Predicting polymorphism in molecular crystals using orientational entropy
arXiv:1806.06006 · doi:10.1073/pnas.1811056115
Abstract
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant polymorphs. This idea, however, conflicts with the fact that crystallization has a time scale much longer than that of molecular simulations. In order to bring the process within affordable simulation time, we enhance the fluctuations of a collective variable by constructing a bias potential with well tempered metadynamics. We use as collective variable an entropy surrogate based on an extended pair correlation function that includes the correlation between the orientation of pairs of molecules. We also propose a similarity metric between configurations based on the extended pair correlation function and a generalized Kullback-Leibler divergence. In this way, we automatically classify the configurations as belonging to a given polymorph using our metric and a hierarchical clustering algorithm. We find all relevant polymorphs for both substances and we predict new polymorphs. One of them is stabilized at finite temperature by entropic effects.
arXiv comment7 pages, 4 figures
References in corpus (7)
- Canonical sampling through velocity-rescaling
- PLUMED 2: New feathers for an old bird
- Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
- Ab initio Random Structure Searching
- Comparing molecules and solids across structural and alchemical space
- Enhancing entropy and enthalpy fluctuations to drive crystallization in atomistic simulations
- The entropy multiparticle-correlation expansion for a mixture of spherical and elongated particles
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