2.1 MD Simulations
The CP2K code [35] was used to perform the ab initio MD
simulations that were conducted using the Perdew-Burke-Ernzerhof (PBE)
exchange-correlation functional [36]. Gaussian and plane waves (GPW)
procedure was used in all MD simulations, employing a DZVP basis set
[37] and a plane wave charge density cut-off of 320 Ry with GTH
pseudo potentials [38]. The systems were equilibrated for
approximately 1.5 ps. A total time of 4 ps was considered for each
trajectory, which contained 2000 snapshots (2 fs per snapshot) for
radicals. The configuration of the system in aqueous solution was
constructed from 55 water molecules and 1 free radical (Fig. 2) at a
periodic unit cell of size 12.0×12.0×12.0 Å3. A CSVR
thermostat [39] was applied along with an NVT ensemble at room
temperature (300 K).
<Fig. 2 >