Understanding the nature of active sites is crucial in heterogeneous catalysis, and dynamic changes of catalyst structures during reaction turnover have brought into focus the dynamic nature of active sites. However, much less is known on how the structural dynamics couples with elementary reactions. Here we report an anomalous decrease in reaction free energies and barriers on dynamical sub-nanometer Au clusters. We calculate temperature dependence of free energies using ab initio molecular dynamics, and find significant entropic effects due to solid-to-liquid phase transitions of the Au clusters induced by adsorption of different states along the reaction coordinate. This finding demonstrates that catalyst dynamics can play an important role in catalyst activity.