The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution
International Journal of Computational and Theoretical Chemistry
Volume 7, Issue 1, June 2019, Pages: 35-48
Received: Jan. 18, 2019; Accepted: Mar. 6, 2019; Published: Apr. 1, 2019
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David Antony Morton-Blake, School of Chemistry, Trinity College, Dublin, Ireland
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In order to investigate the passage of ions through a confined space, two substituted derivatives of a polypyrrole chain are considered in a helical conformation which forms a linear channel. The two species of sidechain on the 3 position of the pyrrole rings differ in their electron-withdrawing power. The system’s response to a pH change by deprotonation of pyrrole rings is discussed in terms of a quantum tunnelling of a proton between two sites at the pyrrole’s N atom. A characteristic ‘inversion time’ is calculated for the mechanism and compared for the two derivatives. In an investigation of the possibility that ions generated by the pH changes may enter the channel, molecular dynamics (MD) calculations are performed to calculate the fluctuating electrostatic potential at points along the axis for the polypyrrole chains in aqueous solution. It is found that although the atoms of the bare two polypyrrole channels derivatives generate very different time-averaged potential profiles along the axis, their polarising effect on the water molecules reorients the dipoles so as to oppose the charges from the polymer chain. It is shown that the charges on the polypyrrole helix imposes a ‘solvent structure’ on the water dipoles in the channel. The MD shows that when an electric field is applied along the channel axis the hydrated H+ is accelerated to a point half way along the channel, where further progress is inhibited; however the passage of the OH− is unimpeded. These results are discussed in relation to the molecular confinement of the migrants through the axial electrostatic potentials and the migrant charges and structure.
Molecular Dynamics, Molecular Channels, Helical Polypyrrole, Electrostatic Potentials, Hydrated Ions, Ion Migration, Proton Tunnelling
To cite this article
David Antony Morton-Blake, The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution, International Journal of Computational and Theoretical Chemistry. Vol. 7, No. 1, 2019, pp. 35-48. doi: 10.11648/j.ijctc.20190701.16
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S_H Chung, O. S. Anderson and V. V. Krishnamurthy (Eds.), Biological Membrane Ion Channels: Dynamics, Structure, and Applications (2007) Springer (2007); R. Pethig and D. B. Kell, ‘The passive electrical properties of biological systems: their significance in physiology, biophysics and biotechnology’, Phys. Med. Biol., 1987, 32 (8) 933-970 (1987).
R. Ballardini, V. Balzani, A. Credi, M. T. Gandolfi, M. Venturi, ‘Artificial molecular-level machines: which energy to make them work?’ Acc. Chem. Res. 34 445–455 (2001).
X. Lin, J. Li, E. Smela and S. Yip ‘Polaron-induced conformation change in single polypyrrole chain: An intrinsic actuation mechanism’ Int. J. of Quantum Chemistry 102 980 (2005).
A. Xie, F. Wu, W. Jiang, K. Zhang, M. San and M. Wang ‘Helical conducting polymers have good optical and electrical activities. Helical polypyrrole is synthesized by a chiral inducing method’ J. Mater. Chem. C 5 2175 (2017).
F. Garnier, G. Tourillon, J. Y. Barraud, H. Dexpert, ‘First evidence of crystalline structure in conducting polythiophene’ J. Mat. Sci. 20 2687 (1985); G. Tourillon and Y. Jugnet, ‘Electronic and structural characteristics of five poly membered heterocycles (polythiophene, polypyrrole): An ultraviolet and x‐ray photoelectron spectroscopy study’, Journal of Chemical Physics 89, 1905 (1988).
Y. Tadesse, R. W Grange and S. Priya, ‘Synthesis and cyclic force characterization of helical polypyrrole actuators for artificial facial muscles’, Smart Mater. Struct. 18 085008 (2009).
M. Chayer, K. Faἲd, M. Leclerc, ‘Highly Conducting Water-Soluble Polythiophene Derivatives’, Chem. Mater. 9 2902-2905 (1997); É. J. Lemieux, M. Leclerc, ‘Sensing via conformational changes of conjugated polythiophenes’ (Chapter 7 pp 231–261) of Conjugated Polyelectrolytes: Fundamentals and Applications, Bin Liu, G. C. Bazan (Eds.) Wiley-VCH Verlag GmbH & Co. (2013).
D. A. Morton-Blake, ‘Ion Selection by Redox Changes in a Soluble Helical Polythiophene Channel’, Diffusion Foundations Vol. 9 pp 1-15 (Zurich 2016).
