Even though the Car-Parrinello molecular dynamics (CPMD) method provides excellent sampling for thermal equilibrium, coupling between ionic motion and the fictitious orbital dynamics leads to an underestimation of ionic vibration frequencies In this letter we examine how this coupling affects calculated rates of energy-barrier crossing. Simulating double-well potentials in 'toy' models based on H3O2- and H5O2+ complexes, we demonstrate that barrier crossing rates can be dramatically affected depending upon how orbitals evolve at the top of the reaction barrier. Thus, it is important that calculated dynamical quantities such as chemical reaction rates be assessed for this coupling effect. (C) 2015 Published by Elsevier B.V.