We give a detailed description of the use of explicit as well as implicit solvation treatments to compute the reduction potentials of biomolecules in a medium. The explicit solvent method involves quantum mechanical/molecular mechanics (QM/MM) treatment of the solvated moiety followed by a Monte-Carlo (MC) simulation of the primary solvent layer. The QM task for considerably large biomolecules is normally carried out by density functional treatment (DFT) along with the MM-assisted evaluation of the most stable configuration for the primary layer and biomolecule complex. The MC simulation accounts for the dynamics of the associated solvent molecules. Contributions of the solvent molecules of the bulk towards the absolute free energy change of the reductive process are incorporated in terms of the Born energy of ion-dielectric interaction, the Onsager energy of dipole-dielectric interaction and the Debye-Hückel energy of ion-ionic cloud interaction. In the implicit solvent treatment, one employs the polarizable continuum model (PCM). Thus the contribution of all the solvent molecules towards the free energy change are incorporated by considering the whole solvent as a dielectric continuum.
As an example, the QM(DFT)/MM/MC-Born/Onsager/Debye-Hückel corrections yielded the oneelectron reduction potential of Pheophytin-a in the solvent DMF as $−0.92 \pm 0.27$ V and the two-electron reduction potential as $−1.34 \pm 0.25$ V at 298.15 K while the DFT-DPCM method yielded the corresponding values as $−1.03 \pm 0.17$ V and $−1.30 \pm 0.17$ V, respectively. The calculated values more or less agree with the observed mid-point potentials of −0.90 V and −1.25 V, respectively. Moreover, a numerical finite difference Poisson-Boltzmann solution along with the DFT-DPCM methodology was employed to calculate the reduction potential of Pheophytin-a within the thylakoid membrane. The calculated reduction potential value of −0.58 V is in agreement with the reported value of −0.61 V that appears in the socalled 𝑍-scheme and is considerably different from the value in vitro.
Volume 135, 2023
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