Transport of molecules through carbon nanotube channels in aqueous environment: A molecular dynamics study


We present molecular dynamics simulation of molecules transporting through carbon nanotubes for applications in engineered flow channels, focusing on the dynamics of molecules spontaneously inserted into the nanotube channel in aqueous environment. The molecules studied include a C60 molecule, a finite segment of carbon nanotube with smaller diameter, and single/double- stranded DNA molecules. We show that in the absence of water solvation, the van der Waals interaction between the molecule and the nanotube wall can induce a rapid spontaneous encapsulation of the molecule inside the nanotube channel. The encapsulation process is strongly impeded for nanotube dissolved in water due to the competition between the van der Waals, hydrophobic and hydrogen bonding interactions in the nanotube/water/molecule complex. Water adsorption inside the nanotube channel plays an important role in determining the dynamics of the spontaneous insertion process.

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  1. 1.

    See, e.g., Issue on Advances in Carbon Nanotubes, MRS Bulletin 29, No. 4, 2004.

  2. 2.

    See, e.g., R.J. Chen et al., Proc. Natl. Acd. Sci. 100, 4984(2003).

    Google Scholar 

  3. 3.

    For a recent review, see E. Katz and I. Willner, ChemPhysChem 5, 1084 (2004).

    CAS  Article  Google Scholar 

  4. 4.

    See, e.g., G. Hummer, J.C. Rasalah, and J.P. Noworyta, Nature 414, 188 (2001); S. Joseph, R.J. Mashl, E. Jakobsson, and N.R. Aluru, Nano Lett. 3, 1399 (2003). I.-C. Yeh and G. Hummer, Proc. Natl. Acad. Sci. 101, 12177 (2004).

    CAS  Article  Google Scholar 

  5. 5.

    J.C.T. Eijkel and A. van den Berg, Microfluid Nanofluid 1, 249(2005).

    CAS  Article  Google Scholar 

  6. 6.

    L.D. Gelb, K.E. Gubbins, R. Radhakrishnan, and M.Sliwinska-Bartkowiak, Rep. Prog. Phys. 62, 1573 (1999).

    CAS  Article  Google Scholar 

  7. 7.

    D.A. Case et al (2004), AMBER 8, University of California, San Francisco.

    Google Scholar 

  8. 8.

    J. Wang, P. Cieplak, and P.A. Kollman, J.comput. Chem. 21, 1049 (2000); W.D. Cornell et al., J. Am. Chem. Soc. 117, 5179 (1995).

    CAS  Article  Google Scholar 

  9. 9.

    W.L. Jorgensen et al., J. Chem. Phys. 79, 926 (1995).

    Article  Google Scholar 

  10. 10.

    T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).

    CAS  Article  Google Scholar 

  11. 11.

    H.J.C. Berendsen et al., J. Chem. Phys. 81, 3684 (1984).

    CAS  Article  Google Scholar 

  12. 12.

    Q. Zhang and Q. Jiang, Phys. Rev. Lett. 88, 45503 (2002); S.B. Legoas et al., ibid. 90, 55504 (2003); Y. Zhao et al., ibid. 91, 175504 (2003); P. Tangnery, S.G. Louie, and M.L. Cohen, ibid. 93, 65503 (2004); P. Liu, Y.W. Zhang, and C. Lu, J. Appl. Phys. 97, 94313 (2005).

    Article  Google Scholar 

  13. 13.

    J.A. McCammon and S.C. Harvey, Dynamics of Proteins and Nucleic Acids (Cambridge University Press, Cambridge, 1987).

    Google Scholar 

  14. 14.

    H. Gao, Y. Kong, D. Cui, and C.S. Ozkan, Nano Lett. 3, 471(2003); H. Gao and Y. Kong, Annu. Rev. Phys. Chem. 34, 123 (2004).

    CAS  Article  Google Scholar 

  15. 15.

    J.H. Walther, R. Jaffe, T. Halicioglu, and P. Koumostsakos, J. Phys. Chem. B 105, 9980 (2001); J. Marti and M.C. Gordillo, Phys. Rev. E 64, 21504 (2001); A. Striolo, A.A. Chialvo, K.E. Gubbins, and P.T. Cummings, J. Chem. Phys. 122, 234712 (2005).

    CAS  Article  Google Scholar 

  16. 16.

    U. Zimmerli, P.G. Gonnet, J.H. Walther, and P. Koumoutsakos, Nano Lett. 5, 1017 (2005).

    CAS  Article  Google Scholar 

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Xue, Y., Chen, M. Transport of molecules through carbon nanotube channels in aqueous environment: A molecular dynamics study. MRS Online Proceedings Library 899, 308 (2005).

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