We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The pi molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wave functions and energies of DNA bases are discussed and then used for calculating the corresponding wave functions of the two B-DNA base-pairs (adenine-thymine and guanine-cytosine). The obtained HOMO and LUMO energies of the bases are in good agreement with available experimental values. Our results are then used for estimating the complete set of charge transfer parameters between neighboring bases and also between successive base-pairs, considering all possible combinations between them, for both electrons and holes. The calculated microscopic quantities can be used in mesoscopic theoretical models of electron or hole transfer along the DNA double helix, as they provide the necessary parameters for a tight-binding phenomenological description based on the pi molecular overlap. We find that usually the hopping parameters for holes are higher in magnitude compared to the ones for electrons. Our findings are also compared with existing calculations from first principles.
The transfer of electrons and holes along DNA dimers, trimers and polymers is described at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters between successive base-pairs. The temporal and spatial evolution of carriers along a N base-pair DNA segment is determined, solving a system of N coupled differential equations. Useful physical quantities are calculated including the pure mean carrier transfer rate k, the inverse decay length β used for exponential fit (k = k0exp(−βd)) of the transfer rate as a function of the charge transfer distance d = N × 3.4Å and the exponent η used for a power law fit (k = k ′ 0 N −η ) of the transfer rate as function of the number of monomers N . Among others, the electron and hole transfer along the polymers poly(dG)-poly(dC), poly(dA)-poly(dT), GCGCGC..., ATATAT... is studied. β (η) falls in the range ≈ 0.2 -2Å −1 (1.7 -17), k0 (k ′ 0 ) is usually ≈ 10 −2 -10 −1 (10 −2 -10 −1 ) PHz although, generally, it falls in the wider range ≈ 10 −4 -10 (10 −4 -10 3 ) PHz. The results are compared with past predictions and experiments. Our approach illustrates to which extent a specific DNA segment can serve as an efficient medium for charge transfer.PACS numbers: 87.14.gk, 82.39. Jn, Charge transfer along DNA is crucial for molecular biology, genetics, and nanotechnology [1][2][3]. Here we present a convenient way to quantify electron or hole transfer along DNA segments using a tight-binding approach which can be easily implemented by interested colleagues. To date all the tight-binding parameters relevant to charge transport along DNA either for electrons (traveling through LUMOs) or for holes (traveling through HOMOs) are available in the literature [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17]. Here we use them to study the temporal and spatial evolution of a carrier along DNA. The transport of electrons or holes can be described at either (I) the base-pair level or (II) the single base level [4]. We need the relevant onsite energies of either (I) the base-pairs or (II) the single bases. In addition, we need the hopping parameters between either (I) successive base-pairs or (II) neighboring bases taking all possible combinations into account [(IIa) successive bases in the same strand, (IIb) complementary bases within a base-pair, (IIc) diagonally located bases of successive base-pairs in opposite strands]. To calculate the temporal and spatial evolution of carriers along a N base-pair segment of DNA one has to solve a system of either (I) N or (II) 2N coupled differential equations. Here we use the simplest approach (I) to examine charge transfer in B-DNA dimers, trimers and polymers. Taking the relevant literature into account [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17], we use the on-site energies and the hopping parameters shown in Tables I-II. We denote adenine (A), thymine (T), guanine (G), cytosine (C), and the relevant base-pairs A-T and G-C. YX signifies two successive base-pairs: the bases Y and X of two succes...
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.
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