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. Drift can take place in a region with all the same bases, for example, A's, by the polaron dropping an A on the trailing edge and picking up an A on the leading edge. For drift that is not too rapid, the necessity of the polarization changing as the polaron moves exerts a drag on the polaron. We calculate the drag by using a model introduced earlier to describe the polaron. We find the drag to be proportional to the velocity of the polaron and to the orientational relaxation time of the water molecules. The drag is also a function of the Coulomb interactions of the fractional charges on the bases constituting the polaron, as modified by the polarization charge induced in the solution. The diffusion rate and mobility for all A polarons, calculated taking into account the drag, are 8 x 10(-5) cm(2)/s and 3 x 10(-3) cm(2)/(V s), respectively. We believe that in the experimental studies that have been carried out on hole propagation in a series of A's it was drift being observed rather than the hopping of a localized hole between adjacent A's, as was assumed to be the case.     

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.     

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 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.     

Elementary steps for charge transport in DNA: thermal activation vs. tunneling

Using stacks of Watson–Crick base pairs as an important example of multichromophoric molecular assemblies, we studied charge migration in DNA with special emphasis on the mechanism of hole hopping between neighboring guanines (G) connected by the adenine–thymine (AT) bridge. The tight-binding model proposed for this elementary step shows that for short AT bridges, hole transfer between two G bases proceeds via quantum mechanical tunneling. By contrast, hopping over long bridges requires thermal activation. The condition for crossover between tunneling and thermal activation near room temperature is specified and applies to the analysis of experimental data. We show that thermal activation dominates, if the bridge between two G bases contains more than three AT pairs. Our theoretical findings predict that the replacement of AT base pairs by GC pairs increases the efficiency of hole transport only in the case of short base pair sequences. For long sequences, however, the opposite effect is expected.     

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.     

Charge carrier photogeneration and transport in poly(methyl-phenylsilylene)

Optical excitations in poly(methyl-phenylsilylene) can be realized within the framework of a chemical bond in the polymer backbone or a side group skeleton. A charge transfer of the electron from the main chain to a side group is necessary to form stable ion-pairs. Dissociation of the ion-pairs can be described in terms of the Onsager theory of geminate recombination. The photogeneration efficiency can be improved by an electron acceptor doping. The charge carrier transport is influenced by two factors: delocalized movement inside the conjugated domains and intra- and interchain hopping. The electrostatic interactions of polar additives with polarons influence the polaron binding energy and the charge hopping.     

Porphyrin Supramolecule as Surface Carrier Modulator Imparts Hole Transporter with Enhanced Mobility for Perovskite Photovoltaics

Modulating the surface charge transport behavior of hole transport materials (HTMs) would be as an potential approach to improve their hole mobility, while yet realized for fabricating efficient photovoltaic devices. Here, an oxygen bridged dimer-based monoamine Fe^III porphyrin supramolecule is prepared and doped in HTM film. Theoretical analyses reveal that the polaron distributed on dimer can be coupled with the parallel arranged polarons on adjacent dimers. This polaron coupling at the interface of supramolecule and HTM can resonates with hole flux to increase hole transport efficiency. Mobility tests reveal that the hole mobility of doped HTM film is improved by 8-fold. Doped perovskite device exhibits an increased efficiency from 19.8 % to 23.2 %, and greatly improved stability. This work provides a new strategy to improve the mobility of HTMs by surface carrier modulation, therefore fabricating efficient photovoltaic devices.     

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.     

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.     

Negative polaron and triplet exciton diffusion in organometallic "molecular wires"

The dynamics of negative polaron and triplet exciton transport within a series of monodisperse platinum (Pt) acetylide oligomers is reported. The oligomers consist of Pt-acetylide repeats, [PtL(2)-C≡C-Ph-C≡C-](n) (where L = PBu(3) and Ph = 1,4-phenylene, n = 2, 3, 6, and 10), capped with naphthalene diimide (NDI) end groups. The Pt-acetylide segments are electro- and photoactive, and they serve as conduits for transport of electrons (negative polaron) and triplet excitons. The NDI end groups are relatively strong acceptors, serving as traps for the carriers. Negative polaron transport is studied by using pulse radiolysis/transient absorption at the Brookhaven National Laboratory Laser-Electron Accelerator Facility (LEAF). Electrons are rapidly attached to the oligomers, with some fraction initially residing upon the Pt-acetylide chains. The dynamics of transport are resolved by monitoring the spectral changes associated with transfer of electrons from the chain to the NDI end group. Triplet exciton transport is studied by femtosecond-picosecond transient absorption spectroscopy. Near-UV excitation leads to rapid production of triplet excitons localized on the Pt-acetylide chains. The excitons transport to the chain ends, where they are annihilated by charge separation with the NDI end group. The dynamics of triplet transport are resolved by transient absorption spectroscopy, taking advantage of the changes in spectra associated with decay of the triplet exciton and rise of the charge-separated state. The results indicate that negative polarons and excitons are transported rapidly, on average moving distances of ~3 nm in less than 200 ps. Analysis of the dynamics suggests diffusive transport by a site-to-site hopping mechanism with hopping times of ~27 ps for triplets and <10 ps for electrons.     

