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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 which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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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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