Coarse-grained molecular dynamics simulations of polymerization with forward and backward reactions,Journal of Computational Chemistry

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Coarse-grained molecular dynamics simulations of polymerization with forward and backward reactions
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2018-06-11 , DOI: 10.1002/jcc.25348
Jakub Krajniak ₁ , Zidan Zhang ₂ , Sudharsan Pandiyan ₂ , Eric Nies ₂ , Giovanni Samaey ₁

Affiliation

We develop novel parallel algorithms that allow molecular dynamics simulations in which byproduct molecules are created and removed because of the chemical reactions during the molecular dynamics simulation. To prevent large increases in the potential energy, we introduce the byproduct molecules smoothly by changing the non‐bonded interactions gradually. To simulate complete equilibrium reactions, we allow the byproduct molecules attack and destroy created bonds. Modeling of such reactions are, for instance, important to study the pore formation due to the presence of e.g. water molecules or development of polymer morphology during the process of splitting off byproduct molecules. Another concept that could be studied is the degradation of polymeric materials, a very important topic in a recycling of polymer waste. We illustrate the method by simulating the polymerization of polyethylene terephthalate (PET) at the coarse‐grained level as an example of a polycondensation reaction with water as a byproduct. The algorithms are implemented in a publicly available software package and are easily accessible using a domain‐specific language that describes chemical reactions in an input configuration file. © 2018 Wiley Periodicals, Inc.

中文翻译：

具有正向和反向反应的聚合的粗粒分子动力学模拟

我们开发了新的并行算法，允许进行分子动力学模拟，其中由于分子动力学模拟过程中的化学反应而产生和去除副产物分子。为了防止势能的大幅增加，我们通过逐渐改变非键相互作用来平滑地引入副产物分子。为了模拟完全的平衡反应，我们允许副产物分子攻击并破坏产生的键。例如，此类反应的建模对于研究由于存在例如水分子或在分解副产物分子的过程中聚合物形态的发展而导致的孔形成是重要的。另一个可以研究的概念是聚合物材料的降解，这是聚合物废物回收中的一个非常重要的主题。我们通过模拟粗粒级聚对苯二甲酸乙二醇酯 (PET) 的聚合来说明该方法，作为与水作为副产物的缩聚反应的示例。这些算法是在一个公开可用的软件包中实现的，并且可以使用描述输入配置文件中的化学反应的特定领域语言轻松访问。© 2018 Wiley Periodicals, Inc.

更新日期：2018-06-11

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