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Int. J. Mol. Sci. 2009, 10(8), 3358-3370; doi:10.3390/ijms10083358
Article

Computational Study on the Conformation and Vibration Frequencies of β-Sheet of ε-Polylysine in Vacuum

1,* , 1, 1, 2
,
1
 and
3,4
1 Key Laboratory of Industrial Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China 2 Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA 3 Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China 4 School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
* Author to whom correspondence should be addressed.
Received: 2 July 2009 / Revised: 21 July 2009 / Accepted: 27 July 2009 / Published: 29 July 2009
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Abstract

Two oligomers, each containing 3 L-lysine residues, were used as model molecules for the simulation of the β-sheet conformation of ε-polylysine (ε-PLL) chains. Their C terminals were capped with ethylamine and N terminals were capped with α-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 α-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°. 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: cyclohepta bifurcated hydrogen bond; ε-polylysine; peptide; ONIOM cyclohepta bifurcated hydrogen bond; ε-polylysine; peptide; ONIOM
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Jia, S.; Mo, Z.; Dai, Y.; Zhang, X.; Yang, H.; Qi, Y. Computational Study on the Conformation and Vibration Frequencies of β-Sheet of ε-Polylysine in Vacuum. Int. J. Mol. Sci. 2009, 10, 3358-3370.

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