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.     

Slow geminate‐charge‐pair recombination dynamics at polymer: Fullerene heterojunctions in efficient organic solar cells

We explore charge recombination dynamics at electron donor‐acceptor heterojunctions, formed between a semiconductor polymer (PCDTBT) and a fullerene derivative (PC₇₀BM), by means of combined time‐resolved photoluminescence and transient absorption spectroscopies. Following prompt exciton dissociation across the heterojunction, a subset of bound electron‐hole pairs recombines with a temperature‐independent rate distribution spanning submicrosecond timescales to produce luminescent charge‐transfer excitons (CTX). At 14 K, this slow mechanism is the dominant geminate charge recombination pathway, whereas we also observe CTX emission on subnanosecond timescales at 293 K. We thus find that at these temperatures, a fraction of the initial charge‐pair population is trapped deeply such that they only recombine slowly over a broad distribution of timescales by quantum tunneling. We identify geminate polaron pairs (GPP) as a reservoir of long‐lived localized states that repopulate the CTX up to microsecond timescales. The observation of such distributed geminate‐charge recombination highlights the importance of the molecular nature of specific donor–acceptor electronic interactions in defining the relaxation pathways of trapped GPP. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012     

Distinct Electron Conductance Regimes in Bacterial Decaheme Cytochromes

Shewanella oneidensis MR‐1 gains energy by extracellular electron transfer to solid surfaces. They employ c‐type cytochromes in two Mtr transmembrane complexes, forming a multiheme wire for electron transport across the cellular outer membrane. We investigated electron‐ and hole‐transfer mechanisms in the external terminal of the two complexes, MtrC and MtrF. Comparison of computed redox potentials with previous voltammetry experiments in distinct environments (isolated and electrode‐bound conditions of PFV or in vivo) suggests that these systems function in different regimes depending on the environment. Analysis of redox potential shifts in different regimes indicates strong coupling between the hemes via an interplay between direct Coulomb and indirect interactions through local structural reorganization. The latter results in the screening of Coulomb interactions and explains poor correlation of the strength of the heme‐to‐heme interactions with the distance between the hemes.     

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.     

Fermi and Coulomb holes of molecules in excited states

Correlation holes of electrons with the same (Fermi hole) and different (Coulomb hole) spins in the ground (X¹Σ⁺), first (A¹Σ⁺) and second (B¹II) excited states of LiH were constructed from full configuration interaction (CI ) wave functions. It was found that the shapes of both the Fermi and Coulomb holes in these states are dependent on the location of the reference electron. When the reference electron is chosen to be close to the Li nucleus, the Fermi correlation results in a large negative hole for all three states. However, the A¹Σ⁺ excited state is further characterized by displaying a second hole around the H nucleus, and in the B¹II state, the hole is elongated along the molecular axis. Coulomb correlation shows up strongly in the A¹Σ⁺ state and, in addition, there is clearly correlation of electrons at the two nuclei. These features of the correlation holes were compared with those from a two-Slater-determinant model wave function. The Hartree, Fermi, and Coulomb screening potentials in these states were also studied in the light of possible modeling of the correlation functionals for the excited states. © 1995 John Wiley & Sons, Inc.     

Photoinduced electron transfer in naphthalimide-pyridine systems: effect of proton transfer on charge recombination efficiencies

