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

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

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
• Public URL: https://durham-repository.worktribe.com/output/1450336