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WIREs Comput Mol Sci
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Methods for exploring reaction space in molecular systems

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The area of reaction mechanism discovery simulation has taken considerable strides in recent years. Novel methods that make hypotheses for elementary steps and complementary means for reaction path and transition state (TS) optimization are lowering the amount of chemical intuition and user effort required to explore reaction networks. The resulting networks lead from reactants to reactive intermediates and products, and are becoming closer representations of physical mechanisms involved in experiments. This review describes several of these approaches, which are categorized based on their overarching TS finding strategies. Future advances are discussed that may revolutionize the ability of simulation to fully predict not just the reaction mechanism but reaction outcomes. WIREs Comput Mol Sci 2018, 8:e1354. doi: 10.1002/wcms.1354 This article is categorized under: Structure and Mechanism > Reaction Mechanisms and Catalysis Software > Quantum Chemistry Software > Simulation Methods
Single elementary step characterization algorithms. (a) IRC, (b) double‐ended, (c) single‐ended.
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Flow chart for molecular dynamics/coordinate driving method of Li and coworkers.
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Example of ZStruct2 reaction types and alignment of reactants at a square planar transition metal center.
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ZStruct2 graphical driving coordinate generation and reaction path searches.
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Reaction pathway discovery using the nanoreactor.
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Flow chart for the reaction path discovery method developed by Reiher and coworkers.
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Graph‐based, dynamical reaction path sampling method.
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Graphical methods used by Zimmerman (bottom pathway) and Green (top pathway) to generate plausible intermediates, followed by reaction path finding.
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Group additivity strategy for transition state geometry estimation and refinement.
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The transition state search using chemical dynamics simulations (TSSCDS) method.
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The artificial force‐induced reaction (AFIR) method.
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The anharmonic downward distortion following (ADDF) method.
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Example of an alkene hydrohalogenation pathway by the Aspuru‐Guzik method.
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Graph‐based reaction network generation using specifically encoded transformations.
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Four categories of automated reaction path exploration methods.
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