We call monomer a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer-and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a tight-binding (TB) approach at the base-pair level to readily determine the spatiotemporal evolution of a single extra carrier along a N base-pair polymer. We study HOMO and LUMO eigenspectra as well as the mean over time probabilities to find the carrier at a particular monomer. We use the pure mean transfer rate k to evaluate the easiness of charge transfer. The inverse decay length β for exponential fits k(d), where d is the charge transfer distance, and the exponent η for power law fits k(N ) are computed; generally power law fits are better. We illustrate that increasing the number of different parameters involved in the TB description, the fall of k(d) or k(N ) becomes steeper and show the range covered by β and η. Finally, both for the time-independent and the time-dependent problem, we analyze the palindromicity and the degree of eigenspectrum dependence of the probabilities to find the carrier at a particular monomer.

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 study hole transfer in open cumulenic and polyynic nanowires made of N carbon atoms, using real-time time-dependent density functional theory (RT-TDDFT) and tight-binding (TB) wire models. For RT-TDDFT, we mainly use functional B3LYP and basis sets cc-pVDZ, cc-pVTZ, and cc-pVQZ, obtaining clear convergence; cc-pVTZ is the smallest basis set of sufficient quality; cc-pVQZ is better with a higher computational cost. For TB, we use a simplistic wire model where all sites are equivalent (TBI) and models with modified initial and final sites, mimicking the existence of one or two or three hydrogens at edge sites (TBImod, TBImodt4times). We compare the ground state energy, E GS , obtained by density functional theory (DFT) for cumulenic molecules with coplanar (co) or perpendicular (pe) methylene end groups as well as polyynic molecules starting with short (sl) or with long (ls) C−C bonds. For odd N, cumulenic pe molecules have lower E GS than cumulenic co molecules, that are probably transition states. We examine energy spectra, density of states, energy gap, charge oscillations, mean over time probabilities to find the hole at each site, coherent transfer rates, electric dipole moment, and frequency content. DFT shows that due to the impact of end groups, there exists a cumulenic energy gap, smaller than the polyynic one. TBI and TBImod reproduce approximately the magnitude of the energy gap in the polyynic case at the limit of large N. TBImod is capable of predicting the same site occupations with the nicely converged RT-TDDFT ones for the cumulenic case. However, charge and dipole moment oscillations as well as transfer rates by RT-TDDFT are approximately four times faster than those by TBImod. The site occupations of polyynic sl and of polyynic ls molecules are modified relative to cumulenic molecules; the trends can be explained qualitatively.

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.