title: Computational study on the conformation and vibration frequencies of β-sheet of ε-polylysine in vacuum.
abstract: 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.
authors.affiliation: Key Laboratory of Industrial Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
authors.forename: Shiru
authors.initials: S
authors.lastname: Jia
authors.affiliation: Key Laboratory of Industrial Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
authors.forename: Zhiwen
authors.initials: Z
authors.lastname: Mo
authors.affiliation: Key Laboratory of Industrial Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
authors.forename: Yujie
authors.initials: Y
authors.lastname: Dai
authors.affiliation: Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.
authors.forename: Xiuli
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Industrial Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
authors.forename: Hongjiang
authors.initials: H
authors.lastname: Yang
authors.affiliation: Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.|School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China.
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Qi
mesh_terms: D006860:Hydrogen Bonding; D008958:Models, Molecular; D011107:Polylysine / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D013055:Spectrophotometry, Infrared; D014618:Vacuum; D014732:Vibration
chemical_list: D011107:Polylysine