Efficient algorithms for the simulation of non-adiabatic electron transfer in complex molecular systems: application to DNA

Abstract

In this work, a fragment-orbital density functional theory-based method is combined with two different non-adiabatic schemes for the propagation of the electronic degrees of freedom. This allows us to perform unbiased simulations of electron transfer processes in complex media, and the computational scheme is applied to the transfer of a hole in solvated DNA. It turns out that the mean-field approach, where the wave function of the hole is driven into a superposition of adiabatic states, leads to over-delocalization of the hole charge. This problem is avoided using a surface hopping scheme, resulting in a smaller rate of hole transfer. The method is highly efficient due to the on-the-fly computation of the coarse-grained DFT Hamiltonian for the nucleobases, which is coupled to the environment using a QM/MM approach. The computational efficiency and partial parallel character of the methodology make it possible to simulate electron transfer in systems of relevant biochemical size on a nanosecond time scale. Since standard non-polarizable force fields are applied in the molecular-mechanics part of the calculation, a simple scaling scheme was introduced into the electrostatic potential in order to simulate the effect of electronic polarization. It is shown that electronic polarization has an important effect on the features of charge transfer. The methodology is applied to two kinds of DNA sequences, illustrating the features of transfer along a flat energy landscape as well as over an energy barrier. The performance and relative merit of the mean-field scheme and the surface hopping for this application are discussed.

Biological charge transfer via flickering resonance

“…Mixed quantum/classical simulations indicate approximately Gaussian distributed site energy distributions (25,29,30) and nearest-neighbor electronic coupling distributions (25,28,(31)(32)(33)(34). However, the site energy fluctuation correlations break the simple connections between σ E , λ, and K B T, and produce values of λ ≈ 1.2 eV.…”

A hybrid approach to simulation of electron transfer in complex molecular systems

“…Following a recent study [36], the SH algorithm based on a local diabatization of the adiabatic states [77] is implemented in this work. We present a brief outline of the method here, and refer to the original work for details [78].…”

“…We note that the efficiency of hole transfer is not limited by the possible distribution of purines between both DNA strands as the electronic coupling can be sufficient in such a case as well [21]. The first application deals with two archetypical DNA species [78], one with a homogeneous sequence AAAA in which the IP of all of the considered fragments are equal, and one with a sequence GAG in which the transfer from one G to the other has to overcome a higher energy region represented by the A.…”

Quantifying Environmental Effects on the Decay of Hole Transfer Couplings in Biosystems

“…Decoherence can be taken into account theoretically by carrying out a simultaneous quantum dynamics of the electrons and the nuclei, 17,18 by ad-hoc corrections of the kinetic constant expression 15,16 or, at least partially, by accounting for the influence of a dissipative environment (phonon bath) which can support or restrict charge motion. 19,20 Theoretically, it has been difficult to provide a clear picture of DNA conductivity due to charge transfer dynamics being inherently non-adiabatic, and its modeling must involve going beyond the Born-Oppenheimer approximation. This was attempted using model Hamiltonians 14,19,[21][22][23][24] as well as full electron-nuclear non-adiabatic dynamics simulations.…”

“…This was attempted using model Hamiltonians 14,19,[21][22][23][24] as well as full electron-nuclear non-adiabatic dynamics simulations. 20,25,26 However, the excess charge localization is dramatically affected by the specific theory employed for handling nonadiabaticity (e.g. Ehrenfest or Surface Hopping).…”