Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [Cl:1][C:2]1[CH:31]=[CH:30][C:5]([CH2:6][N:7]2[C:15]3[C:10](=[CH:11][C:12](/[CH:16]=[C:17]4/[C:18](=[O:29])[N:19]([CH:23]5[CH2:28][CH2:27][NH:26][CH2:25][CH2:24]5)[C:20](=[O:22])[S:21]/4)=[CH:13][CH:14]=3)[CH:9]=[N:8]2)=[C:4]([C:32]([F:35])([F:34])[F:33])[CH:3]=1.Br[CH2:37][CH2:38][OH:39]>>[Cl:1][C:2]1[CH:31]=[CH:30][C:5]([CH2:6][N:7]2[C:15]3[C:10](=[CH:11][C:12](/[CH:16]=[C:17]4/[C:18](=[O:29])[N:19]([CH:23]5[CH2:28][CH2:27][N:26]([CH2:37][CH2:38][OH:39])[CH2:25][CH2:24]5)[C:20](=[O:22])[S:21]/4)=[CH:13][CH:14]=3)[CH:9]=[N:8]2)=[C:4]([C:32]([F:35])([F:34])[F:33])[CH:3]=1
Reactant: OCCBr
Reactant: O=C1S/C(=C\c2ccc3c(cnn3Cc3ccc(Cl)cc3C(F)(F)F)c2)C(=O)N1C1CCNCC1
Product: O=C1S/C(=C\c2ccc3c(cnn3Cc3ccc(Cl)cc3C(F)(F)F)c2)C(=O)N1C1CCN(CCO)CC1

Procedure:
(5Z)-5-({1-[4-Chloro-2-(trifluoromethyl)benzyl]-1H-indazol-5-yl}methylidene)-3-[1-(2-hydroxyethyl)piperidin-4-yl]-1,3-thiazolidine-2,4-dione was prepared from (5Z)-5-({1-[4-chloro-2-(trifluoromethyl)benzyl]-1H-indazol-5-yl}methylidene)-3-piperidin-4-yl-1,3-thiazolidine-2,4-dione (Example 113) and 2-bromoethanol following General Procedure S.
Reaction SMILES: [NH2:1][C@@H:2]1[CH2:8][CH2:7][C:6]2[CH:9]=[CH:10][CH:11]=[CH:12][C:5]=2[NH:4][C:3]1=[O:13].[C:14]([O:18][C:19]([NH:21][C@@H:22]([C:30](O)=[O:31])[CH2:23][C:24]1[CH:29]=[CH:28][CH:27]=[CH:26][CH:25]=1)=[O:20])([CH3:17])([CH3:16])[CH3:15].C(N(CC)CC)C.F[P-](F)(F)(F)(F)F.N1(O[P+](N(C)C)(N(C)C)N(C)C)C2C=CC=CC=2N=N1>C(Cl)Cl.C(OCC)(=O)C>[C:14]([O:18][C:19]([NH:21][C@H:22]([CH2:23][C:24]1[CH:25]=[CH:26][CH:27]=[CH:28][CH:29]=1)[C:30]([NH:1][C@@H:2]1[CH2:8][CH2:7][C:6]2[CH:9]=[CH:10][CH:11]=[CH:12][C:5]=2[NH:4][C:3]1=[O:13])=[O:31])=[O:20])([CH3:17])([CH3:15])[CH3:16]
Reactant: N[C@@H]1CCc2ccccc2NC1=O
Reactant: CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)C(=O)O
Agent: CN(C)[P+](On1nnc2ccccc21)(N(C)C)N(C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CCOC(C)=O
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H]1CCc2ccccc2NC1=O
Reaction time: 2 h
Yield: 100 %

