Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories

Abstract

We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics (MD) simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment (water, backbone, counterions) and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders (differences in base ionization potentials). As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and so does the calculated average transmission. Our analysis further supports the basic intuition of charge-transfer active conformations as proposed by Barton et al. [J. Am. Chem. Soc. 126, 11471 (2004)]. However, not DNA conformations with good stacking contacts leading to large interbase hopping values are necessarily the most important, but rather those where the average fluctuation of ionization potentials along the base stack is small. The reason behind this is that the ensemble of conformations leads to average electronic couplings, which are large enough for sufficient transmission. On the other hand, the alignment of onsite energies is the critical parameter which gates the charge transport.

Thermopower of molecular junctions: Tunneling to hopping crossover in DNA

“…70 . Simulating intermediate coherent dynamics in DNA is an intricate task: This regime can be followed with phenomenological tools 60,[71][72][73] , or by combining classical molecular dynamics simulations (for describing the effect of backbone, solvent, counterions, and he DNA internal structural fluctuations) with quantum mechanics/molecular mechanics methodologies [74][75][76][77][78] . Alternatively, in Ref.…”

π−πorbital resonance in twisting duplex DNA: Dynamical phyllotaxis and electronic structure effects

“…In fact, the study of a possible competition between onsite energy fluctuations arising from environmental effects ͑favoring localization of charge͒ and the existence of offdiagonal correlations in the electronic Hamiltonian stemming from the -orbital overlapping mechanism presented in this work would be a very appealing issue deserving further study, particularly in the light of the recent results reporting on the crucial role of correlated fluctuations of the bps dynamics in the Landauer conductance of DNA chains. 55 Regarding the lattice Hamiltonian one expects that damping effects are not very important, particularly for chains con- taining less than 10 3 bps. 56 Thus, the main dynamical effect on the collective twist motion is expected to arise from the effective-mass enhancement of the bps, leading to a relative increase in the resonance frequencies by just a few percent.…”

Modeling charge transport in C60-based self-assembled monolayers for applications in field-effect transistors

“…This is especially due to fluctuations in the alignment of the fullerenes. To further examine the role of fluctuations on the transport properties, a time-dependent treatment of charge transport 32,33 is required, using, e.g., time-dependent nonequilibrium Green's function (NEGF) theory.…”