(See for example discussions in) C. W. Bunn, E. R. Howell, ’Structures of molecules and crystals of fluorocarbons’, Nature 174 549-551 (1954); A. Azri, P. Giamarchi, Y. Grohens, R. Olier, M. J. Privat, Polyethylene glycol aggregates in water formed through hydrophobic helical structures’, Colloid interface Sci. 329 14-19 (2012).
G. Tourillon, F. Garnier, ‘Morphology and crystallographic structure of polythiophene and its derivatives’ Mol. Cryst. Liq. Cryst. 118 (1985) 221; R. Yang, D. F. Evans, L. Christensen and W. A. Hendrickson, ‘Scanning tunnelling microscopy evidence of semicrystalline and helical conducting polymer structures’ J. Phys. Chem. 94 6117 (1990); G. Caple, B. L. Wheeler, R. Swift, T. L. Porter, S. Jeffers, Scanning tunnelling microscopy of polythiophene, poly(3-methylthiophene) and poly(3-bromolthiophene), ibid 5639-5641; F. Garnier, G. Tourillon, J. Y. Barroud, H. Dexpert, ‘First evidence of crystalline structure in conducting polythiophene’ J. Mat. Sci. 20 (1985) 2687; R. D. McCullough, P. C. Ewbank, Regioregular head to tail coupled poly(3-alkylthiophene) and its derivatives, in T. A. Skotheim, R. L. Elsenbaumer J. R. Reynolds (Eds.), Handbook of Conducting Polymers, Dekker, New York (1998).
O. Bernard and J.-P. Simonin, ‘Association of counterions in polyelectrolytes: Thermodynamic properties in the binding mean sphere approximation’ J. Mol. Liquids 970 14-24 (2018).
E. B. Fleischer, ‘The structure of porphyrins and metalloporphyrins’, EB Fleischer - Accounts of Chemical Research, 3 105-112 (1970).
D. K. Maity, R. L. Bell and T. N. Truong, ‘Mechanism and Quantum Mechanical Tunnelling Effects on Inner Hydrogen Atom transfer in Free Base Porphyrin’, J. Am. Chem. Soc. 122 897-906 (2000).
E. A. Ermilov, B. Büge, S. Jasinski, N. Jux and B. Röder ‘Spectroscopic study of NH-tautomerism in novel cycloketo-tetraphenylporphyrins’, J. Chem. Phys. 130 134509 2018.
U. Langer, C. Hoelger, B. Wehrle, L. Latanowicz, E. Vogel and H.-H. Limbach, ‘15N NMR Study of Proton Localization and Proton Transfer Thermodynamics and Kinetics in Polycrystalline Porphycene’ Journal of Physical Organic Chemistry 13 23-34 (2000).
Q. Pei and R. Qian, ‘Protonation and deprotonation of polypyrrole chain in aqueous solution’ Synthetic Metals 45 35-48 (1991); J. Stejskal, M. Trchová, P. Bober, Z. Morávková, D. Kopecký, M. Vrńata, J. Prokeš, M. Varga and E. Watzlová ‘Polypyrrole salts and bases: superior conductivity of nanotubes and their stability towards the loss of conductivity by deprotonation’ RSC Advances 6 88382 (2006).
P. D. Mitchell, ‘The protonmotive Q cycle: A general formulation’. FEBS Letters. 59 (2): 137–139 (1975); Peter Mitchel’s 1978 Nobel speech. The Nobel Prizes 1978, Editor Wilhelm Odelberg, [Nobel Foundation], Stockholm, 1979; N. Lane, Life: Inevitable or fluke? New Scientist 21 June 2012
See for example ref [16] and) J.-L. Brédas, J. C. Scott, K. Yakushi and G. B. Street ‘Polarons and bipolarons in polypyrrole. Evolution of band structure and optical spectrum upon doping’ Phys. Rev. B 30 1023-5 (1984); P. Pfluger, G. Weiser, J. C. Scott and G. B. Street ‘Electronic structure and transportin the organic “Amorphous semiconductor” polypyrrole’ in ‘Handbook of Conducting polymers’ Vol. 2 (Ed. T. A. Skotheim) Dekker 1986; M. J. L. Santos, A. G. Brolo and E. M. Girotto ‘Study of polaron and bipolaron states in polypyrrole by in situ Raman spectroelectrochemistry’ Electrochim Acta 52 6141-5 (2007) and references theein.
Eds. G. Alefeld and J. Völkl ‘Hydrogen in Metals’, Springer 1978.
