We employ two Tight-Binding (TB) approaches to study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of N monomers (base pairs): (I) at the base-pair level, using the on-site energies of base pairs and the hopping integrals between successive base pairs, i.e., a wire model and (II) at the single-base level, using the on-site energies of the bases and the hopping integrals between neighboring bases, i.e., an extended ladder model since we also include diagonal hoppings. We solve a system of M D ("matrix dimension") coupled equations [(I) M D = N , (II) M D = 2N ] for the time-independent problem, and a system of M D coupled 1 st order differential equations for the time-dependent problem. We study the HOMO and the LUMO eigenspectra, the occupation probabilities, the Density of States (DOS) and the HOMO-LUMO gap as well as the mean over time probabilities to find the carrier at each site [(I) base pair or (II) base)], the Fourier spectra, which reflect the frequency content of charge transfer (CT) and the pure mean transfer rates from a certain site to another. The two TB approaches give coherent, complementary aspects of electronic properties and charge transfer in B-DNA monomer polymers and dimer polymers.

Abstract. We call monomer a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in monomers, dimers and trimers. We employ two Tight Binding (TB) approaches: (I) at the base-pair level, using the on-site energies of the base pairs and the hopping parameters between successive base pairs i.e. a wire model, and (II) at the single-base level, using the on-site energies of the bases and the hopping parameters between neighbouring bases, specifically between (a) two successive bases in the same strand, (b) complementary bases that define a base pair, and (c) diagonally located bases of successive base pairs, i.e. an extended ladder model since it also includes the diagonal hoppings (c). For monomers, with TB II, we predict periodic carrier oscillations with frequency f ≈ 50-550 THz. For dimers, with TB I, we predict periodic carrier oscillations with f ≈ 0.25-100 THz. For trimers made of identical monomers, with TB I, we predict periodic carrier oscillations with f ≈ 0.5-33 THz. In other cases, either with TB I or TB II, the oscillations may be not strictly periodic, but Fourier analysis shows similar frequency content. For dimers and trimers, TB I and TB II are successfully compared giving complementary aspects of the oscillations.

We employ Real-Time Time-Dependent Density Functional Theory to study hole oscillations within a B-DNA monomer (one base pair) or dimer (two base pairs). Placing the hole initially at any of the bases which make up a base pair, results in THz oscillations, albeit of negligible amplitude. Placing the hole initially at any of the base pairs which make up a dimer is more interesting: For dimers made of identical monomers, we predict oscillations with frequencies in the range f ≈ 20-80 THz, with a maximum transfer percentage close to 1. For dimers made of different monomers, f ≈ 80-400 THz, but with very small or small maximum transfer percentage. We compare our results with those obtained recently via our Tight-Binding approaches and find that they are in good agreement.

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The Hartree–Fock (HF) method, widely used for the calculation of ground state properties, in recent years has been extended for calculating excited states. In this article, we develop an approach, which does not require time consuming calculations and can give a good approximation for the excitation energies. The method is based on the fact that the subspaces of the occupied and virtual orbitals are mutually orthogonal. We test the accuracy of our method by evaluating the excited state wavefunctions and the corresponding energies for the Li, N, F, Ne, and Na atoms and for the BeH and CH molecules, and we found good agreement with configuration interaction and experimental results. © 2012 Wiley Periodicals, Inc.