Extracting the mechanisms and kinetic models of complex reactions from atomistic simulation data

Determining reaction mechanisms and kinetic models, which can be used for chemical reaction engineering and design, from atomistic simulation is highly challenging. In this study, we develop a novel methodology to solve this problem. Our approach has three components: (1) a procedure for precisely identifying chemical species and elementary reactions and statistically calculating the reaction rate constants; (2) a reduction method to simplify the complex reaction network into a skeletal network which can be used directly for kinetic modeling; and (3) a deterministic method for validating the derived full and skeletal kinetic models. The methodology is demonstrated by analyzing simulation data of hydrogen combustion. The full reaction network comprises 69 species and 256 reactions, which is reduced into a skeletal network of 9 species and 30 reactions. The kinetic models of both the full and skeletal networks represent the simulation data well. In addition, the essential elementary reactions and their rate constants agree favorably with those obtained experimentally. © 2019 Wiley Periodicals, Inc.

[1]  Mohamed Sassi,et al.  Novel error propagation approach for reducing H2S/O2 reaction mechanism , 2012 .

[2]  Michael J. Pilling,et al.  Evaluated Kinetic Data for Combustion Modelling , 1992 .

[3]  Kyle E. Niemeyer,et al.  Skeletal mechanism generation for surrogate fuels using directed relation graph with error propagation and sensitivity analysis , 2009, 1607.05079.

[4]  Kevin Van Geem,et al.  Comprehensive reaction mechanism for n-butanol pyrolysis and combustion , 2011 .

[5]  Ananth Grama,et al.  Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques , 2012, Parallel Comput..

[6]  Habib N. Najm,et al.  An automatic procedure for the simplification of chemical kinetic mechanisms based on CSP , 2006 .

[7]  A. V. van Duin,et al.  Simulations on the thermal decomposition of a poly(dimethylsiloxane) polymer using the ReaxFF reactive force field. , 2005, Journal of the American Chemical Society.

[8]  C. Westbrook,et al.  Chemical kinetic modeling of hydrocarbon combustion , 1984 .

[9]  Kefeng Yan,et al.  Reactive molecular dynamics simulations of the initial stage of brown coal oxidation at high temperatures , 2013 .

[10]  H. Pitsch,et al.  An efficient error-propagation-based reduction method for large chemical kinetic mechanisms , 2008 .

[11]  R. Kosloff,et al.  Decomposition of condensed phase energetic materials: interplay between uni- and bimolecular mechanisms. , 2014, Journal of the American Chemical Society.

[12]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[13]  Tao Cheng,et al.  Correction to Adaptive Accelerated ReaxFF Reactive Dynamics with Validation from Simulating Hydrogen Combustion , 2014 .

[14]  Zhifeng Jing,et al.  Replica exchange reactive molecular dynamics simulations of initial reactions in zeolite synthesis. , 2015, Physical chemistry chemical physics : PCCP.

[15]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[16]  Donald G. Truhlar,et al.  Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods , 2010 .

[17]  Geraldine J. Heynderickx,et al.  CFD simulations of steam cracking furnaces using detailed combustion mechanisms , 2006, Comput. Chem. Eng..

[18]  Wenjun Zhu,et al.  The intrinsic mechanism of methane oxidation under explosion condition: A combined ReaxFF and DFT study , 2014 .

[19]  Adri C. T. van Duin,et al.  Connectivity-Based Parallel Replica Dynamics for Chemically Reactive Systems: From Femtoseconds to Microseconds , 2013 .

[20]  Huai Sun,et al.  Molecular Dynamics Simulations of Methanol to Olefin Reactions in HZSM-5 Zeolite Using a ReaxFF Force Field , 2012 .

[21]  Jim Pfaendtner,et al.  Car–Parrinello Molecular Dynamics + Metadynamics Study of High-Temperature Methanol Oxidation Reactions Using Generic Collective Variables , 2014 .

[22]  Kyle E. Niemeyer,et al.  Mechanism reduction for multicomponent surrogates: A case study using toluene reference fuels , 2014, 1405.3745.

[23]  Tianfeng Lu,et al.  Experimental counterflow ignition temperatures and reaction mechanisms of 1,3-butadiene , 2007 .

[24]  Kai Leonhard,et al.  Automated discovery of reaction pathways, rate constants, and transition states using reactive molecular dynamics simulations. , 2015, Journal of chemical theory and computation.

[25]  M. Kramer,et al.  Sensitivity Analysis in Chemical Kinetics , 1983 .

[26]  C. Westbrook,et al.  A comprehensive detailed chemical kinetic reaction mechanism for combustion of n-alkane hydrocarbons from n-octane to n-hexadecane , 2009 .

[27]  Gisela Henrici-Olivé,et al.  The Fischer‐Tropsch Synthesis: Molecular Weight Distribution of Primary Products and Reaction Mechanism , 1976 .

[28]  David Weininger,et al.  SMILES. 2. Algorithm for generation of unique SMILES notation , 1989, J. Chem. Inf. Comput. Sci..

[29]  A. V. van Duin,et al.  Thermal decomposition of RDX from reactive molecular dynamics. , 2005, The Journal of chemical physics.

[30]  Xiaolong Liu,et al.  Reaction analysis and visualization of ReaxFF molecular dynamics simulations. , 2014, Journal of molecular graphics & modelling.

[31]  Tsuyoshi Murata,et al.  {m , 1934, ACML.

[32]  Kyle E. Niemeyer,et al.  On the importance of graph search algorithms for DRGEP-based mechanism reduction methods , 2011, ArXiv.

[33]  N. Lümmen ReaxFF-molecular dynamics simulations of non-oxidative and non-catalyzed thermal decomposition of methane at high temperatures. , 2010, Physical chemistry chemical physics : PCCP.

[34]  K. Matyjaszewski Cationic polymerizations : mechanisms, synthesis, and applications , 1996 .

[35]  C. Law,et al.  A directed relation graph method for mechanism reduction , 2005 .

[36]  Harald Bergstriim Mathematical Theory of Probability and Statistics , 1966 .

[37]  P. Cox,et al.  The hydrothermal synthesis of zeolites: Precursors, intermediates and reaction mechanism , 2005 .

[38]  Stephen E. Fienberg,et al.  Testing Statistical Hypotheses , 2005 .

[39]  Tianfeng Lu,et al.  Strategies for mechanism reduction for large hydrocarbons: n-heptane , 2008 .