The motion of local substrate nuclei is incorporated into the quantum hydrogen transfer reaction which occurs in the active site of soybean lipoxygenase-1, modeled within a quantum trajectory ( QT) framework. Interactions within the active site are obtained from on-the-fly electronic structure (ES) calculations at the density-functional tight-binding (DFTB) level. By selectively constraining substrate nuclei, changes in the rate constants and kinetic isotope effect are computed over a 100 K temperature range. Substrate motion, occurring on the time-scale of the hydrogen transfer, enhances both the rate constants and isotope effect, but does not change trends captured in a constrained substrate environment. (C) 2014 Elsevier B.V. All rights reserved.