We studied the effect of proton-coupled electron transfer on lifetimes of the charge-separated radicals produced upon light irradiation of the thiomethyl-naphthalimide donor SMe-NI-H in the presence of nitro-cyano-pyridine acceptor (NO(2)-CN-PYR). The dynamics of electron and proton transfer were studied using femtosecond pump-probe spectroscopy in the UV/vis range. We find that the photoinduced electron transfer between excited SMe-NI-H and NO(2)-CN-PYR occurs with a rate of 1.1 × 10(9) s(-1) to produce radical ions SMe-NI-H(?+) and NO(2)-CN-PYR(?-). These initially produced radical ions in a solvent cage do not undergo a proton transfer, possibly due to unfavorable geometry between N-H proton of the naphthalimide and aromatic N-atom of the pyridine. Some of the radical ions in the solvent cage recombine with a rate of 2.3 × 10(10) s(-1), while some escape the solvent cage and recombine at a lower rate (k = 4.27 × 10(8) s(-1)). The radical ions that escape the solvent cage undergo proton transfer to produce neutral radicals SMe-NI(?) and NO(2)-CN-PYR-H(?). Because neutral radicals are not attracted to each other by electrostatic interactions, their recombination is slower that the recombination of the radical ions formed in model compounds that can undergo only electron transfer (SMe-NI-Me and NO(2)-CN-PYR, k = 1.2 × 10(9) s(-1)). The results of our study demonstrate that proton-coupled electron transfer can be used as an efficient method to achieve long-lived charge separation in light-driven processes.     

Unambiguous Diagnosis of Photoinduced Charge Carrier Signatures in a Stoichiometrically Controlled Semiconducting Polymer‐Wrapped Carbon Nanotube Assembly

Single‐walled carbon nanotube (SWNT)‐based nanohybrid compositions based on (6,5) chirality‐enriched SWNTs ([(6,5) SWNTs]) and a chiral n‐type polymer (S‐PBN(b)‐Ph₄PDI) that exploits a perylenediimide (PDI)‐containing repeat unit are reported; S‐PBN(b)‐Ph₄PDI‐[(6,5) SWNT] superstructures feature a PDI electron acceptor unit positioned at 3 nm intervals along the nanotube surface, thus controlling rigorously SWNT–electron acceptor stoichiometry and organization. Potentiometric studies and redox‐titration experiments determine driving forces for photoinduced charge separation (CS) and thermal charge recombination (CR) reactions, as well as spectroscopic signatures of SWNT hole polaron and PDI radical anion (PDI^?.) states. Time‐resolved pump–probe spectroscopic studies demonstrate that S‐PBN(b)‐Ph₄PDI‐[(6,5) SWNT] electronic excitation generates PDI^?. via a photoinduced CS reaction (τ_CS≈0.4 ps, Φ_CS≈0.97). These experiments highlight the concomitant rise and decay of transient absorption spectroscopic signatures characteristic of the SWNT hole polaron and PDI^?. states. Multiwavelength global analysis of these data provide two charge‐recombination time constants (τ_CR≈31.8 and 250 ps) that likely reflect CR dynamics involving both an intimately associated SWNT hole polaron and PDI^?. charge‐separated state, and a related charge‐separated state involving PDI^?. and a hole polaron site produced via hole migration along the SWNT backbone that occurs over this timescale.     

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 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     

Unpaired electrons at the second‐order reduced density matrix level: Covalent bonding,and coulomb and fermi correlations in closed shell systems

The usual one‐electron populations in atomic orbitals of closed shell systems are split into unpaired and paired at the (spin‐dependent) second‐order reduced density matrix level. The unpaired electron in an orbital is defined as the “simultaneous occurrence of an electron and an electron hole of opposite spins in the same spatial orbital,” which for simplicity is called “electropon.” The electropon population in a given orbital reveals whether and to what degree the Coulomb correlations, and hence, the chemical bonding between this orbital and the remaining orbitals of the system are globally favorable or unfavorable. The interaction of two electropons in two target orbitals reveals the quality (favorable or unfavorable) and the strength of the covalent bonding between these orbitals; this establish a bridge between the notion of “unpaired electrons” and the traditional covalent structure of valence‐bond (VB) theory. Favorable/unfavorable bonding between two orbitals is characterized by the positive/negative (Coulomb) correlation of two electropons of opposite spins, or alternatively, by the negative/positive (Fermi) correlation of two parallel spin electropons. A spin‐free index is defined, and the relationship between the electropon viewpoint for chemical bonding and the well‐known two‐electron Coulomb and Fermi correlations is established. Benchmark calculations are achieved for ethylene, hexatriene, benzene, pyrrole, methylamine, and ammonia molecules on the basis of physically meaningful natural orbitals. The results, obtained in the framework of both orthogonal and nonorthogonal population analysis methods, provide the same conceptual pictures, which are in very good agreement with elementary chemical knowledge and VB theory. © 2013 Wiley Periodicals, Inc.     

