Theoretical investigation of redox species in condensed phase

Abstract

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 ± 0⋅27 V and the two-electron reduction potential as −1⋅34 ± 0⋅25 V at 298⋅15 K while the DFT-DPCM method yielded the corresponding values as −1⋅03 ± 0⋅17 V and −1⋅30 ± 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.

A theoretical study on photomagnetic fluorescent protein chromophore coupled diradicals and their possible applications

“…As a matter of fact, PCM does not explicitly consider any fluctuation effect from the average solvent polarization. 24 For all three diradical pairs PCM optimization calculations have been carried out taking blood plasma (e = 58) as the medium. With the PCM optimized geometry of these diradicals in a high spin state, the BS treatment has been performed to ascertain the magnetic nature of these molecules in blood plasma.…”

Computational electrochemistry: prediction of liquid-phase reduction potentials

“…450 The authors demonstrated that the method could be an efficient approach to free energy simulations of complex electron transfer reactions. 450 Several other enzymatic redox reactions have also been studied recently using the tools of computational electrochemistry, in particular for the following enzymes: photosystem II, 270,[451][452][453] ribonuclease reductase, 454,455 rubredoxin, 456 green fluorescent protein, 457,458 adenosine-5 0 -phosphosulfate reductase, 459 methyltransferases, 460 monoamine oxidase B, 461 and methionine synthase. 462 Billiet et al 463 have studied the thermodynamics of thiol sulfenylation in the sulfenic acid-forming protein human Prx.…”