The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution

David Antony Morton-Blake

doi:doi:10.11648/j.ijctc.20190701.16

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The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution

David Antony Morton-Blake

Received: 18 January 2019 Accepted: 6 March 2019 Published: 1 April 2019

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Abstract

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.

DOI	10.11648/j.ijctc.20190701.16
Published in	International Journal of Computational and Theoretical Chemistry (Volume 7, Issue 1, June 2019)
Page(s)	35-48
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), 2024. Published by Science Publishing Group

Keywords

Molecular Dynamics, Molecular Channels, Helical Polypyrrole, Electrostatic Potentials, Hydrated Ions, Ion Migration, Proton Tunnelling

References

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David Antony Morton-Blake. (2019). The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution. International Journal of Computational and Theoretical Chemistry, 7(1), 35-48. https://doi.org/10.11648/j.ijctc.20190701.16

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David Antony Morton-Blake. The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution. Int. J. Comput. Theor. Chem. 2019, 7(1), 35-48. doi: 10.11648/j.ijctc.20190701.16

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David Antony Morton-Blake. The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution. Int J Comput Theor Chem. 2019;7(1):35-48. doi: 10.11648/j.ijctc.20190701.16

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@article{10.11648/j.ijctc.20190701.16,
  author = {David Antony Morton-Blake},
  title = {The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution},
  journal = {International Journal of Computational and Theoretical Chemistry},
  volume = {7},
  number = {1},
  pages = {35-48},
  doi = {10.11648/j.ijctc.20190701.16},
  url = {https://doi.org/10.11648/j.ijctc.20190701.16},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijctc.20190701.16},
  abstract = {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.},
 year = {2019}
}

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TY  - JOUR
T1  - The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution
AU  - David Antony Morton-Blake
Y1  - 2019/04/01
PY  - 2019
N1  - https://doi.org/10.11648/j.ijctc.20190701.16
DO  - 10.11648/j.ijctc.20190701.16
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  - 35
EP  - 48
PB  - Science Publishing Group
SN  - 2376-7308
UR  - https://doi.org/10.11648/j.ijctc.20190701.16
AB  - 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.
VL  - 7
IS  - 1
ER  -

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David Antony Morton-Blake

School of Chemistry, Trinity College, Dublin, Ireland

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David Antony Morton-Blake. (2019). The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution. International Journal of Computational and Theoretical Chemistry, 7(1), 35-48. https://doi.org/10.11648/j.ijctc.20190701.16

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David Antony Morton-Blake. The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution. Int. J. Comput. Theor. Chem. 2019, 7(1), 35-48. doi: 10.11648/j.ijctc.20190701.16

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David Antony Morton-Blake. The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution. Int J Comput Theor Chem. 2019;7(1):35-48. doi: 10.11648/j.ijctc.20190701.16

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@article{10.11648/j.ijctc.20190701.16,
  author = {David Antony Morton-Blake},
  title = {The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution},
  journal = {International Journal of Computational and Theoretical Chemistry},
  volume = {7},
  number = {1},
  pages = {35-48},
  doi = {10.11648/j.ijctc.20190701.16},
  url = {https://doi.org/10.11648/j.ijctc.20190701.16},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijctc.20190701.16},
  abstract = {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.},
 year = {2019}
}

Copy | Download

TY  - JOUR
T1  - The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution
AU  - David Antony Morton-Blake
Y1  - 2019/04/01
PY  - 2019
N1  - https://doi.org/10.11648/j.ijctc.20190701.16
DO  - 10.11648/j.ijctc.20190701.16
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  - 35
EP  - 48
PB  - Science Publishing Group
SN  - 2376-7308
UR  - https://doi.org/10.11648/j.ijctc.20190701.16
AB  - 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.
VL  - 7
IS  - 1
ER  -

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