One of the simulation engines of an open-source program called the Molecular Workbench which can simulate thermodynamics of chemical reactions is presented. This software calculates time evolution of the system and generates rich, dynamic visual representations of the system that can help students understand the salient features of a dynamic system. This type of real-time, interactive simulation and visualization of chemical reactions at the atomic scale could help students understand the connections between chemical reaction equations and atomic interactions. The addition of chemical reactions to Molecular Dynamics modeling system for educational purposes is also presented so as to build a working model accessible to the majority of chemistry teachers for teaching thermodynamics of chemical reactions.
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