Hole wave functions and transport with deazaadenines replacing adenines in DNA.

Transport of a hole along the base stack of DNA is relatively facile for a series of adenines (As) paired with thymines (Ts) or for a series of guanines (Gs) paired with cytosines (Cs). However, the speed at which a hole was found to travel was much too small to make useful semiconductor-type devices. Quite recently it was found that replacing one of the electronegative nitrogens (N3 or N7) with a carbon and a hydrogen, thus turning A into deazaadenine, increased the hole speed in what was A/T by a factor 30.

Localization of a hole on an adenine-thymine radical cation in B-form DNA in water.

A quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation has been carried out using CP2K for a hole introduced into a B-form DNA molecule consisting of 10 adenine-thymine (A/T) pairs in water. At the beginning of the simulation, the hole wave function is extended over several adenines. Within 20-25 fs, the hole wave function contracts so that it is localized on a single A.

Effect of negative differential conductance in carbon nanotubes.

Measurements of transport at high electric fields in metallic single-walled carbon nanotubes (CNTs) have shown either saturation of the current or a region of negative differential conductance (NDC) characterized by the current, after reaching a maximum, decreasing with further increase in voltage. We point out that both types of behavior are characteristic of NDC, but the NDC is masked in samples showing current saturation due to generation of space charge, leading to a nonuniform electric field. We derive the relation between the carrier concentration, the electric field at which the drift velocity peaks, and the length of the sample that is required for the NDC to be manifest as saturation.

Charge-transfer excitons in DNA.

There have been a number of theoretical treatments of excitons in DNA, most neglecting both the intrachain and interchain wavefunction overlaps of the electron and hole, treating them as Frenkel excitons. Recently, the importance of the intrachain and interchain coupling has been highlighted. Experiments have shown that in (dA)n oligomers and in duplex (dA)n.

Duplex polarons in DNA.

In earlier work we calculated the wavefunction and energy of the solvated polaron in DNA with a simple model in which the charge was taken to be on a single chain of bases at the center of the double helix. To better approximate the actual situation, we have now extended the calculations to the case in which the charge is distributed on two chains of bases, complementary to each other, one on each side of the center. The binding energy of the resulting polaron is somewhat larger than that obtained for the single-chain polaron, the result of each chain of the polaron being closer to some of the polarization charge it induces.

Effect of water drag on diffusion of drifting polarons in DNA.

It has been shown, theoretically and experimentally, that a hole or an excess electron on a DNA molecule in solution forms a delocalized wave function, a polaron. For an all-adenine (A) sequence or a mixed sequence of guanines (G's) and A's, calculations taking into account the polarization of the solution give the wave function spread over approximately four bases, which appears to be in agreement with experiment. The polaron may move by hopping or by drift.

Polarons in DNA: transition from guanine to adenine transport.

Experiments on hole transport in DNA have been interpreted as showing that a hole introduced onto a guanine (G) followed by a series of adenines (As) in a DNA duplex travels through the first three As by tunneling and then, with thermal energy, makes the transition onto the bridge of As. It has been widely believed that, once on the bridge, the hole is localized on a single A and proceeds by hopping between As. In the experiments, the holes on the A bridge diffuse, with little attenuation, until trapped by a GGG sequence.

Base sequence effects on transport in DNA.

Given the success of the polaron model based on solvation in accounting for the width of a hole polaron on an all-adenine (A) sequence on DNA, we extend the calculations to other sequences. We find excellent agreement with the free energy differences measured by Lewis et al. (J.

Charge transport in DNA in solution: the role of polarons.

Since the discovery a decade ago of rapid photoinduced electron transfer in DNA over a distance >4 nm, a large number of experiments and theories have been advanced in the attempt to characterize the transfer, mainly of a radical cation or hole. Particularly influential experiments were carried out by Giese [Giese, B. (2000) Acc.

Self-trapping versus trapping: application to hole transport in DNA.

We address the problem of interplay between self-trapping effects and effects of an external potential, which may be relevant for many physical systems, such as polarons in solids or a Bose-Einstein condensate with attraction. If the potential consists of two different wells, the system initially localized in the shallower well may relax into the deeper well, or may not if stabilized by the self-trapping effect. We show how this picture can be applied to interpret results of recent experiments on electron transfer in the DNA molecule [Giese et al.

Effect of solvation on hole motion in DNA.

An excess charge on a DNA chain in solution interacts with polar solvent molecules and mobile counterions. We give the first theoretical estimate of the resulting hole self-localization energy and calculate the corresponding contribution to hole mobility on a DNA stack consisting of a single base pair repeated.

Stationary polaron motion in a polymer chain at high electric fields.

We study the stationary motion of a polaron in a conducting polymer in the presence of a high electric field. Using the Su-Schrieffer-Heeger model plus an electric field, we find that at polaron velocities not exceeding the sound velocity, the dissipation of the electronic energy into the lattice occurs via emission of phonons with single selected wave vector. For this case the corresponding contribution to the polaron mobility can be calculated analytically.

Hole traps in DNA.

Sequences of guanines, GG and GGG, are known to be readily oxidized, forming radical cations, i.e., hole traps, on DNA.

Polarons in DNA.

Many experiments have been done to determine how far and how freely holes can move along the stack of base pairs in DNA. The results of these experiments are usually described in terms of a parameter beta under the assumption that it describes an exponential decay with distance. The reported values range from beta < 0.