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

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

Feature Ranking Methods Based on Information Entropy with Parzen Windows

A comparison between several feature ranking methods used on artificial and real dataset is presented. Six ranking methods based on entropy and statistical indices are considered. The Parzen window method for estimation of mutual information and other indices gives similar results as discretization based on the separability index, but results strongly dependent on the # smoothing parameter. The quality of the feature subsets with highest ranks is evaluated by using decision tree, Naive Bayes and the nearest neighbour classifiers. Significant differences are found in some cases, but there is no single best index that works best for all data and all classifiers. To be sure that a subset of features giving the highest accuracy has been selected the use of many different indices is recommended

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

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

Structural properties of carboxylic acid dimers confined within the urea tunnel structure: an MD simulation study

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 Å2 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