L. Evangelisti, P. Écija, E. J. Cocinero, F. Castaño, A. Lesarri, W. Caminati and R. Meyer, ‘Proton tunneling in heterodimers of carboxylic acids: A rotational study of the benzoic acid -formic acid bimolecule’, J. Phys. Chem. Lett. 3 3770-5 (2012).
P.-O. Löwdin, ‘Quantum genetics and the aperiodic solid. Some aspects of the biological problems of heredity, aging and tumours in view of the quantum theory of the DNA molecule’. Advances in Quantum Chemistry 2 Pp 213. Academic Press 1965.
See for example A. D. Godbeer, J. S. Al-Khalili and P. D. Stevenson, proton tunnelling in the adenine-thymine base pair’. Phys. Chem. Chem. Phys. 17 13034-44 (2015).
D. F. Brougham, R. Caciuffo and A. J. Horsewill, ‘Coordinated proton tunnelling in a cyclic network network of four hydrogen bonds in the solid state’ Nature 397 241-43 (1999).8.
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.
V. Jelić and F. Marsiglio, ‘The double-well potential in quantum mechanics: a simple, numerically exact formulation’ Europ. J. Phys. 33 1651-66 (2012).
L. Veguilla-Berdecía, ‘Tunnelling in a quartic, symmetric, double-well potential’, J. Chem. Ed. 70 (1993).
W. Smith, T. R. Forester, DL_POLY_2. 0: A general-purpose parallel molecular dynamics simulation package J. Molec. Graphics, 14 136 (1996).
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.
M. W. Mahoney and W. L. Jorgensen, ‘A five-star model for liquid water and the reproduction of the density anomaly by rigid, non-polarizable potential functions, Journal of Chemical Physics, 112 8910-22 (2000)
D. Lankhorst, J. Schriever and J. C. Leyte, ‘Determination of the rotational correlation time of water by proton NMR relaxation in H217O and some related results’ Berichte der Bunsengesellschaft für physikalische Chemie 83 215-21 (1982).
Lorentz, H. A. ‘Über die Anwendung des Satzes vom Virial in der kinetischen Theorie der Gase’. Annalen der Physik. 248 (1): 127–136 (1881).
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 Chemistry 90 445 (2002).
J. Åquist, ‘Ion-water interaction potentials derived from free energy perturnation simulations’, J. Phys. Chem. 94 8021-8024 (1990).
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 1420-5 (1996).
D. A. Morton-Blake, ‘The entry of ions into a molecular synthetic channel in a membrane’, Diffusion Fundamentals 4 195-135 (2015).
G. Zundel and H. Metzger, ‘Energiebänder der tunnelnden Überschuß-Protonen in flüssigen Säuren. Eine IR-spektroskopische Untersuchung der Natur der Gruppierungen H5O2+’, Zeitschrift für Physikalische Chemie. 58 (5_6) 225–245 (1968).
E. Wicke, M. Eigen and Th. Ackermann, ‘Über den Zustand des Protons (Hydroniumions) in wäßriger Lösung’, Zeitschrift für Physikalische Chemie. 1 (5_6): 340–364 (1954).
E. S. Stoyanov, I. Stoyanova, F. S. Tham and C. A. Reed, ‘The nature of the hydrated proton in organic solvents’, J. Amer. Chem. Soc. 130 (36) 12128-38 (2008).
J. S. Hub, M. G. Wolf, C. Caleman, P. J. van Maaren, G. Groenhof and D. van der Spoel, ‘The thermodynamics of hydronium and hydroxide surface solvation’, Chem. Sci. 5 1745-58 (2016).
See for example, Zh. Chen and S. Ghosal, ‘The nonlinear electromigration of analytes into confined spaces’, Proc. R. Soc. A 468, 3139–3152 (2012); Y. Jiang‡, Y. Li‡, W. Sun, W. Huang, J. Liu, B. Xu, C. Jin a, T. Ma, C. Wu and M. Yan, ‘Spatially-confined lithiation–delithiation in highly dense nanocomposite anodes towards advanced lithium-ion batteries‘, Energy Environ. Sci., 2015, 8, 1471-1479; Y. He, ‘Nano-Confined Room-Temperature Ionic Liquids for Electrochemical Applications’ Virginia Polytechnic Institute and State University (2018).
D. A. Morton-Blake and K. Korpela, ‘The trans-membrane mobilities of ions in a synthetic molecular channel under the influence of applied electric fields’, Soft Matter 6 558-67 (2010).
D. A. Morton-Blake, ‘The simulation of the capturing of sodium ions in a monolayer consisting of polythiophene functionalised with crown ether died chains’, J. Mol. Liquids 263 316-23 (2018).
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