Transport through a mixed-valence molecular transistor in the sequential-tunneling regime: Theoretical insight from the two-site Peierls-Hubbard model

Transport through a mixed-valence system in the sequential-tunneling region is investigated using the master equation method and a simple two-site Peierls-Hubbard model that includes electron-phonon (e-p) coupling, electron hopping, and electron-electron (e-e) repulsion. The characteristics of Coulomb diamonds in the conductance spectra under three regimes are discussed. In the regime of zero e-p coupling, we found that the widths of Coulomb diamonds are dominated by the competition of electron-hopping and Coulomb repulsion. In the regime of weak and intermediate e-p coupling, by virtue of the normal-mode transformation we found that coupling to the symmetric-mode decreases the widths of Coulomb diamonds. In the regime of strong e-p coupling, an analytical expression for the widths of Coulomb diamonds can be derived using the small polaron transformation. The derived formula provides a new way to estimate e-e interactions and e-p couplings experimentally.     

Interchain coupling effects on dynamics of photoexcitations in conjugated polymers

Within an extended Su-Schrieffer-Heeger model including interchain interactions and the extended Hubbard model, the dynamical relaxation of photoexcitations in two coupled conjugated polymer chains is investigated by using a nonadiabatic evolution method. Initially, one of the two chains is photoexcited and the other chain is in the dimerized ground state. Due to the interchain interactions, the electron and/or the hole can be transferred from one chain to the other chain. For weak interchain coupling, the dynamical evolution of the lattice on the photoexcited chain is similar to that found in an isolate single chain case. With interchain interactions increasing, the amplitude of the distortions on the photoexcited chain decreases, and simultaneously, that on the other chain gradually increases. Until stronger interchain coupling, the deformations of the two chains have almost the same amplitude. Besides intrachain polaron-excitons and intrachain oppositely charged polaron pairs as found in single chain case, interchain polaron-excitons and interchain separated charged polaron pairs are obtained. The results show that the yield of interchain products increases and that of intrachain products decreases with interchain coupling increasing. Totally, the yield of charged polarons (including intrachain oppositely charged polaron pairs and interchain oppositely charged polaron pairs) is about 25%, in good agreement with results from experiments.     

Theoretical study of long oligothiophene dications: bipolaron vs polaron pair vs triplet state

A series of oligothiophene dications (from the sexithiophene dication to the 50-mer oligothiophene dication, nT2+, n = 6-50) were studied. Density functional theory (DFT) at the B3LYP/6-31G(d) level and, in some cases, also at BLYP/6-31Gd, was applied to study the singlet and triplet states of the whole series. We found that the singlet state is the ground state for all oligothiophene dications up to the 20-mer, and that the singlet and triplet states are degenerate for longer oligomers. Thus, the triplet state is never a pure ground state for these dications. We found that, for short oligothiophenes dication (e.g., 6T2+), the bipolaron state is the more important state, with only a small contribution made by the polaron pair state. For medium size oligothiophene dications (e.g., 14T2+), both the bipolaron state and the polaron-pair state contribute to the electronic structure. Finally, in long oligothiophene dications, such as 30T2+ and 50T2+, the contribution from the polaron pair state becomes dominant, and these molecules can be considered as consisting of two independent cation radicals or a polaron pair. Results from isodesmic reactions show that the stability of oligothiophene cation radicals over dications is inversely proportional to chain length. Small oligothiophene dications (n = 6-12) were studied at the CASSCF(m,m)/6-31G(d) (m = 4, 6, and 10) level. The major conclusions of this paper regarding the relative energy of the singlet state versus the triplet state and regarding the relative stability of the bipolaron versus the polaron pair were also supported by CASSCF calculations.     

