| Peer-Reviewed

The Motion of Ions Confined in a Molecular Channel

Received: 10 December 2020     Accepted: 18 December 2020     Published: 14 May 2021
Views:       Downloads:
Abstract

In order to understand the features governing the motion of ions in a molecular environment the migrational features of Na+ and Cl ions in a molecular channel composed of stacked crown ether 6-CE-18 rings is followed using molecular dynamics, which shows that Na+ is subject to a much greater dynamic hindrance than the Cl ion. The effects of the fluctuating electric fields of the atomic constituents in the channel on the motion of the migrants are investigated by clamping them so as to remove the fluctuations. The dynamic system is simulated both in vacuo and in water. For both it is found that the fluctuating electric fields of the channel and water atoms play a significantly greater role in the ion motions than do fluctuations in the ‘non-bonded’ interactions. The effect of temperature on the dynamics is investigated. Oscillatory trajectories are followed via the force and the potential energy profiles of the system over the timestep range of the molecular dynamics.

Published in International Journal of Computational and Theoretical Chemistry (Volume 9, Issue 1)
DOI 10.11648/j.ijctc.20210901.12
Page(s) 7-18
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2021. Published by Science Publishing Group

Keywords

Ion Migration, Molecular Channel, Molecular Dynamics, Fluctuating Charges, Electric Fields, Migration Direction

References
[1] D. J. Aidley, P. R. Stanfield, Ion Channels, Cambridge University Press, Cambridge, 1996. C. H. Peters, M. R. Ghovanloo, C. G. Gershome, P. C. Ruben, pH modulation of voltage-gated sodium channels, Handbook of Experimental Pharmacology 246 147-160 (2018); B. M. Brown, H. M. Ngyen, H. Wulf, Recent advances in our understanding of the structure and function of more unusual ion channels, F1000 Research (2019) 8, (F1000 Faculty Rev) 123 https//doi.org//10.12688/f1000 research 17163.1); D. L. Bennett, A. J. Clark, S. G. Waxman, S. D. Dib-Hajj, The role of voltage-gated sodium channels in pain signalling, Physiological Reviews 99 (2) 1079-1151 (2019).
[2] J.-C. Olsen, K. E. Griffiths, J. F. Stoddart, A Short History of the Mechanical Bond, in: J.-P. Sauvage, P. Gaspard (Eds.), From Non-Covalent Assemblies to Molecular Machines, Wiley-VCH: Weinheim, Germany, 2011, pp 67-139.
[3] D. A. Morton-Blake, Björn Jenkins and Iwan Blake, The passage on an ion through a synthetic channel, Molecular Simulation, 37, (13), 2011, p 1077 – 1084; D. A. Morton-Blake and C. Kumari-Doyle, The motion of an ion in a synthetic molecular channel, Computational and Theoretical Chemistry 74-82 1008 (2013);; D. A. Morton-Blake, Molecular dynamics of the transport of ions in a synthetic channel, Diffusion foundations 1 (2014) 77-95.
[4] A Einstein, Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen, Annalen der Phys. 17, p. 549, 1905; D. Chowdhuru, 100 years of Einstein’s Theory of Brownian Motion: from Pollen Grains to Protein Trains, Resonance 10 September 2005.
[5] A. K. Rappé, C. J. Casewit, K. S. Colwell, W. A. Goddard III, W. M. Skiff, UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations, J. Amer. Chem. Soc. 114 (1972) 10024-10035.
[6] H. J. C. Berendsen, J. R. Grigera, T. P. Straatsma, The missing term in effective pair potentials, J. Phys. Chem. 91 (1987) 6269-6271.
[7] J. Åquist, Ion-water interaction potentials derived from free energy perturnation simulations, J. Phys. Chem. 94 (1990) 8021-8024.
[8] S. I. Lee, J. C. Rasaiah, Molecular dynamics simulations of ion mobility. 2. Alkali metal and halide ions using the SPC/E model for water at 25°C, J. Phys. Chem. 100 (1996) 1420-5.
[9] M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian 03, Revision B.05, Gaussian, Inc., Pittsburgh PA, 2003.
[10] A. Y. Toukmaji, J. A. Board Jr., Ewald summation techniques in perspective: a survey, Computer Physics Communications 95 (1996) 73–92.
[11] W. Smith, T. R. Forester, DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package, J. Molec. Graphics, 14 (1996) 136-141.
[12] K. C. Gross, P. G. Seybold, C. M. Hadad, ‘Comparison of different atomic charge schemes for predicting pKa variations in substituted anilines and phenols, Internat. J. Quantum Chem. 90 (2002) 445-458.
[13] W. T. Coffey, Yu. P. Kalmykov and J. T. Waldron, The Langevin Equation (Ed. 2), World Scientific (2004).
Cite This Article
  • APA Style

