Computational Procedure for Analysis of Crystallites in Polycrystalline Solids of Quasilinear Molecules

Abstract

In the current work, a comprehensive procedure for structural analysis of quasilinear organic molecules arranged in a polycrystalline sample generated by molecular dynamics is developed. A linear alkane, hexadecane, is used as a test case because of its interesting behavior upon cooling. Instead of a direct transition from isotropic liquid to the solid crystalline phase, this compound forms first a short-lived intermediate state known as a “rotator phase”. The rotator phase and the crystalline one are distinguished by a set of structural parameters. We propose a robust methodology to evaluate the type of ordered phase obtained after a liquid-to-solid phase transition in a polycrystalline assembly. The analysis starts with the identification and separation of the individual crystallites. Then, the eigenplane of each of them is fit and the tilt angle of the molecules relative to it is computed. The average area per molecule and the distance to the nearest neighbors are estimated by a 2D Voronoi tessellation. The orientation of the molecules with respect to each other is quantified by visualization of the second molecular principal axis. The suggested procedure may be applied to different quasilinear organic compounds in the solid state and to various data compiled in a trajectory.