Automated reaction kinetics and network exploration (Arkane): A statistical mechanics, thermodynamics, transition state theory, and master equation software

IF 1.5 4区 化学 Q4 CHEMISTRY, PHYSICAL
Alon Grinberg Dana, Matthew S. Johnson, Joshua W. Allen, Sandeep Sharma, Sumathy Raman, Mengjie Liu, Connie W. Gao, Colin A. Grambow, Mark J. Goldman, Duminda S. Ranasinghe, Ryan J. Gillis, A. Mark Payne, Yi-Pei Li, Xiaorui Dong, Kevin A. Spiekermann, Haoyang Wu, Enoch E. Dames, Zachary J. Buras, Nick M. Vandewiele, Nathan W. Yee, Shamel S. Merchant, Beat Buesser, Caleb A. Class, Franklin Goldsmith, Richard H. West, William H. Green
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引用次数: 9

Abstract

The open-source statistical mechanics software described here, Arkane–Automated Reaction Kinetics and Network Exploration–facilitates computations of thermodynamic properties of chemical species, high-pressure limit reaction rate coefficients, and pressure-dependent rate coefficient over multi-well molecular potential energy surfaces (PES) including the effects of collisional energy transfer on phenomenological kinetics. Arkane can use estimates to fill in information for molecules or reactions where quantum chemistry information is missing. The software solves the internal energy master equation for complex unimolecular reaction systems. Inputs to the software include converged electronic structure computations performed by the user using a variety of supported software packages (Gaussian, Molpro, Orca, TeraChem, Q-Chem, Psi4). The software outputs high-pressure limit rate coefficients and pressure-dependent phenomenological rate coefficients, as well as computed thermodynamic properties (enthalpy, entropy, and constant pressure heat capacity) with added energy corrections. Some of the key features of Arkane include treatment of 1D, 2D or ND hindered internal rotation modes, treatment of free internal rotation modes, quantum tunneling effect consideration, transition state theory (TST) and Rice-Ramsperger-Kassel-Marcus (RRKM) rate coefficient computations, master equation solution with four implemented methods, inverse-Laplace transform of high-pressure limit rate coefficients into the energy domain, energy corrections based on bond-additivity or isodesmic reactions, automated and efficient PES exploration, and PES sensitivity analysis. The present work describes the design of Arkane, how it should be used, and refers to the theory that it employs. Arkane is distributed via the RMG-Py software suite (https://github.com/ReactionMechanismGenerator/RMG-Py).

Abstract Image

自动化反应动力学和网络探索(Arkane):统计力学、热力学、过渡态理论和主方程软件
本文介绍的开源统计力学软件arkane——自动反应动力学和网络探索——有助于计算化学物质的热力学性质、高压极限反应速率系数和多井分子势能面(PES)上的压力相关速率系数,包括碰撞能量传递对现象动力学的影响。Arkane可以利用估计来填补量子化学信息缺失的分子或反应信息。该软件解决了复杂的单分子反应系统的内能主方程。软件的输入包括由用户使用各种支持的软件包(Gaussian, Molpro, Orca, TeraChem, Q-Chem, Psi4)执行的聚合电子结构计算。该软件输出高压极限速率系数和压力相关的现象速率系数,以及计算的热力学性质(焓、熵和恒压热容)与添加的能量校正。Arkane的一些关键特性包括对一维、二维或ND受限内旋转模式的处理、对自由内旋转模式的处理、量子隧道效应的考虑、过渡态理论(TST)和Rice-Ramsperger-Kassel-Marcus (RRKM)速率系数的计算、四种实现方法的主方程解、高压极限速率系数在能量域的反拉普拉斯变换、基于键加性或等速反应的能量修正,自动化和高效的PES勘探,以及PES敏感性分析。本工作描述了Arkane的设计,它应该如何使用,并提到了它所采用的理论。Arkane是通过RMG-Py软件套件(https://github.com/ReactionMechanismGenerator/RMG-Py)发布的。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
CiteScore
3.30
自引率
6.70%
发文量
74
审稿时长
3 months
期刊介绍: As the leading archival journal devoted exclusively to chemical kinetics, the International Journal of Chemical Kinetics publishes original research in gas phase, condensed phase, and polymer reaction kinetics, as well as biochemical and surface kinetics. The Journal seeks to be the primary archive for careful experimental measurements of reaction kinetics, in both simple and complex systems. The Journal also presents new developments in applied theoretical kinetics and publishes large kinetic models, and the algorithms and estimates used in these models. These include methods for handling the large reaction networks important in biochemistry, catalysis, and free radical chemistry. In addition, the Journal explores such topics as the quantitative relationships between molecular structure and chemical reactivity, organic/inorganic chemistry and reaction mechanisms, and the reactive chemistry at interfaces.
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