Efficient Calculation of Charge-Transfer Matrix Elements for Hole Transfer in DNA

• Published in: The journal of physical chemistry. B 2008-07, Vol.112 (26), p.7937-7947
• Main Authors: Kubař, Tomáš, Woiczikowski, P. Benjamin, Cuniberti, Gianaurelio, Elstner, Marcus
• Format: Article
• Language: English
• Subjects: B: Biophysical Chemistry; Computer Simulation; DNA - chemistry; Ions - chemistry; Models, Molecular; Nucleic Acid Conformation
• ISSN: 1089-5647; 1520-6106; 1520-5207
• DOI: 10.1021/jp801486d

We present a new computational strategy to evaluate the charge-transfer (CT) parameters for hole transfer in DNA. On the basis of a fragment-orbital approach, site energies and coupling integrals for a coarse-grained tight-binding description of the electronic structure of DNA are rapidly calculated using the approximative density functional method SCC-DFTB. The methodology is validated by extensive test calculations in comparison with DFT and ab initio reference data, demonstrating its high accuracy at low computational cost. Environmental effects are captured using a quantum mechanics−molecular mechanics (QM/MM) coupling scheme, and dynamical effects are included by evaluating the CT parameters along classical molecular dynamics simulations. This combined methodology allows for a realistic treatment of CT processes in DNA.