Between Superexchange and Hopping: An Intermediate Charge-Transfer Mechanism in Poly(A)-Poly(T) DNA Hairpins

Abstract

We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within the framework of the stochastic surrogate Hamiltonian approach, give values for the arrival rate in good agreement with experimental data. Theoretical results obtained for hairpins with fewer than three A:T base pairs suggest that hole transfer along short hairpins occurs via superexchange. This mechanism is characterized by the exponential distance dependence of the arrival rate on the donor/acceptor distance, k(a) ≃ e(-βR), with β = 0.9 Å(-1). For longer systems, up to six A:T pairs, the distance dependence follows a power law k(a) ≃ R(-η) with η = 2. Despite this seemingly clear signature of unbiased hopping, our simulations show the complete delocalization of the hole density along the entire hairpin. According to our analysis, the hole transfer along relatively long sequences may proceed through a mechanism which is distinct from both coherent single-step superexchange and incoherent multistep hopping. The criterion for the validity of this mechanism intermediate between superexchange and hopping is proposed. The impact of partial localization on the rate of hole transfer between neighboring A bases was also investigated.

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.…”

Quantum dynamics of a vibronically coupled linear chain using a surrogate Hamiltonian approach

“…16 The surrogate Hamiltonian method [47][48][49] provides another means to study dissipative quantum dynamics without assuming a weak system-bath coupling or Markov approximation and has been shown to successfully model quantum dynamics of a variety of physical processes. 47,48,[50][51][52][53][54][55][56][57][58] The basic idea of the surrogate Hamiltonian approach is to construct a finite system-bath Hamiltonian, which can reproduce the true system dynamics in the limit of an infinite number of bath modes for a finite time interval, by using the representative bath modes that span the typical energy range of the system. 47,50 Truncation of the infinite number of bath modes into the finite representative modes limits the description of system dynamics to short time evolution and recurrence eventually appears.…”

“…[50][51][52][53][54][55] In order to model exciton and charge transport in large systems such as photosynthetic complexes, for which the grid propagation method can be numerically expensive, 56 eigen-(site-)basis set has been introduced in the surrogate Hamiltonian method. [56][57][58] In those studies only electronic states were accounted for in the primary system and vibrational states were included in the bath. Herein we employ surrogate Hamiltonian method on a vibronic basis where the effective vibrational mode is explicitly incorporated into the primary system.…”

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

“…[11][12][13] In this interpretation, the excess charges are assumed to be localized on single nucleobases, and no polarons are invoked. Recently, 14 a hybrid mechanism that cannot be classified as hopping nor as coherent superexchange has been theoretically proposed for the long range CT in DNA. Incoherent mechanisms are also significant in DNA charge transport.…”