Procedure:
To a solution of 30 mg (0.17 mmol) 3(R)-amino-2,3,4,5-tetrahydro-1H-1-benzazepin-2-one (Example 1; Step B) in 2 mL methylene chloride at room temperature was added 50 mg (0.19 mmol, 1.1 eq) N-(t-butoxycarbonyl)-D-phenylalanine followed by 0.047 mL (34 mg, 0.34 mmol, 2 eq) of triethylamine and 113 mg (0.26 mmol, 1.5 eq) benzotriazol-1-yloxytris(dimethylamino)phosphonium hexafluorophosphate. After 2 hours at room temperature, the mixture was added to 30 mL of ethyl acetate and washed with 5% citric acid (2×), saturated aqueous sodium bicarbonate and brine. The organic layer was removed, dried over magnesium sulfate, filtered and solvents removed under vacuum. The residue was purified by medium pressure liquid chromatography on silica, eluting with ethyl acetate to afford 71 mg (0.17 mmol, 100%) of the product. 1H NMR (200 MHz, CDCl3): 1.38 (s,9H), 1.9 (m,1H), 2.6-3.1 (m,5H), 4.44 (m,2H), 5.10 (br d,7 Hz,1H), 6.95 (d,8 Hz,1H), 7.1-7.3 (m,8H), 8.33 (br s,1H). FAB-MS: calc. for C24H29N3O4 423; found 424 (M+H,65%).
Reaction SMILES: [Br:1][C:2]1[S:3][C:4]([C:11]2[CH:16]=[CH:15][CH:14]=[CH:13][CH:12]=2)=[C:5]([C:7]([O:9]C)=O)[N:6]=1.[NH2:17][CH2:18][CH2:19][NH:20][C:21](=[O:27])[O:22][C:23]([CH3:26])([CH3:25])[CH3:24].NC1SC(C2C=CC=CC=2)=C(C(OC)=O)N=1>>[Br:1][C:2]1[S:3][C:4]([C:11]2[CH:16]=[CH:15][CH:14]=[CH:13][CH:12]=2)=[C:5]([C:7]([NH:17][CH2:18][CH2:19][NH:20][C:21](=[O:27])[O:22][C:23]([CH3:25])([CH3:24])[CH3:26])=[O:9])[N:6]=1
Reactant: CC(C)(C)OC(=O)NCCN
Reactant: COC(=O)c1nc(Br)sc1-c1ccccc1
Agent: COC(=O)c1nc(N)sc1-c1ccccc1
Product: CC(C)(C)OC(=O)NCCNC(=O)c1nc(Br)sc1-c1ccccc1
Yield: 20.3 %

Procedure:
2.0 g (6.7 mmol) of methyl 2-bromo-5-phenyl-4-thiazolecarboxylate and 1.61 g (10.1 mmol) of t-butyl (2-aminoethyl)carbamate were stirred under reduced pressure for 2.5 hours at 110° bath temperature, whereby the methanol formed was distilled off continuously. After chromatography on 100 g of silica gel with methylene chloride and a 4:1 mixture of methylene chloride and ethyl acetate there was obtained 0.58 g (26%) of t-butyl [2-(2-bromo-5-phenyl-4-thiazolecarboxamido)ethyl]carbamate as a pale yellow, crystallizing oil which was used directly.
Reaction SMILES: [CH2:1]([CH:8]1[CH2:13][CH:12]([NH2:14])[CH2:11][CH2:10][N:9]1[C:15](=[O:24])[C:16]1[CH:21]=[C:20]([Cl:22])[CH:19]=[C:18]([Cl:23])[CH:17]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[C:25]([C:33]1[CH:38]=[CH:37][CH:36]=[CH:35][CH:34]=1)(=O)[C:26]1[CH:31]=[CH:30][CH:29]=[CH:28][CH:27]=1.C([BH3-])#N.[Na+].C(O)(=O)C>C1(C)C=CC=CC=1>[CH2:1]([C@@H:8]1[CH2:13][C@@H:12]([NH:14][CH:25]([C:26]2[CH:31]=[CH:30][CH:29]=[CH:28][CH:27]=2)[C:33]2[CH:38]=[CH:37][CH:36]=[CH:35][CH:34]=2)[CH2:11][CH2:10][N:9]1[C:15](=[O:24])[C:16]1[CH:21]=[C:20]([Cl:22])[CH:19]=[C:18]([Cl:23])[CH:17]=1)[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: O=C(c1ccccc1)c1ccccc1
Reactant: NC1CCN(C(=O)c2cc(Cl)cc(Cl)c2)C(Cc2ccccc2)C1
Agent: [BH3-]C#N
Agent: [Na+]
Solvent: CC(=O)O
Solvent: Cc1ccccc1
Product: O=C(c1cc(Cl)cc(Cl)c1)N1CC[C@H](NC(c2ccccc2)c2ccccc2)C[C@H]1Cc1ccccc1
Temperature: 25 °C
Reaction time: 68 h