Charge Carrier Transport Mechanism in Ta2O5, TaON,and Ta3N5 Studied by Applying Polaron Hopping and Bandlike Models

TaON and Ta₃N₅ are considered promising materials for photocatalytic and photoelectrochemical water splitting. In contrast, their counterpart Ta₂O₅ does not exhibit good photocatalytic performance. This may be explained with the different charge carrier transport mechanisms in these materials, which are not well understood yet. Herein, we investigate the charge transport properties in Ta₂O₅, TaON, and Ta₃N₅ by polaron hopping and bandlike models. First, the polaron binding energies were calculated to evaluate whether the small polaron occurs in these materials. Then we performed calculations to localize the excess carriers as small polarons using a hybrid density functional. We find that the small polaron hopping is the charge transfer mechanism in Ta₂O_5, whereas our calculations indicate that this mechanism may not occur in TaON and Ta₃N₅. We also investigated the bandlike model mechanism by calculating the charge carrier mobility of these materials using the effective mass approximation, but the calculated mobility is not consistent with experimental results. This study is a first step towards understanding charge transport in oxynitrides and nitrides and furthermore establishes a simple rule to determine whether a small polaron occurs in a material.     

Poly(silylene)s: charge carrier photogeneration and transport

An Erratum has been published for this article in Polymers for Advanced Technologies 12(10)2001, 603. Poly(diorganylsilylene)s can be excited within the framework of Si bonds in the polymer backbone as well as within a side group skeleton. An electron transfer from the main chain to a side group or an interchain electron transfer is necessary to form a quasi‐stable ion‐pair. Dissociation of the ion‐pair in the external electric field can be described in terms of the Onsager theory of geminate recombination. The charge carrier transport proceeds predominantly along σ‐delocalized Si backbone with participation of interchain hopping and polaron formation. A model of disordered polarons seems to be adequate to describe the charge carrier transport properties. Copyright © 2001 John Wiley & Sons, Ltd.     

Sequence dependence of charge transport through DNA domains

Here we examine the photooxidation of two kinetically fast electron hole traps, N4-cyclopropylcytosine (CPC) and N2-cyclopropylamine-guanosine (CPG), incorporated in DNA duplexes of various sequence using different photooxidants. DNA oxidation studies are carried out either with noncovalently bound [Ru(phen)(dppz)(bpy')]3+ (dppz = dipyridophenazine) and [Rh(phi)2(bpy)]3+ (phi = phenanthrenequinone diimine) or with anthraquinone tethered to DNA. Because the cyclopropylamine-substituted bases decompose rapidly upon oxidation, their efficiency of decomposition provides a measure of relative hole localization. Consistent with a higher oxidation potential for CPC versus CPG in DNA, CPC decomposes with photooxidation by [Rh(phi)2(bpy)]3+, while CPG undergoes ring-opening both with photoexcited [Rh(phi)2(bpy)]3+ and with [Ru(phen)(dppz)(bpy')]3+. Anthraquinone-modified DNA assemblies of identical base composition but different base sequence are also probed. Single and double base substitutions within adenine tracts modulate CPC decomposition. In fact, the entire sequence within the DNA assembly is seen to govern CPC oxidation, not simply the bases intervening between CPC and the tethered photooxidant. These data are reconciled in the context of a mechanistic model of conformationally gated charge transport through delocalized DNA domains. Photooxidations of anthraquinone-modified DNA assemblies containing both CPC and CPG, but with varied distances separating the modified bases, point to a domain size of at least three bases. Our model for DNA charge transport is distinguished from polaron models. In our model, delocalized domains within the base pair stack form transiently based upon sequence-dependent DNA structure and dynamics. Given these results, DNA charge transport is indeed remarkably sensitive to DNA sequence and structure.     

Temperature dependence of small polaron population decays in iron-doped lithium niobate by Monte Carlo simulations

The population decay of light-induced small polarons in iron-doped lithium niobate is simulated by a Monte-Carlo method on the basis of Holstein's theory. The model considers random walks of both bound polarons (Nb_Li⁴⁺) and free polarons (Nb_Nb⁴⁺) ending to deep traps (Fe_Li³⁺). The thermokinetic interplay between polaron species is introduced by trapping and de-trapping rates at niobium antisites (Nb_Li). The decay of the Nb_Li⁴⁺ population proceeds by three possible channels: direct trapping at Fe_Li³⁺ sites, hopping on niobium antisites and hopping on Nb regular sites after conversion to the free state. Up to three regimes, each one reflecting the predominance of one of these processes, appear with different activation energies in the Arrhenius plots of the decay time. The influence of Fe_Li and Nb_Li concentrations on the transition temperatures is evidenced. For both polaron species, the length of the final hop (trapping length) is found much larger than the usual hopping length and decreases at rising temperature. This trap size effect is a natural consequence of Holstein's theory and may explain some unclear features of polaron-related light-induced phenomena, such as the temperature-dependent stretching exponent of light-induced absorption decays and the anomalous increase of the photoconductivity at high doping levels.     

