Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of a wire model versus an extended ladder model

Abstract

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.

RT-TDDFT study of hole oscillations in B-DNA monomers and dimers

“…Charge transfer in DNA is important for DNA damage and repair [3][4][5][6] and it may be used as an indicator for the separation between cancer tumor and healthy tissue [7]. Although (unbiased) charge transfer in DNA nearly vanishes after 10 to 20 nm [8][9][10], DNA is still a promising component for (biased) charge transport in molecular electronics, e.g., as a short molecular wire [11]. It may also be exploited in nanotechnology for nanosensors [12] and molecular wires [13,14].…”

“…For dimers made of different Net charge versus time for the monomer where the hole was initially placed: (upper panel) dimers made of identical monomers, (lower panel) dimers made of different monomers. The notation(10) means that the hole is initially placed at the 1st base pair of the dimer, while the notation (01) means that the hole is initially placed at the 2nd base pair of the dimer.…”

Periodic, quasiperiodic, fractal, Kolakoski, and random binary polymers: Energy structure and carrier transport

“…The on-site energies are taken E A−T = −8.3 eV for the A-T base pair and E G−C = −8.0 eV for the G-C base pair. 5,6,17,36,49 The hopping integrals between successive base pairs that are involved in the segments studied here are shown in Table I. 5,6,17,36,49 The values of the parameters correspond to the HOMO of the base pairs and are discussed in Ref.…”

“…using various natural and artificial nucleobases with different highest occupied molecular orbital (HOMO) levels 4 . Transfer rates can be increased by many orders of magnitude with appropriate sequence choice [5][6][7] . Furthermore, dynamical fluctuations, arising from either solvent fluctuations or base-pair vibrations can gate charge transport, counteracting the intrinsic disordered potential profile of the sequence 8 .…”

“…Several works have been devoted to the study of transfer and transport in specific DNA structures (periodic [5][6][7]28,29 , quasiperiodic [30][31][32] , random and natural 19,20,[33][34][35] ) using variants of the Tight-Binding (TB) method. Here, we employ the TB wire model, with the sites of the chain being the base pairs, to study the spectral, localization and charge transport properties of periodic, deterministic aperiodic [Thue-Morse (TM), Fibonacci (F), Period Doubling (PD), Rudin-Shapiro (RS), Cantor set (CS), generalized Cantor set (GCS), Kolakoski (KOL)] and random DNA binary segments.…”