Procedure:
A solution of 200 mg (0.551 mmol) of (2R*,45*)-2-benzyl-1-(3,5-dichlorobenzoyl)-4-piperidinamine and 110 mg (0.606 mmol) of benzophenone in 5 ml of toluene are kept at reflux for 18 hours. The reaction mixture is then concentrated in a rotary evaporator and dissolved in 3 ml of methanol, and 69 mg (1.10 mmol) of sodium cyanoborohydride are added at RT. The reaction mixture is adjusted to pH=5 with 80 μl of acetic acid and stirred at RT for 68 hours. The title compound ##STR98## is obtained as white foam (120 mg, 41%). TLC:toluene/ethyl acetate (7:3) Rf =0.79, FD-MS:M+ =528, 530; IR:1630 cm-1.
Reaction SMILES: Cl.Cl.Cl.[O:4]1[C:12]2[CH:11]=[CH:10][N:9]=[C:8]([N:13]3[CH2:18][CH2:17][N:16]([CH2:19][CH2:20][C@H:21]4[CH2:26][CH2:25][C@H:24]([NH2:27])[CH2:23][CH2:22]4)[CH2:15][CH2:14]3)[C:7]=2[CH2:6][CH2:5]1.[O:28]1[CH2:33][CH2:32][O:31][CH2:30][CH:29]1[CH2:34][C:35](O)=[O:36]>>[O:4]1[C:12]2[CH:11]=[CH:10][N:9]=[C:8]([N:13]3[CH2:18][CH2:17][N:16]([CH2:19][CH2:20][C@H:21]4[CH2:26][CH2:25][C@H:24]([NH:27][C:35](=[O:36])[CH2:34][CH:29]5[CH2:30][O:31][CH2:32][CH2:33][O:28]5)[CH2:23][CH2:22]4)[CH2:15][CH2:14]3)[C:7]=2[CH2:6][CH2:5]1
Reactant: O=C(O)CC1COCCO1
Reactant: N[C@H]1CC[C@H](CCN2CCN(c3nccc4c3CCO4)CC2)CC1
Agent: Cl
Product: O=C(CC1COCCO1)N[C@H]1CC[C@H](CCN2CCN(c3nccc4c3CCO4)CC2)CC1

Procedure:
The title compound, white solid (107 mg, 78%), MS (ISP) m/z=459.4 [(M+H)+], mp 186° C., was prepared in accordance with the general method of example 32 from trans-4-{2-[4-(2,3-dihydrofuro[3,2-c]pyridin-4-yl)-piperazin-1-yl]-ethyl}-cyclohexanamine trihydrochloride (intermediate C) (132 mg, 0.3 mmol) and rac-(1,4-dioxan-2-yl)-acetic acid.
Reaction SMILES: [CH2:1]([O:3][C:4]([CH:6]1[C:15]([CH:16]=O)=[CH:14][C:13]2[C:8](=[CH:9][CH:10]=[CH:11][C:12]=2[Cl:18])[O:7]1)=[O:5])C.[CH3:19][O:20][C:21](=[O:28])[C@@H:22]([NH2:27])[CH2:23][CH:24]([CH3:26])[CH3:25].CCN(C(C)C)C(C)C.C([BH3-])#N.[Na+].C(O)(=O)C>CO>[CH3:1][O:3][C:4]([CH:6]1[C:15]([CH2:16][NH:27][C@H:22]([C:21]([O:20][CH3:19])=[O:28])[CH2:23][CH:24]([CH3:26])[CH3:25])=[CH:14][C:13]2[C:8](=[CH:9][CH:10]=[CH:11][C:12]=2[Cl:18])[O:7]1)=[O:5]
Reactant: CCOC(=O)C1Oc2cccc(Cl)c2C=C1C=O
Reactant: COC(=O)[C@@H](N)CC(C)C
Agent: [BH3-]C#N
Agent: [Na+]
Solvent: CO
Solvent: CC(=O)O
Solvent: CCN(C(C)C)C(C)C
Product: COC(=O)C1Oc2cccc(Cl)c2C=C1CN[C@@H](CC(C)C)C(=O)OC
Temperature: 25 °C
Reaction time: 10 h
Yield: 55.9 %

Procedure:
To a solution of 5-chloro-3-formyl-2H-chromene-2-carboxylic acid ethyl ester (1.5 g, 5.62 mmol) (from Example 1, Step 1) in methanol (20 mL) containing molecular sieves (0.7 g) was added commercially available (S)-2-amino-4-methyl-pentanoic acid methyl ester (1.2 g, 5.62 mmol) and N,N′-diisopropylethylamine (2 mL, 11.24 mmol). The mixture was stirred at 25° C. for 10 hours. At this time, sodium cyanoborohydride (0.706 g, 11.24 mmol) and acetic acid (0.70 mL, 11.24 mmol) were added simultaneously to the reaction mixture, and the reaction mixture was stirred for additional 16 hours at 25° C. The reaction mixture was then filtered through celite and washed with methanol. The filtrate was concentrated in vacuo and the residue was purified using flash column chromatography over neutral alumina (eluant-ethyl acetate:petroleum ether 1:19, Rf=0.7) to afford 5-chloro-3-[((S)-1-methoxycarbonyl-3-methyl-butylamino)-methyl]-2H-chromene-2-carboxylic acid methyl ester (1.2 g, 54.5%) as an oil.
Reaction SMILES: [C:1]([NH:9][CH2:10][C:11]([OH:13])=O)(=[O:8])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.Cl.CN(CCCN=C=N)C.O.ON1C2C=CC=CC=2N=N1.Cl.Cl.[NH2:37][CH:38]1[CH2:42][CH2:41][N:40]([CH2:43][C:44]2[CH:49]=[CH:48][C:47]([Cl:50])=[CH:46][CH:45]=2)[CH2:39]1>C(Cl)(Cl)Cl.CCN(CC)CC>[C:1]([NH:9][CH2:10][C:11]([NH:37][CH:38]1[CH2:42][CH2:41][N:40]([CH2:43][C:44]2[CH:49]=[CH:48][C:47]([Cl:50])=[CH:46][CH:45]=2)[CH2:39]1)=[O:13])(=[O:8])[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: NC1CCN(Cc2ccc(Cl)cc2)C1
Reactant: O=C(O)CNC(=O)c1ccccc1
Agent: CN(C)CCCN=C=N
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: CCN(CC)CC
Solvent: ClC(Cl)Cl
Solvent: O
Product: O=C(CNC(=O)c1ccccc1)NC1CCN(Cc2ccc(Cl)cc2)C1
Temperature: 25 °C
Reaction time: 16 h