A unified theory for charge-carrier transport in organic crystals

To characterize the crossover from bandlike transport to hopping transport in molecular crystals, we study a microscopic model that treats electron-phonon interactions explicitly. A finite-temperature variational method combining Merrifield's transformation with Bogoliubov's theorem is developed to obtain the optimal basis for an interacting electron-phonon system, which is then used to calculate the bandlike and hopping mobilities for charge carriers. Our calculations on the one dimensional (1D) Holstein model at T=0 K and finite temperatures show that the variational basis gives results that compared favorably to other analytical methods. We also study the structures of polaron states at a broad range of parameters including different temperatures. Furthermore, we calculate the bandlike and hopping mobilities of the 1D Holstein model in different parameters and show that our theory predicts universal power-law decay at low temperatures and an almost temperature independent behavior at higher temperatures, in agreement with experimental observations. In addition, we show that as the temperature increases, hopping transport can become dominant even before the polaron state changes its character. Thus, our result indicates that the self-trapping transition studied in conventional polaron theories does not necessarily correspond to the bandlike to hopping transition in the transport properties in organic molecular crystals. Finally, a comparison of our 1D results with experiments on ultrapure naphthalene crystals suggests that the theory can describe the charge-carrier mobilities quantitatively across the whole experimental temperature range.     

On the Distance‐Independent Hole Transfer over Long (A⋅T)n‐Sequences in DNA

Electron holes can travel through DNA double strands over long distances in a multistep ‘hopping’ process. But the influence of the DNA sequence on this process is still not understood in all details. We have carried out new experiments to understand the recent observation that the efficiency of the hole transport between guanines (G), which are separated from each other by long adenine?thymine (A?T) sequences, is nearly independent of the length of the (A?T)_n sequence for n ≥ 4. For this purpose, a new synthesis of the modified adenosine 16 and its incorporation into a DNA double strand was worked out. Subsequent experiments demonstrated that the hole transport between GGG units and the H₂O trapping of the guanine radical cation display similar rates. We conclude that the charge must be already partially equilibrated before being trapped by H₂O. Thus, the weak distance effect is caused not only by the rate of the hole transport, but also by its equilibration over the (A ? T)_n sequence.     

Hole polarons in poly(G)-poly(C) and poly(A)-poly(T) DNA molecules

The polaron might play an important role in the process of charge migration through duplex DNA stack. In the present work, we investigate properties of hole polarons in DNA molecules containing identical base pairs, such as poly(G)-poly(C) and poly(A)-poly(T), An extended tight-binding model (extended Su-Schrieffer-Heeger model), which involves the effect of an electric field in the direction of DNA stack, will be introduced. The transfer integral and electron-phonon coupling parameters in this model are obtained according to ab initio calculation for different base pair dimers. Calculations reveal that the polaron in poly(A)-poly(T) has a wider shape and a higher mobility under a specific electric field than that in poly(G)-poly(C) DNA stack.     

Computational model of hole transport in DNA

A computational model based on the molecular dynamics (MD) simulation for the hole transport in DNA has been developed and applied to study hole current in DNA strands consisting of different numbers of GC pairs. The approach is based on the hopping mechanism which is thermally activated. The calculations show that the hole hopping intensifies with the temperature and the transport rate increases in agreement with the experimental evidence. It is also determined that the degree of structural ordering in the DNA strand enhances the hole conductivity and reasons are provided why this may occur.     

DNA hole transport on an electrode: application to effective photoelectrochemical SNP typing

A useful feature of DNA is that long-range hole transport through DNA is readily achieved. Photostimulated long-range hole transport through DNA has prospective use in the development of a conceptually new electrochemical single-nucleotide polymorphism (SNP) typing method for use as a versatile platform for gene diagnostics and pharmacogenetics. We have applied artificial DNAs designed for photostimulated long-range hole transport through DNA to SNP typing. By hybridizing photosensitizer-equipped DNA probes, immobilized on gold working electrodes, with a target DNA strand containing an SNP site, we observed a cathodic photocurrent, which markedly changed depending on the nature of the base at the specific site. The use of a combination of hole-transporting bases constitutes a very powerful method for a single-step electrochemical assay applicable to SNP typing of all types of sequences.