Reaction SMILES: [CH2:1]([O:3][C:4]1[CH:30]=[CH:29][C:7]([CH2:8][C:9]2[N:13]([CH2:14][CH2:15][CH:16]3[CH2:20][CH2:19][CH2:18][N:17]3[CH3:21])[C:12]3[CH:22]=[CH:23][C:24]([N+:26]([O-])=O)=[CH:25][C:11]=3[N:10]=2)=[CH:6][CH:5]=1)[CH3:2].I.CS[C:34]([C:36]1[S:37][CH:38]=[CH:39][CH:40]=1)=[NH:35]>C(O)C.[Pd]>[CH2:1]([O:3][C:4]1[CH:30]=[CH:29][C:7]([CH2:8][C:9]2[N:13]([CH2:14][CH2:15][CH:16]3[CH2:20][CH2:19][CH2:18][N:17]3[CH3:21])[C:12]3[CH:22]=[CH:23][C:24]([NH:26][C:34]([C:36]4[S:37][CH:38]=[CH:39][CH:40]=4)=[NH:35])=[CH:25][C:11]=3[N:10]=2)=[CH:6][CH:5]=1)[CH3:2]
Reactant: CSC(=N)c1cccs1
Reactant: CCOc1ccc(Cc2nc3cc([N+](=O)[O-])ccc3n2CCC2CCCN2C)cc1
Agent: [Pd]
Agent: I
Solvent: CCO
Product: CCOc1ccc(Cc2nc3cc(NC(=N)c4cccs4)ccc3n2CCC2CCCN2C)cc1
Temperature: 25 °C
Reaction time: 20 h

Procedure:
2-(4-Ethoxy-benzyl)-1-[2-(1-methyl-pyrrolidin-2-yl)-ethyl]-5-nitro-1H-benzimidazole 34 (45 mg, 0.110 mmol) was dissolved in anhydrous ethanol (5 mL) in a dry argon purged flask. Palladium, 10 wt % on activated carbon (15 mg, 0.014 mmol) is quickly added and the atmosphere from the flask evacuated by vacuum pump and replaced with hydrogen from a balloon. The atmosphere is evacuated from the flask and replaced with hydrogen twice more and the mixture stirred under a hydrogen atmosphere at room temperature. After 20 hours, thin layer chromatography in a solvent system of (5% 2M NH3 in methanol/95% dichloromethane) shows complete conversion to 35 2-(4-Ethoxy-benzyl)-1-[2-(1-methyl-pyrrolidin-2-yl)-ethyl]-1H-benzoimidazol-5-ylamine, which is utilized without isolation. The mixture is filtered through a pad of celite to remove insolubles, the pad washed with anhydrous ethanol (5 mL) and the ethanolic solution of the amine 35 is charged to a small, argon purged flask fitted with a magnetic stirbar. Thiophene-2-carboximidothioic acid methyl ester hydroiodide 9a (110.6 mg, 0.388 mmol) is added to the flask and the reaction was stirred under Ar at ambient temperature for 67 hours. The solvent was removed and the residue partitioned between H2O and ethyl acetate and 3M sodium hydroxide solution added to adjust pH to 10. The mixture was transferred to a separatory funnel and the organic layer collected. The aqueous layer was further extracted with ethyl acetate and the combined organic layers were washed with brine (twice), dried over magnesium sulphate, filtered and concentrated to afford crude product. The reaction was repeated on a 67 mg scale and the combined crudes purified using silica gel dry column chromatography with a solvent system of (2.5% 2M NH3 in methanol/97.5% dichloromethane to 10% 2M NH3 in methanol/90% dichloromethane) then a second silica gel dry column with a solvent system of (10% methanol/90% dichloromethane to 100% methanol) to afford a beige solid 36 N-{2-(4-Ethoxy-benzyl)-1-[2-(1-methyl-pyrrolidin-2-yl)-ethyl]-1H-benzoimidazol-5-yl}-thiophene-2-carboxamidine. Yield: 48 mg (35.9%). 1H NMR (DMSO) δ: 1.29 (t, 3H, J=6.9), 1.35-1.49 (m, 2H), 1.54-1.69 (m, 3H), 1.77-1.90 (m, 1H), 1.95-2.05 (m, 2H), 2.08 (s, 3H), 2.84-2.95 (m, 1H), 3.98 (q, 2H, J=6.9), 4.06 (t, 2H, J=7.7), 4.20 (s, 2H), 6.33 (br s, 2H), 6.73 (dd, 1H, J=8.7, 1.6), 6.87 (d, 2H, J=8.8), 7.00 (d, 1H, J=1.6), 7.09 (dd, 1H, J=5.2, 3.8), 7.19 (d, 2H, J=8.6), 7.33 (d, 1H, J=8.4), 7.59 (d, 1H, J=5.4), 7.73-7.74 (m, 1H); MS (ESI): 488 (MH+, 60%), 244 (100%).