Procedure:
N-Benzoylglycine (9.9 mg, 0.055 mmol), 3-ethyl-1-(3-(dimethylaminopropyl)carbodiimide hydrochloride (EDCI) (10.5 mg) and 1-hydroxybenzotriazole hydrate (HOBt) (7.4 mg) were added to a solution of 3-amino-1-(4-chlorobenzyl)pyrrolidine dihydrochloride (14.2 mg, 0.050 mmol) and Et3N (15.2 mg) in CHCl3 (2.5 mL). The reaction mixture was stirred at 25° C. for 16 h, washed with 2 N aqueous NaOH (2 mL×2) and brine (1 mL). After filtration through a PTFE membrane filter, the solvent was removed under reduced pressure to afford 3-(N-benzoylglycyl)amino-1-(4-chlorobenzyl)pyrrolidine (compound No. 1) as a pale yellow oil (17.7 mg, 95%): The purity was determined by RPLC/MS (95%); ESI/MS m/e 372.0 (M++H, C20H22ClN3O2).
Reaction SMILES: [CH:1]1([CH2:4][NH:5][CH2:6][C:7]2[NH:8][C:9](=[O:17])[C:10]3[CH2:16][O:15][CH2:14][CH2:13][C:11]=3[N:12]=2)[CH2:3][CH2:2]1.[CH2:18]([O:22][C:23]1[CH:40]=[CH:39][C:26]([C:27]([CH:29]2[CH2:34][CH2:33][N:32]([CH2:35][C:36](O)=[O:37])[CH2:31][CH2:30]2)=[O:28])=[CH:25][CH:24]=1)[C:19]#[C:20][CH3:21]>>[CH2:18]([O:22][C:23]1[CH:40]=[CH:39][C:26]([C:27]([CH:29]2[CH2:34][CH2:33][N:32]([CH2:35][C:36]([N:5]([CH2:4][CH:1]3[CH2:3][CH2:2]3)[CH2:6][C:7]3[NH:8][C:9](=[O:17])[C:10]4[CH2:16][O:15][CH2:14][CH2:13][C:11]=4[N:12]=3)=[O:37])[CH2:31][CH2:30]2)=[O:28])=[CH:25][CH:24]=1)[C:19]#[C:20][CH3:21]
Reactant: CC#CCOc1ccc(C(=O)C2CCN(CC(=O)O)CC2)cc1
Reactant: O=c1[nH]c(CNCC2CC2)nc2c1COCC2
Product: CC#CCOc1ccc(C(=O)C2CCN(CC(=O)N(Cc3nc4c(c(=O)[nH]3)COCC4)CC3CC3)CC2)cc1
Yield: 28.6 %