    David Antony Morton-Blake. (2021). The Motion of Ions Confined in a Molecular Channel. International Journal of Computational and Theoretical Chemistry, 9(1), 7-18. https://doi.org/10.11648/j.ijctc.20210901.12

    Copy | Download

    ACS Style

    David Antony Morton-Blake. The Motion of Ions Confined in a Molecular Channel. Int. J. Comput. Theor. Chem. 2021, 9(1), 7-18. doi: 10.11648/j.ijctc.20210901.12

    Copy | Download

    AMA Style

    David Antony Morton-Blake. The Motion of Ions Confined in a Molecular Channel. Int J Comput Theor Chem. 2021;9(1):7-18. doi: 10.11648/j.ijctc.20210901.12

    Copy | Download

  • @article{10.11648/j.ijctc.20210901.12,
      author = {David Antony Morton-Blake},
      title = {The Motion of Ions Confined in a Molecular Channel},
      journal = {International Journal of Computational and Theoretical Chemistry},
      volume = {9},
      number = {1},
      pages = {7-18},
      doi = {10.11648/j.ijctc.20210901.12},
      url = {https://doi.org/10.11648/j.ijctc.20210901.12},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijctc.20210901.12},
      abstract = {In order to understand the features governing the motion of ions in a molecular environment the migrational features of Na+ and Cl− ions in a molecular channel composed of stacked crown ether 6-CE-18 rings is followed using molecular dynamics, which shows that Na+ is subject to a much greater dynamic hindrance than the Cl− ion. The effects of the fluctuating electric fields of the atomic constituents in the channel on the motion of the migrants are investigated by clamping them so as to remove the fluctuations. The dynamic system is simulated both in vacuo and in water. For both it is found that the fluctuating electric fields of the channel and water atoms play a significantly greater role in the ion motions than do fluctuations in the ‘non-bonded’ interactions. The effect of temperature on the dynamics is investigated. Oscillatory trajectories are followed via the force and the potential energy profiles of the system over the timestep range of the molecular dynamics.},
     year = {2021}
    }
    

    Copy | Download

  • TY  - JOUR
    T1  - The Motion of Ions Confined in a Molecular Channel
    AU  - David Antony Morton-Blake
    Y1  - 2021/05/14
    PY  - 2021
    N1  - https://doi.org/10.11648/j.ijctc.20210901.12
    DO  - 10.11648/j.ijctc.20210901.12
    T2  - International Journal of Computational and Theoretical Chemistry
    JF  - International Journal of Computational and Theoretical Chemistry
    JO  - International Journal of Computational and Theoretical Chemistry
    SP  - 7
    EP  - 18
    PB  - Science Publishing Group
    SN  - 2376-7308
    UR  - https://doi.org/10.11648/j.ijctc.20210901.12
    AB  - In order to understand the features governing the motion of ions in a molecular environment the migrational features of Na+ and Cl− ions in a molecular channel composed of stacked crown ether 6-CE-18 rings is followed using molecular dynamics, which shows that Na+ is subject to a much greater dynamic hindrance than the Cl− ion. The effects of the fluctuating electric fields of the atomic constituents in the channel on the motion of the migrants are investigated by clamping them so as to remove the fluctuations. The dynamic system is simulated both in vacuo and in water. For both it is found that the fluctuating electric fields of the channel and water atoms play a significantly greater role in the ion motions than do fluctuations in the ‘non-bonded’ interactions. The effect of temperature on the dynamics is investigated. Oscillatory trajectories are followed via the force and the potential energy profiles of the system over the timestep range of the molecular dynamics.
    VL  - 9
    IS  - 1
    ER  - 

    Copy | Download

Author Information
  • School of Chemistry, Trinity College, Dublin, Ireland

  • Sections