Description of proton transfer in soybean lipoxygenase-1 employing approximate quantum trajectory dynamics

The effect of local substrate motion on quantum hydrogen transfer in soybean lipoxygenase-1 modeled with QTES-DFTB dynamics

“…The trajectories are evolved for 1000 imaginary time steps with d = (4k B T) −1 /1000 a.u., followed by 500 real time steps with dt = 1 a.u. This timescale was chosen to be comparable to the double-well oscillation period in the reduced active site model [18], and the total number of time steps was chosen to yield rate constant results converged to less than 1% deviation at the lowest temperature examined, T = 250 K.…”

“…This study was performed as a generalization of the fixed-substrate donor/acceptor dynamics, employed in a previous study [18]. A density-functional tight-binding method was used to calculate electronic structure on-the-fly after modification of the O-H repulsive spline to match a more expensive ab initio PES.…”

“…A decrease of R OH describes advancement toward a product state along the minimum energy path. For reaction dynamics, the geometry corresponding to a constraint of R OH = 1.50Å was chosen for rate constant calculations as it corresponds to a nearly equal donor and acceptor well depth, and the donor-acceptor barrier produced in this configuration is most conducive to tunneling [16,15,18]. This configuration is therefore referred to as a quantum transition state (QTS), represented by the bold curve in Figure 2.…”

“…By explicitly including the motion of local substrate atoms and the quantum flux formalism, we can improve upon our previous model of Ref. [18].…”

“…In our previous work [18], a KIE of 51 was estimated at zero temperature from the dynamics of the quantum proton/deuteron, initially localized in the donor well of the potential energy surfaces (PES) associated with fixed active site configurations. While different active site geometries correspond to different PESs of the proton, the dynamic interplay between local motion of activesite nuclei and proton tunneling remains controversial [19][20][21].…”