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. Am. Chem. Soc. 2000, 122, 12037-12038) between a guanine (G) cation and a pair of bases, GG, or a triple of bases, GGG, in all cases surrounded by As, by treating AGGA and AGGGA as solvated polarons. There is additional support for hole polaron formation in DNA from experiments in which oxidative damage due to injected holes is investigated in sequences involving Gs and As. Theory and comparison with transport measurements on repeated sequences involving multiple thymines (Ts) or combinations such as ATs or GCs, where C is cytosine, led to the suggestion that the basic sequences in these cases must be polarons whose wave functions have substantial amplitudes on both chains in a duplex. The size of an electron polaron in DNA is predicted to be similar to that of a hole polaron, approximately 4 or 5 bases. Although experiments have shown that polaron hopping is the dominant mode of charge transport in DNA with repeated sequences such as AGGA, further investigations, particularly of temperature dependence of site energies and transfer integrals, are needed to determine to what extent hole transport takes place by polaron hopping for arbitrary DNA sequences.     

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. The trapping probability of GG is less than that of GGG. Lewis et al. (J. Am. Chem. Soc. 2000, 122, 12037) have used measurements on synthetic hairpins to determine the free energy liberated when a hole goes from the radical cation G(+) to GG or to GGG. They find these free energies to be of the order of thermal energy at room temperature, in contradiction to the expectation by many of much greater trap depths. We have calculated the wave function of a hole on G, on GG, and on GGG surrounded by adenines, as in the Lewis et al. experiments, using a simple tight-binding model. We find that to account for the shallow traps found by them it is necessary that the difference in ionization potentials of contiguous guanine and adenine be smaller by about 0.2 eV than the 0.4 eV found for isolated bases. Using this value and taking into account polaron formation, we find the wave functions of holes trapped on G, GG, or GGG to extend over approximately 6 sites (bases) and with energy level differences in good agreement with the values found by Lewis et al.     

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. Carrying out the calculations for a number of different sequences, we find that the polaron wavefunction is predominantly on one of the two chains, this usually being the one on which the charge was originally placed, despite the availability of lower energy sites on the other chain. This finding is in agreement with recent experiments of Schuster's group(Joy, A.; Ghosh, A. K.; Schuster, G. B. J. Am. Chem. Soc. 2006, 128, 5346-5347). Thus, in contradiction to the ideas of many researchers, there is no transport in which a hole zigzags from one chain to the other, as has been suggested for a sequence of guanines and cytosines (GCGCGC....), for example.     

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. Recently, it has been discovered by Bixon and Jortner that the model of tunneling followed by hopping between As cannot account for the very weak dependence on bridge size of the relative chemical yields and the ratios of the rates for the two processes. In earlier calculations, we have shown that interaction with water results in the hole becoming a polaron spread over approximately four As. According to these calculations, the energy of the hole on the polaron is decreased so much that it is lower than that of the hole on G and even that of GGG. Estimates of energy fluctuations, due to fluctuations in the environment and conformational changes of the DNA, find them to be large enough so that GGG, and even G, can still act as hole traps, but trapping on the former is still very much more likely because of its lower energy.     

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.(dT)n, to be abbreviated (A/T), where A is adenine and T is thymine, the exciton wavefunction is delocalized over several bases. In duplexes it is possible to have charge-transfer (CT) excitons. Theoretical calculations have suggested that CT excitons in DNA may have lower energy than single chain excitons. In all the calculations of excitons in DNA, the polarization of the surrounding water has been neglected. Calculations have shown, however, that polarization of the water by an excess electron or a hole in DNA lowers its energy by approximately 1/2 eV, causing it to become a polaron. It is therefore to be expected that polarization charge induced in the surrounding water has a significant effect on the properties of the exciton. In what follows, we present calculations of some properties CT excitons would have in an A/T duplex taking into account the wavefunction overlaps, the effect of the surrounding water, which results in the electron and hole becoming polarons, and the ions in the water. As expected, the CT exciton has lowest energy when the electron and hole polarons are directly opposite each other. By appropriate choice of the dielectric constant, we can obtain a CT exciton delocalized over the number of sites found in photoinduced absorption experiments. The absorption threshold that we then calculate for CT exciton creation in A/T is in reasonable agreement with the lowest singlet absorption deduced from available data.     

