Coarse-Grained Time-Dependent Density Functional Simulation of Charge Transfer in Complex Systems: Application to Hole Transfer in DNA

• Published in: The journal of physical chemistry. B 2010-09, Vol.114 (34), p.11221-11240
• Main Authors: Kubař, Tomáš, Elstner, Marcus
• Format: Article
• Language: English
• Subjects: Adenine - chemistry; B: Biophysical Chemistry; DNA - chemistry; Electrons; Molecular Dynamics Simulation; Quantum Theory; Solvents - chemistry; Static Electricity; Time Factors
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp102814p

We present a coarse-grained tight-binding method based on density functional theory (DFT) for the simulation of charge transfer in complex materials. The charge-transfer parameters are computed using a fragment-orbital approach combined with the approximative DFT method self-consistent charge density functional tight binding (SCC-DFTB), which allows to follow the dynamics of excess charge along nanosecond MD trajectories, still accounting for the important impact of structural fluctuations and solvent effects. Since DFT suffers from the self-interaction error, which would lead to a delocalization of the hole charge over the entire system, we study the effect of an empirical self-interaction correction in detail. The wave function of the excess charge is propagated within the framework of time-dependent DFT, where the electron (hole) and the atomic system are propagated simultaneously according to the derived coupled equations of motion. In the case of DNA, the solvent polarization effects are a dominant factor affecting the hole transport. The hole charge polarizes the surrounding water, which in turn supports a localization of the hole chargea water polaron is formed, extended dynamically over several nucleobases. As this polarization of water accompanies the migrating hole, the motion of hole is significantly slowed down due to the solvent reorganization energy involved. The estimated hopping rate between neighboring adenines in poly(A)-DNA is in the order of 100 ns−1, and our simulations clearly show that the charge transfer occurs in a nonadiabatic fashion, due to the small average electronic coupling of around 0.06 eV.