Procedure:
The title compound (90 mg) was prepared following the general procedure of Example 1 from 2-[(cyclopropylmethyl-amino)-methyl]-3,5,7,8-tetrahydro-pyrano[4,3-d]pyrimidin-4-one (140 mg, 0.59 mmol) and [4-(4-but-2-ynyloxy-benzoyl)-piperidin-1-yl]-acetic acid (187 mg, 0.59 mmol). 1H NMR (400 MHz, MeOD) δ: 8.01 (d, J=8.6 Hz, 2H), 7.08 (d, J=9.1 Hz, 2H), 4.79-4.76 (m, 2H), 4.66 (s, 1H), 4.57 (s, 1H), 4.50-4.45 (m, 2H), 4.39 (s, 2H), 3.92 (t, J=5.6 Hz, 2H), 3.80-3.67 (m, 2H), 3.36 (d, J=7.1 Hz, 2H), 3.33-3.28 (m, 6H), 2.69-2.58 (m, 2H), 2.22-2.02 (m, 4H), 1.83 (t, J=2.5 Hz, 3H), 1.11-0.89 (m, 1H), 0.66-0.43 (m, 2H), 0.34-0.19 (m, 2H). HRMS calculated for C33H38N4O3=533.2764. found (ESI, [M+H]+), 533.2788. LRMS m/z: ES+=533.7 (M+H), retention time 1.08.
Reaction SMILES: [I:1][C:2]1[C:10]([CH3:11])=[CH:9][CH:8]=[CH:7][C:3]=1[C:4]([OH:6])=O.Cl.[CH2:13]([O:15][C:16]([C:18]1([NH2:29])[CH2:26][C:25]2[C:20](=[C:21]([F:28])[CH:22]=[CH:23][C:24]=2[F:27])[CH2:19]1)=[O:17])[CH3:14].CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.CCN(C(C)C)C(C)C>CN(C=O)C.CCOC(C)=O>[CH2:13]([O:15][C:16]([C:18]1([NH:29][C:4](=[O:6])[C:3]2[CH:7]=[CH:8][CH:9]=[C:10]([CH3:11])[C:2]=2[I:1])[CH2:26][C:25]2[C:20](=[C:21]([F:28])[CH:22]=[CH:23][C:24]=2[F:27])[CH2:19]1)=[O:17])[CH3:14]
Reactant: CCOC(=O)C1(N)Cc2c(F)ccc(F)c2C1
Reactant: Cc1cccc(C(=O)O)c1I
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: Cl
Agent: F[P-](F)(F)(F)(F)F
Solvent: CN(C)C=O
Solvent: CCN(C(C)C)C(C)C
Solvent: CCOC(C)=O
Product: CCOC(=O)C1(NC(=O)c2cccc(C)c2I)Cc2c(F)ccc(F)c2C1
Temperature: 25 °C
Reaction time: 48 h
Yield: 75.4 %

Procedure:
To a solution of 2-iodo-3-methyl-benzoic acid (1.31 g, 5 mmol), 2-amino-4,7-difluoro-indan-2-carboxylic acid ethyl ester HCl salt (1.38 g, 5 mmol), HATU [O-(7-Azabenzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium PF6, 3.80 g, 10 mmol) in anhydrous DMF (20 mL) is added DIPEA (N,N-diisopropylethylamine, 3.3 mL, 15 mmol). The resulting solution is stirred at RT for two days. After the removal of DMF in vacuo, the residue obtained is dissolved in EtOAc (200 mL) and washed with saturated NaHCO3 (1×100 mL) and brine (2×100 mL). The organic layer is dried over anhydrous Na2SO4 and concentrated in vacuo. The obtained residue is purified by flash column chromatography (40 g silica gel, gradient elution: 0%-50% EtOAc in heptane) to give a pure product (390) as white solid (1.83 g, 75%).
Reaction SMILES: [CH3:1][O:2][C:3]1[C:11]([CH3:12])=[CH:10][CH:9]=[C:8]2[C:4]=1[CH:5]=[C:6]([C:13]([NH2:15])=O)[NH:7]2.P(Cl)(Cl)(Cl)=O.C(Cl)(Cl)Cl>O>[CH3:1][O:2][C:3]1[C:11]([CH3:12])=[CH:10][CH:9]=[C:8]2[C:4]=1[CH:5]=[C:6]([C:13]#[N:15])[NH:7]2
Reactant: COc1c(C)ccc2[nH]c(C(N)=O)cc12
Solvent: O=P(Cl)(Cl)Cl
Solvent: ClC(Cl)Cl
Solvent: O
Product: COc1c(C)ccc2[nH]c(C#N)cc12
Reaction time: 1 h
Yield: 70.2 %

Procedure:
A mixture of 79 mg of 4-methoxy-5-methyl-1H-indole-2-carboxamide (0.39 mmol), 0.19 mL of phosphorus oxychloride (2 mmol) and 1.5 mL of chloroform was refluxed for 2 hs. Then cooled solution was poured into 10 mL of water and stirred for 1 hr. After separation the organic layer was dried over sodium sulfate and concentrated. The residue was purified on silica gel column using hexane-ethyl acetate 5:1 to afford 51 mg of 4-methoxy-5-methyl-1H-indole-2-carbonitrile.
Reaction SMILES: C1(S([N:10]2[C:14]3=[N:15][CH:16]=[C:17]([Br:19])[CH:18]=[C:13]3[C:12]([C:20]3[CH:21]=[N:22][N:23]([C:25]([C:38]4[CH:43]=[CH:42][CH:41]=[CH:40][CH:39]=4)([C:32]4[CH:37]=[CH:36][CH:35]=[CH:34][CH:33]=4)[C:26]4[CH:31]=[CH:30][CH:29]=[CH:28][CH:27]=4)[CH:24]=3)=[CH:11]2)(=O)=O)C=CC=CC=1.[H-].[Na+].[CH3:46][Si:47]([CH2:50][CH2:51][O:52][CH2:53]Cl)([CH3:49])[CH3:48].C(OCC)(=O)C>CN(C=O)C>[Br:19][C:17]1[CH:18]=[C:13]2[C:12]([C:20]3[CH:21]=[N:22][N:23]([C:25]([C:32]4[CH:33]=[CH:34][CH:35]=[CH:36][CH:37]=4)([C:38]4[CH:43]=[CH:42][CH:41]=[CH:40][CH:39]=4)[C:26]4[CH:31]=[CH:30][CH:29]=[CH:28][CH:27]=4)[CH:24]=3)=[CH:11][N:10]([CH2:53][O:52][CH2:51][CH2:50][Si:47]([CH3:49])([CH3:48])[CH3:46])[C:14]2=[N:15][CH:16]=1
Reactant: C[Si](C)(C)CCOCCl
Reactant: O=S(=O)(c1ccccc1)n1cc(-c2cnn(C(c3ccccc3)(c3ccccc3)c3ccccc3)c2)c2cc(Br)cnc21
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: CCOC(C)=O
Product: C[Si](C)(C)CCOCn1cc(-c2cnn(C(c3ccccc3)(c3ccccc3)c3ccccc3)c2)c2cc(Br)cnc21
Reaction time: 0.5 h
Yield: 54.8 %

