Well-Tempered Metadynamics as a Tool for Characterizing Multi-Component, Crystalline Molecular Machines

Ilott, Andrew J.; Palucha, Sebastian; Hodgkinson, Paul; Wilson, Mark R.

doi:10.1021/jp4045995

Well-Tempered Metadynamics as a Tool for Characterizing Multi-Component, Crystalline Molecular Machines

Ilott, Andrew J.; Palucha, Sebastian; Hodgkinson, Paul; Wilson, Mark R.

Authors

Andrew J. Ilott

Sebastian Palucha

Professor Paul Hodgkinson paul.hodgkinson@durham.ac.uk
Professor

Professor Mark Wilson mark.wilson@durham.ac.uk
Professor

Abstract

The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster than unbiased molecular dynamics runs. The metadynamics collective variables used have also been expanded to include the simultaneous orientations of three neighboring octafluoronaphthalene molecules. Analysis of the resultant three-dimensional free energy surface, which is sampled to a very high degree despite its significant complexity, demonstrates that there are strong correlations between the molecular orientations. Although this correlated motion is of limited applicability in terms of exploiting dynamical motion in octafluoronaphthalene, the approach used is extremely well suited to the investigation of the function of crystalline molecular machines.

Citation

Ilott, A. J., Palucha, S., Hodgkinson, P., & Wilson, M. R. (2013). Well-Tempered Metadynamics as a Tool for Characterizing Multi-Component, Crystalline Molecular Machines. Journal of Physical Chemistry B (Soft Condensed Matter and Biophysical Chemistry), 117(40), 12286-12295. https://doi.org/10.1021/jp4045995

Journal Article Type	Article
Publication Date	Oct 10, 2013
Deposit Date	Jun 10, 2014
Publicly Available Date	Jul 18, 2014
Journal	Journal of Physical Chemistry B (Soft Condensed Matter and Biophysical Chemistry)
Print ISSN	1520-6106
Electronic ISSN	1520-5207
Publisher	American Chemical Society
Peer Reviewed	Peer Reviewed
Volume	117
Issue	40
Pages	12286-12295
DOI	https://doi.org/10.1021/jp4045995

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Copyright Statement
This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of Physical Chemistry, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp4045995