Parametrization of an effective correlated hamiltonian for hole transfer in large DNA strands

The hybrid valence-bond/Hartree–Fock model (VB/HF) [F. Castet, A. Fritsch and L. Ducasse, J. Phys. I (France), 1996, 6, 583; F. Castet, L. Ducasse and A. Fritsch, Chem. Phys., 1998, 232, 37] is used to derive an effective model for conduction holes along DNA nucleoside stacks. The extraction procedure which gives the transfer integrals from the off-diagonal elements of the VB/HF matrix was presented in the first paper of this series [G. Brunaud, F. Castet, A. Fritsch, M. Kreissler and L. J. Ducasse, Phys. Chem. B, 2001, 105, 12 665.]. The remaining electrostatic parameters, introduced here, provide a complete set of transferable intrasite and intersite parameters for the effective hamiltonian. The sensitivity of the effective parameters to the chemical nature of the interacting nucleosides as well as to geometrical fluctuations of the DNA strands is analyzed. It is shown that conformational changes can induce sizeable variations on the effective parameters, in particular on penetration integral values which play a leading role in hole localization properties [G. Brunaud, F. Castet, A. Fritsch and L. Ducasse, Phys. Chem. Chem. Phys., 2002, 4, 6072]. However, these variations do not affect the nature of the most efficient trapping sites, so that the experimental sampling of the charge on guanine sites are quite satisfactorily simulated using the effective parameters calculated from canonical geometries. This point is illustrated in the last part of the paper, in which electron distributions in the ground state of charged DNA sequences are calculated and compared to experimental data.