An analysis method has been developed for identifying reaction events that occur within molecular dynamics (MD) simulations. This method can be used to discover novel theoretical isomers of complex molecules. The procedure for finding unique isomers was developed through the study of a group of iron carbonyls, including an Fe<sub>3</sub>(CO)<sub>9</sub> complex. Theoretical isomers of compounds of interest can be found using local energy minimization methods. However, these methods can only locate the isomers within the local environment of the initial structure. The ability to find isomers that exist throughout a molecule’s potential energy surface requires the crossing of energy barriers that separate neighboring local minima. MD simulations can be used to overcome these reaction barriers. The reaction events that occur within the simulations can be detected through analysis of bond order data. The bond order between two atoms over time can be processed with a threshold parameter to indicate whether the two atoms are bonded or not bonded, creating a binary time series. The transitions in the binary series shows where a reaction has taken place. Rapid transitions that occur very close to each other can be eliminated using delay parameters so that only lasting changes in atomic bonding are shown in the binary series. The binary transitions that remain in the binary time series correspond to the conversion of one constitutional isomer into another.

Using molecular dynamics simulations to investigate novel reaction events: A case study with iron carbonyls

253rd National Meeting (2017)

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