Two oligomers, each containing 3 l-lysine residues, were used as model molecules for the simulation of the beta-sheet conformation of varepsilon-polylysine (varepsilon-PLL) chains. Their C terminals were capped with ethylamine and N terminals were capped with alpha-l-aminobutanoic acid, respectively. The calculations were carried out with the hybrid two-level ONOIM (B3LYP/6-31G:PM3) computational chemistry method. The optimized conformation was obtained and IR frequencies were compared with experimental data. The result indicated that the two chains were winded around each other to form a distinct cyclohepta structure through bifurcated hydrogen bonds. The groups of amide and alpha-amidocyanogen coming from one chain and the carbonyl group from the other chain were involved in the cyclohepta structure. The bond angle of the bifurcated hydrogen bonds was 66.6 degrees . The frequency analysis at ONIOM [B3LYP/6-31G (d):PM3] level showed the IR absorbances of the main groups, such as the amide and amidocyanogen groups, were in accordance with the experimental data.
Keywords: ONIOM; cyclohepta bifurcated hydrogen bond; peptide; ɛ-polylysine.