The Entry of Ions into a Molecular Synthetic Channel in a Membrane

Abstract:

A molecular dynamics simulation is conducted to describe the behaviour of sodium and chloride ions as they enter a synthetic ion channel (mounted in a bilayer membrane) from aqueous NaCl solutions on either side of the membrane. The channel consists of an α-helical peptide chain scaffold with six aligned crown ether (CE) rings (18-CE-6) as side groups, forming a molecular chamber between each neighbouring pair. Responding to the channel’s axial −2 to −1 V electric potential, the Na⁺ ions, but not Cl⁻, enter the channel spontaneously but they do not proceed beyond the first chamber formed between CE rings 1 and 2. The application of an axial electric field promotes the entry of a Na⁺ ion and its migration over the internal length of the channel. The forces that drive the migration phenomena are predominantly coulombic. Although the same electric field simultaneously allows a Cl⁻ ion initially to access the channel the ion is subsequently expelled from the first chamber into the bilayer. Although a Na⁺ ion may make a facile or even spontaneous entry to the channel it requires an energy estimated from Coulomb forces as ~5 eV to pass subsequent CE rings, and considerably more to exit the channel. An important role is found for the vibrational activity of the ether rings’ C-O-C units in their facilitating contribution to the migration of Na⁺ in the channel.

• Periodical: Diffusion Foundations (Volume 4)
• Pages: 119-135
• DOI: https://doi.org/10.4028/www.scientific.net/DF.4.119
• Online since: July 2015
• Authors: D.A. Morton-Blake
• Keywords: Electric Field, Electrostatic Potential, Ion Migration, Molecular Dynamics, Synthetic Ion Channel, Thermally-Induced Channel Entry

References

[1] G.G. Hammes, Physical chemistry for the biological sciences, Wiley-Interscience, Hoboken, New Jersey 2007, Chapter 3.

[2] J. -C. Olsen, K. E. Griffiths, J. F. Stoddart, A Short History of the Mechanical Bond, in From Non-Covalent Assemblies to Molecular Machines, J. -P. Sauvage, P. Gaspard (Eds. ), Wiley-VCH: Weinheim, Germany (2011), pp.67-139.

DOI: 10.1002/9783527632817.ch8

[3] D.A. Morton-Blake, Molecular dynamics of the transport of ions in a synthetic channel, Diffusion Fundamentals 1 (2014) 77-95.

[4] D.A. Morton-Blake, Conan Kumari-Doyle, The motion of an ion in a synthetic molecular ion channel, Computational and Theoretical Chemistry 1008 (2013).

DOI: 10.1016/j.comptc.2012.12.007

[5] N. Sakai, S. Matile, Synthetic ion channels, Langmuir 29 (2013).

[6] V.E. Carmichel, P. Dutton, T. Fyles, T. James, J. Swan, M. Zojaji, Biomimetic ion transport: A functional model of a unimolecular ion channel, J. Amer. Chem. Soc. 111 (1989) 767-769.

DOI: 10.1021/ja00184a075

[7] N. Voyer, M. Robitaille, A novel functional artificial channel, J. Am. Chem. Soc. 117 (1995) 6599-6600.

DOI: 10.1021/ja00129a027

[8] W. Kabsch, C. Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers. 22 (1983) 2577-2637.

DOI: 10.1002/bip.360221211

[9] W. Smith, T.R. Forester, DL_POLY_2. 0: a general-purpose parallel molecular dynamics simulation package, J. Molec. Graphics 14 (1996) 136.

DOI: 10.1016/s0263-7855(96)00043-4

[10] Gaussian 03, Revision E. 01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., 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, V. Bakken, 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, J. A. Pople, Gaussian, Inc., Wallingford CT, (2004).

[11] J. Åqvist, Ion-water interaction potentials derived from free energy perturbation simulations, J. Phys. Chem. 94 (1990) 8021-8024.

DOI: 10.1021/j100384a009

[12] S.H. Lee, J.C. Rasaiah, Molecular dynamics simulation of ion mobility. 2. Alkali metal halide ions using the SPC/E model for water at 25°C, J. Chem. Phys. 100 (1996) 1420-1425.

DOI: 10.1021/jp953050c

[13] S. L. Mayo, B. D. Olafson, W.A. Goddard III, DREIDING: A generic force field for molecular simulations, J. Phys. Chem. 94 (1990) 8897-8909.

DOI: 10.1021/j100389a010

[14] H. J. C. Berendsen, J. R. Grigera, T. P. Straatsma, The missing term in effective pair potentials, J. Phys. Chem. 91 (1987) 6269-6271.

DOI: 10.1021/j100308a038

[15] W.T. Coffey, Yu.P. Kalmykov, J.T. Waldron, The Langevin Equation: with Applications to Stochastic Problems in Physics, Chemistry and Electrical Engineering, second edition, World Scientific Singapore, 2004, Chapter 1.

DOI: 10.1142/5343

[16] A.R. Tiller, Dielectric relaxation in polymers by molecular dynamics simulation, Macromolecules 25 (1992) 4605-4611.

DOI: 10.1021/ma00044a022

[17] E. Samson, J. Marchand K.A. Snyder, Calculation of ionic diffusion coefficients on the basis of migration test results, Materials and Structures 36 (2003) 156-165.

DOI: 10.1007/bf02479554

[18] P. Atkins, J. de Paula, Physical Chemistry, eighth edition, Oxford University Press, Oxford 2006 , Chapter 21.

[19] A. Faracone, L. Liu, C. -Y. Mou, P.C. Shih, J.R.D. Copley, S.H. Chen, Translational and rotational dynamics of water in mesoporous silica materials, J. Chem. Phys. 119 (2003) 3963-3971.

DOI: 10.1063/1.1584653

[20] R. A. Fouracre, M. J. Given, B. H. Crichton, The effect of alternating fields on ion migration in solid dielectrics, J. Phys. C: Solid State Phys. 19 (1986) 1949-(1958).

DOI: 10.1088/0022-3719/19/12/009

[21] L. Gammaitoni, P. Hänggi, P. Jung, F. Marchesoni, Stochastic resonance, Rev. Mod. Phys. 70 (1998) 224-287.

DOI: 10.1103/revmodphys.70.223