Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations

Abstract

We developed a new multi-resolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multi-resolution model, in which an atomic-level layer of water molecules around redox center is solvated in supra-molecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multi-layer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

An interaction energy driven biased sampling technique: A faster route to ionization spectra in condensed phase

“…The computational prediction of ionization energies (IEs), EAs, and redox potentials has been challenging in condensed phases, due to: (i) difficulty in treating both the ground and electron attached/detached states in a balanced manner, (ii) large number of degrees of freedom in condensed phases, (iii) long range electrostatics and polarization as crucial components of the solute‐solvent interactions, and (iv) important role played by solvent re‐organization in the case of redox potential. There has been significant progress in modeling the redox reactions accurately using Marcus theory and linear response approximations …”

From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field

“…In this scheme, the MM region is treated at two different resolutions at the same time. This strategy proved to be as good as QM/ MM/CG in the calculation of redox potentials for aqueous ruthenium and iron complexes [83].…”

“…An alternative scheme, called QM/(AA þ CG), has been derived from the AA þ CG adaptive resolution scheme (figure 1j ) [83]. In this method, the Hamiltonian of the QM subsystem is preserved, while the QM/MM and MM interactions are described by a multi-resolution scheme according to the relative interparticle distances.…”

Theoretical estimation of redox potential of biological quinone cofactors

“…), DFT (e.g., Refs. ), and so forth. Historically, the alternative relying on parameterized model Hamiltonian like the empirical valence bond approach have been shown to be extremely powerful .…”