We present charge transfer characteristics of DNA by evaluating the electronic parameters in the presence of water and counterions. Motivated by the recent experiment by Guo et al. [1], we investigate three types of dsDNA oligomers; a well matched 15 base pair sequence and single mismatched base pairs (GT, CA) in sequence. Charge transfer parameters are obtained using a fragment orbital approach [2] on the coarse-grained level, where a fragment consists of a pair of nucleotides from each DNA strand. In order to fully take into account the effect of dynamical fluctuations [3] the electronic structure calculation is performed using a hybrid QM/MM method for each snapshot along the MD trajectory. From the electronic structure parameters the current is obtained for both coherent and incoherent transport [4] contribution to see the effect of single base pair mismatch.
[1] X. Guo et al., Nature Nanotech. 3, 163 (2008).
[2] D. G. Fedorov and K. Kitaura, J. Phys. Chem. A 111, 6904 (2007).
[3] R. Gutierrez, et al., Phys. Rev. Lett. 102, 208102 (2009);
P. B. Woiczikowski et al., J. Chem. Phys. 130, 215104 (2009);
P. B. Woiczikowski et al., J. Phys. Chem. B 112, 7937 (2008).
[4] J. L. D'Amato and H. M. Pastawski, Phys. Rev. B 41, 7411 (1990).