Procedure:
To a solution of 21 (0.5 g, 0.99 mmol) in DMF (2.5 mL) was added NaH (60% w/w in mineral oil, 59.4 mg, 1.48 mmol) portionwise. Then the reaction mixture was stirred for 0.5 h. SEM-Cl (263 μL, 1.48 mmol) was then added and the reaction mixture stirred overnight. It was poured cautiously onto a stirred mixture of ethyl acetate (20 mL)/sat. aq. NH4Cl (20 mL) and the layers separated. The aqueous layer was extracted with AcOEt (2×30 mL), the combined organic extracts dried (MgSO4) and concentrated. The residue was purified by SGC using AcOEt:hexane (gradient elution up to 8:92, v/v) to give 22 as a white foam (345 mg, 55%); 1H NMR (400 MHz, CDCl3) δ 0.002 (9H, s), 0.97 (t, J=8.3 Hz, 2H), 3.58 (t, J=8.3 Hz, 2H), 5.69 (s, 2H), 7.30 (m, 6H), 7.40 (m, 9H), 7.46 (s, 1H), 7.65 (s, 1H), 7.98 (d, J=0.7 Hz, 1H), 8.06 (d, J=2.1 Hz, 1H), 8.41 (d, J=2.2 Hz, 1H).
Reaction SMILES: [C:1]([O:5][C:6](=[O:17])[CH2:7][O:8][C:9]1[CH:14]=[CH:13][CH:12]=[C:11]([CH2:15][NH2:16])[CH:10]=1)([CH3:4])([CH3:3])[CH3:2].[N:18]1[CH:23]=[CH:22][CH:21]=[N:20][C:19]=1[C:24]1[CH:31]=[CH:30][C:27]([CH:28]=O)=[CH:26][CH:25]=1>C(N(CC)CC)C>[C:1]([O:5][C:6](=[O:17])[CH2:7][O:8][C:9]1[CH:14]=[CH:13][CH:12]=[C:11]([CH2:15][NH:16][CH2:28][C:27]2[CH:26]=[CH:25][C:24]([C:19]3[N:18]=[CH:23][CH:22]=[CH:21][N:20]=3)=[CH:31][CH:30]=2)[CH:10]=1)([CH3:4])([CH3:2])[CH3:3]
Reactant: O=Cc1ccc(-c2ncccn2)cc1
Reactant: CC(C)(C)OC(=O)COc1cccc(CN)c1
Solvent: CCN(CC)CC
Product: CC(C)(C)OC(=O)COc1cccc(CNCc2ccc(-c3ncccn3)cc2)c1