Electrical properties of σ-conjugated polymers with additives and their applications in sensors

The charge carrier transport in poly[methyl(phenyl)silylene] (PMPSi) proceeds predominantly along the σ-delocalized Si backbone with participation of interchain hopping and polaron formation. The charge carrier mobility increases with increasing electron affinity of acceptor dopands having zero dipole moments. On the other band, the hole drift mobility is influenced by the dipole moment of the dopand. The electrostatic charge-dipole interactions cause a broadening of the energy distribution of transport states, which results in a decrease in the charge carrier mobility. An addition of organic salts leads, under the conditions of increased humidity, to an increase in electrical conductivity and capacitance. This is demonstrated on the layers PMPSi/1,5-dimorpholino-1,5-diphenylpentamethinium perchlorate.     

Conjugated chromophore arrays with unusually large hole polaron delocalization lengths

We report variable temperature X-band EPR spectroscopic data for the cation radical states of meso-to-meso ethyne-bridged (porphinato)zinc(II) (PZnn) oligomers. These [PZn2-PZn7]+ species span an average 18-75 A length scale and display peak-to-peak EPR line widths (DeltaBp-p) that diminish with conjugation length. Analysis of these EPR data show that PZnn+ structures possess the largest hole polaron delocalization lengths yet measured; experiments carried out over a 4-298 K temperature domain demonstrate remarkably that the charge delocalization length remains invariant with temperature. These cation radical EPR data are well described by a stochastic, near barrierless, one-dimensional charge hopping model developed by Norris for N equivalent sites on a polymer chain, where the theoretical EPR line width is given by DeltaBp-p(N-mer) = (1/N1/2)DeltaBp-p(monomer); PZnn+ oligomers are the first such systems to verify a Norris-type hole delocalization mechanism over a substantial ( approximately 75 A) length scale. Given the time scale of the EPR measurement, these data show that either (i) Franck-Condon effects are incapable of driving charge localization in [PZn2-PZn7]+, resulting in cation radical wave functions which are globally delocalized over a spatial domain that is large with respect to established benchmarks for hole-doped conjugated materials, or (ii) polaron hopping rates in these oligomers exceed 107 s-1, even at 4 K. Finally, this study demonstrates that polymeric building blocks having low magnitude inner sphere reorganization energies enable the development of electronic materials having long polaron delocalization lengths.     

Electrical Conductivity in Poly(vinyl Chloride)

Conductivity and Seebeck coefficient measurements have been made on commerically-available molded PVC samples containing a range of impurities and on much purer specimens recast from tetrahydrofuran solution. Activation energies measured in the latter materials were not very reproducible; it seems likely that the evaporation of gold electrodes thermally initiates a dehydrochlorination reaction which renders the samples unstable. A range of activation energies from 1.4 to 1.8 eV was observed in the impure samples. The Seebeck coefficient measurements indicated that the majority carriers were negatively charged; the linearity of the current-voltage relationship up to applied field strengths of 80,000 V/cm then suggested an electronic conduction mechanism, although considerable polarization effects were observed in both pure and impure samples. The Seebeck coefficient results also showed that even the purest PVC obtainable is unlikely to be an intrinsic semiconductor, and that the electron transport mechanism probably corresponds more closely to the small polaron hopping model than to the conventional energy-band formation model commonly applied to inorganics.     

Charge hopping in DNA.

