The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. Structure and dynamics in octafluoronaphthalene tally essential. The reasons why a process on the timescale of µs, and associated with such a large activation barrier, can be accessed via classical molecular dynamics simulations are also discussed.

Large-scale molecular dynamics simulations have been performed on solid inclusion compounds formed between urea and alkane (dodecane) and alkanoic acid (dodecanoic acid) guest molecules. The incommensurate nature of the guest and host substructures means that simulations of these systems are challenging, and our results call into question some of the simplifying assumptions made in earlier simulations on the urea inclusion compounds. Detailed information is obtained on the structural properties of the carboxylic acid dimers and alkyl chains confined within the nanoscale tunnels of the urea host structure, including the chirality of the guest conformation induced by the chiral nature of the urea tunnels. Diffusion coefficients (at 300 K) of the guest molecules along the tunnel axis were determined to be 0.091 ± 0.031 (dodecane) and 0.0063 ± 0.0013 Å(2) ps(-1) (dodecanoic acid), in good agreement with experimental measurements on alkane/urea systems. Weak ordering is observed between guests in neighboring tunnels, which is compatible with experimental measurements on the alkane/urea systems, although the simulations provide more detailed molecular-level insights into the nature of this supramolecular ordering.

Publisher's copyright statement:This document is the Accepted Manuscript version of a Published Work that appeared in nal form in the Journal of Physical Chemistry, copyright c American Chemical Society after peer review and technical editing by the publisher. To access the nal edited and published work see http://dx.doi.org/10.1021/jp4045995Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. 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 four 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 threedimensional 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.

No abstract