Procedure:
The title compound of Step A was prepared from (3-aminomethyl-phenoxy)-acetic acid tert-butyl ester, of Preparation 20, and 4-pyrimidin-2-yl-benzaldehyde, of Preparation 21, using the method described in Example 3, Step A, except no triethylamine was used. 1H NMR (400 MHz, CDCl3) δ 8.89 (d, 2H), 8.38 (d, 2H), 7.46 (d, 2H), 7.23 (m, 1H), 7.17 (m, 1H), 6.95 (m, 2H), 6.78 (dd, 1H), 4.51 (s, 2H), 3.86 (s, 2H), 3.79 (s, 2H), 1.47 (s, 9H); MS 406 (M+1).
Reaction SMILES: Cl.[CH2:2]([NH:4][CH2:5][C:6]([F:9])([F:8])[F:7])[CH3:3].Cl[C:11]1[C:16]([C:17]#[N:18])=[C:15]([C:19]2[CH:24]=[CH:23][C:22]([O:25][CH2:26][CH2:27][OH:28])=[CH:21][CH:20]=2)[C:14]([C:29]#[N:30])=[C:13]([S:31][CH2:32][C:33]2[N:34]=[C:35]([C:38]3[CH:43]=[CH:42][C:41]([Cl:44])=[CH:40][CH:39]=3)[S:36][CH:37]=2)[N:12]=1.Cl.FC(F)(F)CNC>CN(C=O)C.O.C1COCC1>[Cl:44][C:41]1[CH:40]=[CH:39][C:38]([C:35]2[S:36][CH:37]=[C:33]([CH2:32][S:31][C:13]3[C:14]([C:29]#[N:30])=[C:15]([C:19]4[CH:20]=[CH:21][C:22]([O:25][CH2:26][CH2:27][OH:28])=[CH:23][CH:24]=4)[C:16]([C:17]#[N:18])=[C:11]([N:4]([CH2:2][CH3:3])[CH2:5][C:6]([F:9])([F:8])[F:7])[N:12]=3)[N:34]=2)=[CH:43][CH:42]=1
Reactant: CCNCC(F)(F)F
Reactant: N#Cc1c(Cl)nc(SCc2csc(-c3ccc(Cl)cc3)n2)c(C#N)c1-c1ccc(OCCO)cc1
Agent: CNCC(F)(F)F
Agent: Cl
Solvent: O
Solvent: C1CCOC1
Solvent: CN(C)C=O
Product: CCN(CC(F)(F)F)c1nc(SCc2csc(-c3ccc(Cl)cc3)n2)c(C#N)c(-c2ccc(OCCO)cc2)c1C#N
Temperature: 25 °C
Reaction time: 0.5 h

Procedure:
133 mg (0.81 mmol) of N-ethyl-2,2,2-trifluoroethanamine hydrochloride were dissolved in 2 ml of DMF, 130 mg Amberlyst A-21 were added and the mixture was stirred at RT for 30 min. The mixture was filtered off and added to 100 mg (0.14 mmol, purity about 74%) of 2-chloro-6-({(2-(4-chlorophenyl)-1,3-thiazol-4-yl)methyl}sulfanyl)-4-(4-(2-hydroxyethoxy)phenyl)pyridine-3,5-dicarbonitrile (Example 2A), and the solution was stirred at RT overnight. The mixture was then warmed to 60° C. and stirred at this temperature overnight. In a separate flask, another 87 mg (0.54 mmol) of 2,2,2-trifluoro-N-methylethanamine hydrochloride were then dissolved in 0.5 ml of DMF, 88 mg of Amberlyst A-21 were added and the mixture was stirred at RT for 30 min. The mixture was filtered off and added to the first solution. The reaction mixture obtained was stirred at 100° C. for 4.5 h. The mixture was then diluted with a little water/THF and purified by preparative HPLC (acetonitrile/water+0.1% TFA). This gave 37 mg (41% of theory) of the target compound.
Reaction SMILES: C[Si](C)(C)[N-][Si](C)(C)C.[Li+].O1CCC[CH2:12]1.CI.[Br:18][C:19]1[C:27]2[C:22](=[CH:23][C:24]([N+:28]([O-:30])=[O:29])=[CH:25][CH:26]=2)[NH:21][CH:20]=1>CN(C)C=O>[Br:18][C:19]1[C:27]2[C:22](=[CH:23][C:24]([N+:28]([O-:30])=[O:29])=[CH:25][CH:26]=2)[N:21]([CH3:12])[CH:20]=1
Reactant: O=[N+]([O-])c1ccc2c(Br)c[nH]c2c1
Reactant: C1CCOC1
Agent: C[Si](C)(C)[N-][Si](C)(C)C
Agent: [Li+]
Solvent: CN(C)C=O
Solvent: CI
Product: Cn1cc(Br)c2ccc([N+](=O)[O-])cc21
Temperature: 25 °C
Reaction time: 5 h
Yield: 77.9 %