The efficiency of charge migration through stacked Watson-Crick base pairs is analyzed for coherent hole motion interrupted by localization on guanine (G) bases. Our analysis rests on recent experiments, which demonstrate the competition of hole hopping transitions between nearest neighbor G bases and a chemical reaction of the cation G(+) with water. In addition, it has been assumed that the presence of units with several adjacent stacked G bases on the same strand leads to the additional vibronic relaxation process (G(+)G...G) --> (GG...G)(+). The latter may also compete with the hole transfer from (G(+)G...G) to a single G site, depending on the relative positions of energy levels for G(+) and (G(+)G...G). A hopping model is proposed to take the competition of these three rate steps into account. It is shown that the model includes two important limits. One corresponds to the situation where the charge relaxation inside a multiple guanine unit is faster than hopping. In this case hopping is terminated by several adjacent G bases located on the same strand, as has been observed for the GGG triple. In the opposite, slow relaxation limit the GG...G unit allows a hole to migrate further in accord with experiments on strand cleavage exploiting GG pairs. We demonstrate that for base pair sequences with only the GGG triple, the fast relaxation limit of our model yields practically the same sequence- and distance dependencies as measurements, without invoking adjustable parameters. For sequences with a certain number of repeating adenine:thymine pairs between neighboring G bases, our analysis predicts that the hole transfer efficiency varies in inverse proportion to the sequence length for short sequences, with change to slow exponential decay for longer sequences. Calculations performed within the slow relaxation limit enable us to specify parameters that provide a reasonable fit of our numerical results to the hole migration efficiency deduced from experiments with sequences containing GG pairs. The relation of the results obtained to other theoretical and experimental studies of charge transfer in DNA is discussed. We propose experiments to gain a deeper insight into complicated kinetics of charge-transfer hopping in DNA.     

共轭聚合物薄膜中光生载流子的产生及输运机制

对共轭聚合物光生载流子的产生机制进行了初步探讨,分析了由最初产生的电子 空穴对经过晶格驰豫之后形成极化子 激子的热离化过程,认为同一链上的激子会迅速复合,只有链间激子对光电流作出贡献.研究了共轭聚合物中载流子的输运机制,导出了共聚物的电导率公式,其计算值与实验结果符合,我们认为是极化子的链间跃迁实现了整个共聚物的电导和光致发光,较好地解释了实验事实.     

Charge-transfer and spin dynamics in DNA hairpin conjugates with perylenediimide as a base-pair surrogate

A perylenediimide chromophore (P) was incorporated into DNA hairpins as a base-pair surrogate to prevent the self-aggregation of P that is typical when it is used as the hairpin linker. The photoinduced charge-transfer and spin dynamics of these hairpins were studied using femtosecond transient absorption spectroscopy and time-resolved EPR spectroscopy (TREPR). P is a photooxidant that is sufficiently powerful to quantitatively inject holes into adjacent adenine (A) and guanine (G) nucleobases. The charge-transfer dynamics observed following hole injection from P into the A-tract of the DNA hairpins is consistent with formation of a polaron involving an estimated 3-4 A bases. Trapping of the (A 3-4) (+*) polaron by a G base at the opposite end of the A-tract from P is competitive with charge recombination of the polaron and P (-*) only at short P-G distances. In a hairpin having 3 A-T base pairs between P and G ( 4G), the radical ion pair that results from trapping of the hole by G is spin-correlated and displays TREPR spectra at 295 and 85 K that are consistent with its formation from (1*)P by the radical-pair intersystem crossing mechanism. Charge recombination is spin-selective and produces (3*)P, which at 85 K exhibits a spin-polarized TREPR spectrum that is diagnostic of its origin from the spin-correlated radical ion pair. Interestingly, in a hairpin having no G bases ( 0G), TREPR spectra at 85 K revealed a spin-correlated radical pair with a dipolar interaction identical to that of 4G, implying that the A-base in the fourth A-T base pair away from the P chromophore serves as a hole trap. Our data suggest that hole injection and transport in these hairpins is completely dominated by polaron generation and movement to a trap site rather than by superexchange. On the other hand, the barrier for charge injection from G (+*) back onto the A-T base pairs is strongly activated, so charge recombination from G (or even A trap sites at 85 K) most likely proceeds by a superexchange mechanism.     

