Abstract by Jordan Jenkins
Chemistry and Biochemistry
Python Tools for Analysis of Direct Molecular Dynamics Simulations, and Application to the Dynamics of Rhodium Reductive Coupling
Molecular dynamics provide information of how molecular structures change over time. This information is being used in our lab to understand nonstatistical effects in chemical reactions, specifically organometallic reaction mechanisms. Our quasiclassical direct dynamics C++ software (DynSuite) provides the ability to examine complete reaction pathways, including transition states. However, until now plotting the output of these simulations was tedious. I will present a suite of Python tools that provides the ability to analyze the geometries as a function of time from dynamics simulations. This will be demonstrated for a rhodium-methyl reductive coupling reaction.