Hopping conductivity in nucleotide base stacks*

Abstract

ABSTRACT:The frequency-dependent complex hopping conductivities of single nucleotide base stacks and base pair stacks were calculated on the following basis:(1) The determination of the density of states of these disordered systems with the help of the matrix block negative counting method. (2) Using the inverse iteration technique, the Anderson localization of the one-electron functions belonging to the physically interesting levels were computed. (3) With the help of the latter quantities the hopping frequencies corresponding to the relative motion of the base pairs with respect to each other (acoustic phonons) were determined. (4) Finally, using a random-walk theory the frequency-dependent complex conductivities [σ (ω)] were computed. The |σ (ω)| − ω curves show a saturation at ω ≈ 10 10 s −1 . The |σ (ω)|'s have the values in the base pairs case (taking into account the role of the sugar-phosphate backbone, basis set, and correlation effects) are a few times 1 −1 cm −1 for ω > 10 10 s −1 . This room temperature result is in excellent agreement with the energy loss (in a resonant cavity) experiment on lambda phage deoxyribonucleic acid (DNA) of Gruner and co-workers.

An effective hamiltonian for hole transfer along B-DNA double strands

“…The theoretical efforts towards this goal explore different overlapping approaches. Ladik and coworkers calculated the conduction gap by performing ab initio band structure calculations at the HF and MP2 levels on homonucleoside polymers 13,14 and aperiodic nucleotide base stacks. 15,16 HF calculations within a 6-31g* basis set were performed by Jortner and colleagues, [17][18][19][20][21] essentially in order to evaluate the donor-acceptor coupling term of the Marcus theory.…”