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Molecular dynamics studies on the influences of a gradient electric field on the water chain in a peptide nanotube

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Abstract

The structure and transportation characteristics of the water chain inside a 8 × cyclo-(WL)4 peptide nanotube (PNT) were simulated under a gradient electric (GE) field. The gradient was defined by the ratio of a constant (E a) and the z-directional length (L z) of the simulation box. E a varies from 0.0 to 0.9 V nm−1. As the gradient increases, the probabilities of finding two water molecules in an α-plane zone and three in a midplane region increase. To accommodate more water molecules, the axial array of channel water molecules becomes more compact. Meanwhile, the H-bonded network between the channel water is greatly intensified when E a increases from 0.3 to 0.9 V nm−1. Nevertheless, the proportion of strong H-bonds does not increase significantly following the formation of a more compact axial array of water molecules. When E a reaches 0.9 V nm−1, the water molecule in an α-plane zone may be dragged by its neighboring water molecules into the midplane region, resulting in a significant deviation from the channel axis. With the augment of the gradient, the dipoles of channel water are gradually oriented along the tube axis in the sequence from gap 1 to 7, namely along the direction of the electric field. Nevertheless, even when E a reaches 0.9 V nm−1, the dipole orientation of the channel water is not complete, and dipole flips still occur in gap 7. Under a GE field, the rightward and leftward hopping rates of channel water are no longer equal to each other, i.e., channel water performs an asymmetric transportation.

MD studies on the influences of a gradient electric field on water chain in a peptide nanotube

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Acknowledgments

This work was supported by the National Natural Science Foundation of China under Grant No. 21173154; and the Priority Academic Program Development of Jiangsu Higher Education Institutions. The authors are grateful to Mr. Jan Liu, Xuezeng Song for their insightful suggestions, and indebted to School of Computer Science & Technology in Soochow University for providing us with generous amounts of computer facilities assigned to high-powered computers.

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  1. College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, China

    Hui Li, Jianfen F. Fan, Rui Li, Yi Yu & Xiliang L. Yan

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  1. Hui Li
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Correspondence to Jianfen F. Fan.

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Li, H., Fan, J.F., Li, R. et al. Molecular dynamics studies on the influences of a gradient electric field on the water chain in a peptide nanotube. J Mol Model 20, 2370 (2014). https://doi.org/10.1007/s00894-014-2370-x

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