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Molecular Dynamic Simulations of Cyclo-hexa-peptides (CHPs) at the Water/cyclohexane Interface

Author: ZuoMin
Tutor: FanJianFen
School: Suzhou University
Course: Physical and chemical
Keywords: Cyclo-Hexa-Peptides (CHPs) Molecular dynamics Water/cyclohexane interface
CLC: O643.1
Type: Master's thesis
Year: 2012
Downloads: 25
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Abstract


Molecular dynamic simulations have been performed to study the behaviors of tenkinds of cyclo-hexa-peptides (CHPs), composed of amino acids with the diversehydrophilic/hydrophobic side chains at the water/cyclohexane interface. The researchwas focused on the CHPs’ structures, orientations, distributions, dynamic characteristicsand interactions with the two solvents.It was found that the CHPs adopt the "horse-saddle" conformations at thewater/cyclohexane interface. Cyclo-(PP)3and cyclo-(HH)3peptides with the rigid sidechains and cyclo-(GG)3peptide without side chain almost lay flat at the interface.Among all the CHPs, cyclo-(GG)3peptide exhibits the biggest deformation. Thehydrophilicity/hydrophobicity of the side chains influences the CHPs’ orientations anddistributions at the interface. The CHPs with the hydrophilic side chains tend to pluginto the water phase and their backbones tilt to the water phase.RDF analysis shows that the strong H-bonds were formed between the Oc atoms ofthe CHPs’ backbones and Hw atoms of water molecules. N atoms of the CHPs’backbones formed the weak H-bonds or van der Waals interactions with the watersolvent.The translational diffusions of CHPs at the water/cyclohexane interface showanisotropic features. The hydrophilicity/hydrophobicity of the side chains influences theCHPs’ translational diffusions and reorientational dynamics. Cyclo-(EE)3peptide withthe strong hydrophilic side chain shows the slowest lateral translational diffusion andrelaxational motion, while cyclo-(FF)3peptide with the strong hydrophobic side chaindiffuses and relaxes fastest. There is a parallel relationship between the lateral diffusioncoefficients (Dxy) of the CHPs at the interface and the differences (ΔΔE) of theinteraction energies of CHPs with the two solvents.The simulations present direct information of the structural and dynamiccharacteristics of CHPs at the water/cyclohexane interface, and the results will be helpful for better understanding of the interfacial behaviors andhydrophilic/hydrophobic properties of CHPs at the micro atomic level.

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CLC: > Mathematical sciences and chemical > Chemistry > Physical Chemistry ( theoretical chemistry ),chemical physics > Chemical kinetics,catalysis > Chemical kinetics
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