1.532 mmol) and sealed with a rubber septum. Anhyd THF (30 mL) and DIPA (30.8 mL, 219 mmol) were added via syringe and the mixture was degassed 10 min by sparging with N2 while immersed in an ultrasonic bath. Ethynyltrimethylsilane (3.40 mL, 24.07 mmol) was added via syringe and the septum was replaced with a PTFE bushing. The mixture was stirred in an oil bath at 40° C. After 40 h, the mixture was cooled, diluted with EtOAc and filtered through a pad of Celite. The filtrate was washed (satd NH4Cl×2, water, brine), dried over Na2SO4 and concentrated in vacuo. The residue was purified by low pressure liquid chromatography (silica gel, EtOAc/hexanes, gradient elution) affording ((2,3-dibromo-6-fluorophenyl)ethynyl)trimethylsilane (6.08 g, 17.37 mmol, 79% yield) as a yellow oil: 1H NMR (400 MHz, CDCl3) δ 7.53 (dd, J=8.9, 5.4 Hz, 1H), 6.95 (dd, J=8.9, 8.1 Hz, 1H), 0.29 (s, 9H); MS (GCMS EI) m/z 348 ([M]+, Br isotopes, 18%), 350 ([M]+, Br isotopes, 34%), 352 ([M]+, Br isotopes, 18%), 333 ([M-CH3]+, Br isotopes, 56%), 335 ([M-CH3]+, Br isotopes, 100%), 337 ([M-CH3]+, Br isotopes, 54%).