Procedure:
Method A Add 1M lithium hexamethyldisilazide in tetrahydrofuran (31.2 mL, 31.17 mmol) and methyl iodide (2.6 mL, 41.56 mmol) to a solution of 3-bromo-6-nitro-1H-indole 2 (5.01 g, 20.78 mmol) in N,N-dimethylformamide (100 mL) at 0° C. Warm the reaction mixture to room temperature and allow it to stir for 5 hr. Quench with saturated aqueous ammonium chloride (100 mL), dilute with ethyl acetate (200 mL), and separate the layers. Sequentially, wash the organic layer with 10% aqueous lithium chloride (75 mL), saturated aqueous sodium bicarbonate (75 mL), water (75 mL×2), and brine (75 mL). Dry the resulting organic layer over Na2SO4 and filter. Concentrate the filtrate to provide a residue. Adsorb the residue with the crude product onto silica gel. Chromatograph the residue on a silica gel column eluting with dichloromethane in hexane (5-50 v/v %) to give 4.13 g of the title compound (78%). LRMS (API ES+)=255.0 (M+H).
Reaction SMILES: FC(F)(F)C(O)=O.O.[C:9]([C:13]1[CH:64]=[CH:63][C:16]2[NH:17][C:18]([CH2:20][CH2:21][CH:22]3[CH2:25][CH:24]([N:26]([CH2:31][C@@H:32]4[C@H:36]5[O:37]C(C)(C)[O:39][C@H:35]5[C@H:34]([N:42]5[C:46]6[N:47]=[CH:48][N:49]=[C:50]([NH:51]CC7C=CC(OC)=CC=7OC)[C:45]=6[CH:44]=[CH:43]5)[CH2:33]4)[CH2:27][CH:28]([CH3:30])[CH3:29])[CH2:23]3)=[N:19][C:15]=2[CH:14]=1)([CH3:12])([CH3:11])[CH3:10].C([SiH](CC)CC)C.C([O-])([O-])=O.[K+].[K+]>CO.O>[NH2:51][C:50]1[C:45]2[CH:44]=[CH:43][N:42]([C@@H:34]3[CH2:33][C@H:32]([CH2:31][N:26]([CH:24]4[CH2:23][CH:22]([CH2:21][CH2:20][C:18]5[NH:17][C:16]6[CH:63]=[CH:64][C:13]([C:9]([CH3:12])([CH3:11])[CH3:10])=[CH:14][C:15]=6[N:19]=5)[CH2:25]4)[CH2:27][CH:28]([CH3:29])[CH3:30])[C@@H:36]([OH:37])[C@H:35]3[OH:39])[C:46]=2[N:47]=[CH:48][N:49]=1
Reactant: COc1ccc(CNc2ncnc3c2ccn3[C@@H]2C[C@H](CN(CC(C)C)C3CC(CCc4nc5cc(C(C)(C)C)ccc5[nH]4)C3)[C@H]3OC(C)(C)O[C@H]32)c(OC)c1
Agent: CC[SiH](CC)CC
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CO
Solvent: O
Solvent: O=C(O)C(F)(F)F
Product: CC(C)CN(C[C@H]1C[C@@H](n2ccc3c(N)ncnc32)[C@H](O)[C@@H]1O)C1CC(CCc2nc3cc(C(C)(C)C)ccc3[nH]2)C1
Reaction time: 8 h
Yield: 47.8 %

Procedure:
Trifluoroacetic Acid (20 ml, 300 mmol) added to a mixture of Water (2 ml, 100 mmol) and 7-((3aS,4R,6R,6aR)-6-(((3-(2-(5-(tert-butyl)-1H-benzo[d]imidazol-2-yl)ethyl)cyclobutyl)(isobutyl)amino)methyl)-2,2-dimethyltetrahydro-3aH-cyclopenta[d][1,3]dioxol-4-yl)-N-(2,4-dimethoxybenzyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (0.9 g, 1 mmol) at RT. The reaction was stirred overnight and Triethylsilane (0.38 ml, 2.4 mmol) was added. The volatiles were removed in vacuo and resulting residue was taken up in MeOH (15 ml), 500 mgs of K2CO3 and 8 drops H2O were added and reaction stirred at RT for 1 hour. The mixture was filtered and filter cake washed with 10 ml MeOH. The filtrate was concentrated and the resulting residue purified by flash chromatography (DCM/7N NH3 in MeOH 90:10) to yield the desired product (0.274 g) as an off white foam. MS (ESI+) for C33H47N7O2 m/z 574.6 [M+H]+; MS (EST) for C33H45N7O2 m/z 572.4 [M−H]−; HPLC purity >86% (ret. time, 2.918 min.) 1H NMR (400 MHz, d4-MeOH) δH 8.078 (s, 1H), 7.497 (s, 1H), 7.416-7.396 (m, 1H), 7.305-7.284 (m, 1H), 7.216-7.200 (m, 1H), 6.621-6.612 (d, J=3.6 Hz, 1H), 4.368-4.334 (m, 1H), 3.930-3.894 (m, 1H), 2.934-2.918 (m, 1H), 2.866-2.797 (m, 2H), 2.652-2.583 (m, 1H), 2.444-2.361 (m, 2H), 2.287-2.199 (m, 2H), 2.166-2.119 (m, 3.5H (contains methine of trans isomer)), 2.048-2.012 (m, 1H), 1.921-1.748 (m, 3.5H (contains methine of cis isomer)), 1.622-1.494 (m, 2H), 1.380 (s, 9H), 1.269-1.252 (m, 1H), 0.932-0.879 (m, 6H).