Experimental determination of the absorption cross-section and molar extinction coefficient of CdSe and CdTe nanowires

Absorption cross-sections and corresponding molar extinction coefficients of solution-based CdSe and CdTe nanowires (NWs) are determined. Chemically grown semiconductor NWs are made via a recently developed solution-liquid-solid (SLS) synthesis, employing low melting Au/Bi bimetallic nanoparticle "catalysts" to induce one-dimensional (1D) growth. Resulting wires are highly crystalline and have diameters between 5 and 12 nm as well as lengths exceeding 10 microm. Narrow diameters, below twice the corresponding bulk exciton Bohr radius of each material, place CdSe and CdTe NWs within their respective intermediate to weak confinement regimes. Supporting this are solution linear absorption spectra of NW ensembles showing blue shifts relative to the bulk band gap as well as structure at higher energies. In the case of CdSe, the wires exhibit band edge emission as well as strong absorption/emission polarization anisotropies at the ensemble and single-wire levels. Analogous photocurrent polarization anisotropies have been measured in recently developed CdSe NW photodetectors. To further support fundamental NW optical/electrical studies as well as to promote their use in device applications, experimental absorption cross-sections are determined using correlated transmission electron microscopy, UV/visible extinction spectroscopy, and inductively coupled plasma atomic emission spectroscopy. Measured CdSe NW cross-sections for 1 microm long wires (diameters, 6-42 nm) range from 6.93 x 10(-13) to 3.91 x 10(-11) cm2 at the band edge (692-715 nm, 1.73-1.79 eV) and between 3.38 x 10(-12) and 5.50 x 10(-11) cm2 at 488 nm (2.54 eV). Similar values are obtained for 1 microm long CdTe NWs (diameters, 7.5-11.5 nm) ranging from 4.32 x 10(-13) to 5.10 x 10(-12) cm2 at the band edge (689-752 nm, 1.65-1.80 eV) and between 1.80 x 10(-12) and 1.99 x 10(-11) cm2 at 2.54 eV. These numbers compare well with previous theoretical estimates of CdSe/CdTe NW cross-sections far to the blue of the band edge, having order of magnitude values of 1.0 x 10(-11) cm2 at 488 nm. In all cases, experimental NW absorption cross-sections are 4-5 orders of magnitude larger than those for corresponding colloidal CdSe and CdTe quantum dots. Even when volume differences are accounted for, band edge NW cross-sections are larger by up to a factor of 8. When considered along with their intrinsic polarization sensitivity, obtained NW cross-sections illustrate fundamental and potentially exploitable differences between 0D and 1D materials.     

Synthesis and electrical transport of single-crystal NH4V3O8 nanobelts

Monoclinic NH(4)V(3)O(8) single-crystalline nanobelts with widths of 80-180 nm, thicknesses of 50-100 nm, and lengths up to tens of micrometers have been synthesized at large scale in an ammonium metavanadate solution by a templates/catalysts-free route. Such nanobelts grow along the direction of [010]. The individual NH(4)V(3)O(8) nanobelt exhibits nonlinear, symmetric current/voltage (I/V) characteristics, with a conductivity of 0.1-1 S/cm at room temperature and a dielectric constant of approximately 130. The dominant conduction mechanism is based on small polaron hopping due to ohmic mechanism at low electric field below 249 V/cm due to Schottky emission at medium electric field between 249 and 600 V/cm and due to the Poole-Frenkel emission mechanism at high field above 600 V/cm.     

Small polaron hopping in Li(x)FePO4 solid solutions: coupled lithium-ion and electron mobility

Transition metal phosphates such as LiFePO(4) have been recognized as very promising electrodes for lithium-ion batteries because of their energy storage capacity combined with electrochemical and thermal stability. A key issue in these materials is to unravel the factors governing electron and ion transport within the lattice. Lithium extraction from LiFePO(4) results in a two-phase mixture with FePO(4) that limits the power characteristics owing to the low mobility of the phase boundary. This boundary is a consequence of low solubility of the parent phases, and its mobility is impeded by slow migration of the charge carriers. In principle, these limitations could be diminished in a solid solution, Li(x)FePO(4). Here, we show that electron delocalization in the solid solution phases formed at elevated temperature is due to rapid small polaron hopping and is unrelated to consideration of the band gap. We give the first experimental evidence for a strong correlation between electron and lithium delocalization events that suggests they are coupled. Furthermore, the exquisite frequency sensitivity of M?ssbauer measurements provides direct insight into the electron hopping rate.     

