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Molecular Simulation of Chemical Reaction Equilibrium by Computationally Efficient Free Energy Minimization
ACS Central Science ( IF 18.2 ) Pub Date : 2018-08-23 00:00:00 , DOI: 10.1021/acscentsci.8b00361
William R. Smith 1, 2, 3, 4 , Weikai Qi 1
Affiliation  

The molecular simulation of chemical reaction equilibrium (CRE) is a challenging and important problem of broad applicability in chemistry and chemical engineering. The primary molecular-based approach for solving this problem has been the reaction ensemble Monte Carlo (REMC) algorithm [Turner et al. Molec. Simulation 2008, 34, (2), 119−146], based on classical force-field methodology. In spite of the vast improvements in computer hardware and software since its original development almost 25 years ago, its more widespread application is impeded by its computational inefficiency. A fundamental problem is that its MC basis inhibits the implementation of significant parallelization, and its successful implementation often requires system-specific tailoring and the incorporation of special MC approaches such as replica exchange, expanded ensemble, umbrella sampling, configurational bias, and continuous fractional component methodologies. We describe herein a novel CRE algorithm (reaction ensemble molecular dynamics, ReMD) that exploits modern computer hardware and software capabilities, and which can be straightforwardly implemented for systems of arbitrary size and complexity by exploiting the parallel computing methodology incorporated within many MD software packages (herein, we use GROMACS for illustrative purposes). The ReMD algorithm utilizes these features in the context of a macroscopically inspired and generally applicable free energy minimization approach based on the iterative approximation of the system Gibbs free energy function by a mathematically simple convex ideal solution model using the composition at each iteration as a reference state. Finally, we additionally describe a simple and computationally efficient a posteriori method to estimate the equilibrium concentrations of species present in very small amounts relative to others in the primary calculation. To demonstrate the algorithm, we show its application to two classic example systems considered previously in the literature: the N2–O2–NO system and the ammonia synthesis system.

中文翻译:

计算有效自由能最小化的化学反应平衡的分子模拟

化学反应平衡(CRE)的分子模拟是在化学和化学工程中广泛应用的具有挑战性和重要的问题。解决此问题的主要基于分子的方法是反应集成蒙特卡洛(REMC)算法[Turner等。Molec。仿真 2008年34(2),[119-146],基于经典力场方法。尽管自从将近25年前最初的发展以来,计算机硬件和软件有了巨大的改进,但由于计算效率低,阻碍了其更广泛的应用。一个基本问题是它的MC基础阻碍了显着并行化的实现,并且其成功实现通常需要特定于系统的定制,并且需要合并特殊的MC方法,例如副本交换,扩展集合,伞状抽样,配置偏差和连续小数部分方法论。我们在这里描述了一种利用现代计算机硬件和软件功能的新型CRE算法(反应整体分子动力学,ReMD),并且可以通过利用许多MD软件包中集成的并行计算方法直接将其用于任意大小和复杂性的系统(在此,我们使用GROMACS进行说明)。ReMD算法在宏观启发和普遍适用的自由能最小化方法的上下文中利用了这些特征,该方法基于系统吉布斯自由能函数的迭代近似,通过数学上简单的凸理想解模型,使用每次迭代时的成分作为参考状态。最后,我们还描述了一个简单且计算效率高的 ReMD算法在宏观启发和普遍适用的自由能最小化方法的上下文中利用了这些特征,该方法基于系统吉布斯自由能函数的迭代近似,通过数学上简单的凸理想解模型,使用每次迭代时的成分作为参考状态。最后,我们还描述了一个简单且计算效率高的 ReMD算法在宏观启发和普遍适用的自由能最小化方法中利用了这些特征,该方法基于系统吉布斯自由能函数的迭代逼近,该数学上是数学上简单的凸理想解模型,使用每次迭代时的成分作为参考状态。 。最后,我们还描述了一个简单且计算效率高的一种后验方法,用于估计在初始计算中相对于其他物种而言很少存在的物种的平衡浓度。为了演示该算法,我们展示了其在文献中先前考虑的两个经典示例系统中的应用:N 2 -O 2 -NO系统和氨合成系统。
更新日期:2018-08-23
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