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Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation

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Abstract

Molecular dynamic (MD) simulations have been performed to study the behaviors of ten kinds of cyclo-hexa-peptides (CHPs) composed of amino acids with the diverse hydrophilic/hydrophobic side chains at the water/cyclohexane interface. All the CHPs take the “horse-saddle” conformations at the interface and the hydrophilicity/hydrophobicity of the side chains influences the backbones’ structural deformations. The orientations and distributions of the CHPs at the interface and the differences of interaction energies (ΔΔE) between the CHPs and the two liquid phases have been determined. RDF analysis shows that the H-bonds were formed between the OC atoms of the CHPs’ backbones and Hw atoms of water molecules. N atoms of the CHPs’ backbones formed the H-bonds or van der Waals interactions with the water solvent. It was found that there is a parallel relationship between ΔΔE and the lateral diffusion coefficients (D xy ) of the CHPs at the interface. The movements of water molecules close to the interface are confined to some extent, indicating that the dynamics of the CHPs and interfacial water molecules are strongly coupled.

Scheme of the ten kinds of CHPs formed by even alternating D- and L- amino acids with the different hydrophilic/hydrophobic side chains. The letters in the parentheses stand for the abbreviations of the composed amino acids in the CHPs

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Acknowledgments

This work has been supported by the National Natural Science Foundation of China (Grant No. 21173154) and the Priority Academic Program Development of Jiangsu Higher Education Institutions. The authors are grateful to College of Computer Science & Technology in Soochow University for providing amounts of computer facilities assignment on its high-powered computers.

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Authors and Affiliations

  1. College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, People’s Republic of China

    Min Cen, Jian Fen Fan, Dong Yan Liu, Xue Zeng Song & Wei Qun Zhou

  2. Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800–204, Shanghai, 201800, People’s Republic of China

    Jian Liu

  3. College of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, People’s Republic of China

    He Ming Xiao

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  1. Min Cen
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  2. Jian Fen Fan
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  5. Jian Liu
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Correspondence to Jian Fen Fan.

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Cen, M., Fan, J.F., Liu, D.Y. et al. Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation. J Mol Model 19, 601–611 (2013). https://doi.org/10.1007/s00894-012-1588-8

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  • DOI: https://doi.org/10.1007/s00894-012-1588-8

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