Electric field independent mobilities in molecular crystals

It is experimentally demonstrated that the electron drift mobility among the c' direction of anthracene and naphthalene is independent of the electric field to high electric fields (≈17 V/μm)at low temperatures (≈100 K). These data provide additional evidence against the applicability of small polaron models to molecular crystals and provide a challenge to recently proposed hopping models of charge transport which can account for the temperatures independence of the drift mobility.     

Drifting undulations in an achiral smectic C liquid crystal driven by a static electric field

We report a novel dc field-driven propagative instability associated with the thermally induced layer undulations of the smectic C phase in a phenyl benzoate. While the undulations are two-dimensional, the drift is observed only along the wave vector q parallel to the c director; undulations with orthogonal q and c remain stable. The drift, which is nonhysteretic, takes place in a hopping way between equilibrium positions; it has a well-defined threshold in a given region, but the threshold varies rather widely for different regions. The average propagation velocity increases linearly from zero with the control parameter epsilon until epsilon approximately 2 but tends to saturate thereafter. Significantly, the drift direction reverses on switching the field polarity. The mechanism responsible for the drift appears to involve a coupling between the transverse field gradients due to the conductivity anisotropy and the transverse component of the flexoelectric polarization.     

Thermoelectric power of superionic conductors

A technique for the calculation of the thermoelectric power in many-particle systems exhibiting hopping conduction is presented. It is shown that the combination of thermopower and conductivity data provides very useful information about the microscopic nature of the ion hopping process in solid electrolytes. There are two main qualitative features of the transport data. In most systems the heat of transport (determined from the thermopower) and the activation energy for conduction are nearly equal, and in systems exhibiting lattice gas order-disorder transitions, these parameters may change across the phase boundary. An extended polaron lattice gas model is presented which is consistent with these features of the data and which allows a determination of the relative strengths of static barrier and polaron effects on the hopping. The results of the model suggest that polaron coupling is relatively small in most materials except for those based on organic halides.     

Influence of silver doping on the electrical and magnetic behavior of La0.7Ca0.3MnO3 manganites

A systematic investigation of structural, magnetic and magnetotransport behavior of La_0.7Ca_0.3?xAg_xMnO₃ manganites has been undertaken. The X-ray diffraction shows a structural transformation from orthorhombic to rhombohedral with increasing Ag concentration. The undoped and 10% Ag substituted samples exhibit double transition in M–T curves. The electrical resistivity in the entire temperature range is fitted to effective medium approximation and phase separation models. The sign of S changes from negative to positive with increase in Ag doping. The low temperature thermopower data has been fitted to an equation containing diffusion, magnon drag and phonon drag terms. The paramagnetic insulting part of the TEP data has been analyzed using small polaron hopping mechanism.     

Hole polarons in pure BaTiO3 studied by computer modeling

Self‐trapped hole polarons in technologically important perovskite‐type ceramic of BaTiO₃ have been modeled by means of the quantum chemical method modified for crystal calculations. The computations are carried out in the self‐consistent field (SCF) manner using the embedded molecular cluster model. The spatial configuration of a hole polaron, displacement of defect‐surrounding atoms, and wave functions of the polaron ground and excited states are obtained and analyzed. The probability of spontaneous hole self‐trapping is estimated in the perfect lattice of the BaTiO₃ crystal by calculating the value of the hole self‐trapping energy as a difference of the atomic relaxation energy and the hole localization energy. This value is found to be negative, −1.49 eV, which demonstrates the preference of the self‐trapped polaron state. The calculated polaron absorption energy, 0.5 eV, is discussed in light of the available experimental data. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 358–366, 2000     

Charge transport in poly(methylphenylsilane): The case for superimposed disorder and polaron effects

Careful analysis of the temperature dependence of the hole mobility in poly (methylphenylsilane) indicates that the functional dependence is between an Arrhenius law and a ln μ ∝ T^?2 law as predicted by a model of disorder-controlled hopping. This is attributed to the superposition of disorder and polaron effects. A method is presented for separating the two contributions. The evolution of time-of-flight photocurrent transients with decreasing temperature is consistent with the disorder parameter derived from the temperature dependence of the mobility. © 1994 John Wiley & Sons, Inc.