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Computational study on the conformation and vibration frequencies of β-sheet of ε-polylysine in vacuum.

Jia S, Mo Z, Dai Y, Zhang X, Yang H, Qi Y - Int J Mol Sci (2009)

Bottom Line: The optimized conformation was obtained and IR frequencies were compared with experimental data.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.

View Article: PubMed Central - PubMed

Affiliation: Tianjin University of Science and Technology, China. jiashiru@tust.edu.cn <jiashiru@tust.edu.cn>

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.

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Related in: MedlinePlus

Parallel β-sheet form of ɛ-PLL double chains.(a). Proton donors and acceptors are arranged in the chains alternately.(b). Proton donors and acceptors are arranged in the separate chains.
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f2-ijms-10-03358: Parallel β-sheet form of ɛ-PLL double chains.(a). Proton donors and acceptors are arranged in the chains alternately.(b). Proton donors and acceptors are arranged in the separate chains.

Mentions: Parallel β-sheet form - the two molecular chains are arranged in parallel. The C terminals of the double chains are at one end, while the N terminals are at the opposite [Figures 2 (a) and (b)].


Computational study on the conformation and vibration frequencies of β-sheet of ε-polylysine in vacuum.

Jia S, Mo Z, Dai Y, Zhang X, Yang H, Qi Y - Int J Mol Sci (2009)

Parallel β-sheet form of ɛ-PLL double chains.(a). Proton donors and acceptors are arranged in the chains alternately.(b). Proton donors and acceptors are arranged in the separate chains.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2812828&req=5

f2-ijms-10-03358: Parallel β-sheet form of ɛ-PLL double chains.(a). Proton donors and acceptors are arranged in the chains alternately.(b). Proton donors and acceptors are arranged in the separate chains.
Mentions: Parallel β-sheet form - the two molecular chains are arranged in parallel. The C terminals of the double chains are at one end, while the N terminals are at the opposite [Figures 2 (a) and (b)].

Bottom Line: The optimized conformation was obtained and IR frequencies were compared with experimental data.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.

View Article: PubMed Central - PubMed

Affiliation: Tianjin University of Science and Technology, China. jiashiru@tust.edu.cn <jiashiru@tust.edu.cn>

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.

Show MeSH
Related in: MedlinePlus