Enhanced Computational Sampling of Perylene and Perylothiophene Packing with Rigid-Body Models
Enhanced Computational Sampling of Perylene and Perylothiophene Packing with Rigid-Body Models
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DOI：
10.1021/acsomega.6b00371
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发表时间：
2017-01-01
期刊：
影响因子：
4.1
通讯作者：
Jankowski, Eric
中科院分区：
文献类型：
--
作者：
Miller, Evan D.;Jones, Matthew L.;Jankowski, Eric
分子模拟有可能促进对如何通过选择化学成分来设计有机材料结构的理解，但受计算成本的限制。通过使用捕获系统相关特征的建模近似，同时降低算法复杂性或通过降低必须集成的自由度，可以显著降低计算成本。这些方法包括粗粒化技术，用短程电位近似远程静电，以及使用刚体代替原子之间的柔性键约束。为了了解这些技术是否以及在多大程度上可以用来增强对平面有机分子的理解，我们使用简化的苝和过氧噻吩分子模型研究了分子动力学模拟预测的形态。使用刚性和柔性模型进行了大约10000小时的图形处理单元加速模拟，以测试它们的效率和两种化学物质的预测能力。我们使用模拟x射线衍射和聚类分析来区分结构转变，并通过四种相图来描述1191种结果的形貌。我们发现苝和过氧噻吩的刚性模型所产生的形貌与柔性模型所产生的形貌相匹配。我们发现有序的、六边形排列的柱状相在很大的密度和温度范围内对这两种分子都有利，在定性上与实验一致。此外，我们发现刚性模型对两种分子的计算效率更高，每秒提供更多的样品和更短的平衡时间。由于将多芳烃基建模为刚体的结构精度和计算效率的提高，我们推荐采用这种建模方法来提高多芳烃分子模拟中的采样精度。
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.