Charge transport in DNA strands using fragment orbital theory

A semi-empirical Valence-Bond/Hartree–Fock (VB/HF) method is developed to calculate one- and two-electron interactions between molecular fragments in conducting supramolecular stacks. This fragment orbital-based formalism allows for the consistent extraction of an effective hamiltonian defined as a “frontier orbital” model. This hamiltonian quantitatively describes transfer and electrostatic interactions between conducting electrons while reducing the active space so dramatically that the electronic eigenstates of very large systems may be investigated. The VB/HF formalism is applied here to the derivation an effective model for conduction holes along doped DNA double strands. Transferable intra and intersite parameters are first evaluated from VB/HF calculations carried out on nucleoside pairs. From this interaction databank, the effective hamiltonian of any kind of nucleoside sequence can eventually be defined. The thermalized charge distribution for a single hole delocalized along DNA sequences is then calculated and compared to the experimental yields of damage revealed by photocleavage experiments.