Automatic Construction And Visualization Of Chemical Reaction Networks Based On ReaxFF MD Simulation Results

Reactive molecular dynamics(ReaxFF MD)is a promising new method that can be applied to study complex chemical reactions in large scale reactive molecular systems(>10,000 atoms).There are huge amount of underlying chemical reactions in the trajectory and bond order files obtained in ReaxFF MD simulations,from which is not practical to discover reactions manually.VARxMD is a reaction analysis and visualization tool for ReaxFF MD developed by the author's research group.VARxMD can automatically obtain unique species,detailed chemical reaction lists with detailed reaction sites from ReaxFF MD simulation results.In addition,reactions can be classified into different groups based on the characteristics of substructures and reaction sites of specified species.On the basis of the analysis data of VARxMD,this work extends the functions of reaction pathway search and construction of the chemical reaction network between specified reactant and product in the reaction list.Two strategies based on reaction lists and based on atoms for automatic identification of reaction paths are proposed.The advantages and disadvantages of these two strategies are further analyzed.The strategy based on the reaction lists needs to be performed based on complete reaction lists and with the limitation of single set of search targets designation In contrast,the strategy based on atoms supports multi-target search and the detailed network can be obtained.An atom-based reaction path search algorithm is designed and implemented that supports searching targets of atoms,chemical bonds,molecules and species,which is beneficial to explore the reaction mechanisms from different perspectives.The reaction search algorithm is based on breadth-first search(BFS).The results and reaction pathways of reaction search during specified period between the range of two timesteps can be fiurther analyzed for understanding of reaction mechanisms.The visualization of obtained chemical reaction network is implemented with Sugiyama algorithm for directed graph layout and Qt-based view framework.The visualization of the chemical reaction network supports both the reduced reaction pathway network without time stamps or detailed reaction pathway with time stamps.The Qt-based signal and slot mechanism are employed to realize the interactive depiction of the reaction network diagram,which is beneficial to obtain the rich information of reactive species and chemical reaction sites for the contained in the chemical reaction network.Based on the existing functions of VARxMD,this work expands the function of automatic retrospect of reaction pathways and construction of chemical reaction networks.The extended functions for construction and visualization of c:hemical reaction network in this work is general and can be widely applied in ReaxFF MD simulations.