Enhanced Computational Sampling of Perylene and Perylothiophene Packing with Rigid-Body Models
posted on 31.01.2017, 19:18 by Evan D. Miller, Matthew L. Jones, Eric Jankowski
Molecular simulations have the potential to advance the understanding of how the structure of organic materials can be engineered through the choice of chemical components but are limited by computational costs. The computational costs can be significantly lowered through the use of modeling approximations that capture the relevant features of a system, while lowering algorithmic complexity or by decreasing the degrees of freedom that must be integrated. Such methods include coarse-graining techniques, approximating long-range electrostatics with short-range potentials, and the use of rigid bodies to replace flexible bonded constraints between atoms. To understand whether and to what degree these techniques can be leveraged to enhance the understanding of planar organic molecules, we investigate the morphologies predicted by molecular dynamic simulations using simplified molecular models of perylene and perylothiophene. Approximately, 10 000 wall-clock hours of graphics processing unit-accelerated simulations are performed using both rigid and flexible models to test their efficiency and predictive capability with the two chemistries. We characterize the 1191 resulting morphologies using simulated X-ray diffraction and cluster analysis to distinguish structural transitions, summarized by four phase diagrams. We find that the morphologies generated by the rigid model of perylene and perylothiophene match with those generated by the flexible model. We find that ordered, hexagonally packed columnar phases are thermodynamically favored over a wide range of densities and temperatures for both molecules, in qualitative agreement with experiments. Furthermore, we find the rigid model to be more computationally efficient for both molecules, providing more samples per second and shorter times to equilibrium. Owing to the structural accuracy and improved computational efficiency of modeling polyaromatic groups as rigid bodies, we recommend this modeling choice for enhancing the sampling in polyaromatic molecular simulations.
perylothiopheneRigid-Body Models Molecular simulationsPerylothiophene PackingperyleneX-ray diffraction10 000understandingefficiency10 000 wall-clock hoursmorphologiegraphics processing unit-accelerated simulationschemical componentsEnhanced Computational Samplingmodeling choicecolumnar phasescoarse-graining techniquescluster analysismodeling approximationsphase diagramsalgorithmic complexitymoleculeSuch methodsmodeling polyaromatic groups