Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories.
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.
Woiczikowski
P Benjamin
PB
Department of Physical and Theoretical Chemistry, Technische Universitat Braunschweig, D-38106 Braunschweig, Germany.
Kubar
Tomás
T
Gutiérrez
Rafael
R
Caetano
Rodrigo A
RA
Cuniberti
Gianaurelio
G
Elstner
Marcus
M
D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004579:Electron Transport; D008958:Models, Molecular; D009068:Movement; D009690:Nucleic Acid Conformation; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D013997:Time Factors; D014867:Water / Q000737:chemistry
D012997:Solvents; D014867:Water; D004247:DNA