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.     

The Interplay Between Lead Vacancy and Water Rationalizes the Puzzle of Charge Carrier Lifetimes in CH3NH3PbI3: Time‐Domain Ab Initio Analysis

The perovskite CH₃NH₃PbI₃ excited‐state lifetimes exhibit conflicting experimental results under humid environments. Using ab initio nonadiabatic (NA) molecular dynamics, we demonstrate that the interplay between lead vacancy and water can rationalize the puzzle. The lead vacancy reduces NA coupling by localizing holes, slowing electron–hole recombination. By creating a deep electron trap state, the coexistence of a neutral lead vacancy and water molecules enhances NA coupling, accelerating charge recombination by a factor of over 3. By eliminating the mid‐gap state by accepting two photoexcited electrons, the negatively charged lead vacancy interacting with water molecules increases the carrier lifetime over 2 times longer than in the pristine system. The simulations rationalize the positive and negative effects of water on the solar cell performance exposure to humidity.     

Exciton dissociation and charge carrier recombination processes in organic semiconductors

Exciton dissociation and charge recombination processes in organic semiconductors, with thermal effects taken into account, are described in this paper. Here, we analyzed the mechanisms of polaron-excitons dissociation into free charge carriers and the consequent recombination of those carriers under thermal effects on two parallel π-conjugated polymers chains electronically coupled. Our results suggest that exciton dissociation in a single molecule give rise to localized, polaron-like charge carrier. Besides, we concluded that in the case of interchain processes, the bimolecular polaron recombination does not lead to an usual exciton state. Rather, this type of recombination leads to an oscillating dipole between the two chains. The recombination time obtained here for these processes are in agreement with the experimental results. Finally, our results show that temperature effects are essential to the relaxation process leading to polaron formation in a single chain, as in the absence of temperature, this process was not observed. In the case of two chains, we conclude that temperature effects also help the bimolecular recombination process, as observed experimentally.     

Intact Four‐atom Organic Tetracation Stabilized by Charge Localization in the Gas Phase

Several features distinguish intact multiply charged molecular cations (MMCs) from other species such as monocations and polycations: high potential energy, high electron affinity, a high density of electronic states with various spin multiplicities, and charge‐dependent reactions. However, repulsive Coulombic interactions make MMCs quite unstable, and hence small organic MMCs are currently not readily available. Herein, we report that the isolated four‐atom molecule diiodoacetylene survives after the removal of four electrons via tunneling. We show that the tetracation remains metastable towards dissociation because of the localization (91–95 %) of the positive charges on the terminal iodine atoms, ensuring minimum Coulomb repulsion between adjacent atoms as well as maximum charge‐induced attractive dipole interactions between iodine and carbon. Our approach making use of iodines as the positively charged sites enables small organic MMCs to remain intact.     

Role of structural order and excess energy on ultrafast free charge generation in hybrid polythiophene/Si photovoltaics probed in real time by near-infrared broadband transient absorption

Despite the central role of light absorption and the subsequent generation of free charge carriers in organic and hybrid organic-inorganic photovoltaics, the precise process of this initial photoconversion is still debated. We employ a novel broadband (UV-Vis-NIR) transient absorption spectroscopy setup to probe charge generation and recombination in the thin films of the recently suggested hybrid material combination poly(3-hexylthiophene)/silicon (P3HT/Si) with 40 fs time resolution. Our approach allows for monitoring the time evolution of the relevant transient species under various excitation intensities and excitation wavelengths. Both in regioregular (RR) and regiorandom (RRa) P3HT, we observe an instant (<40 fs) creation of singlet excitons, which subsequently dissociate to form polarons in 140 fs. The quantum yield of polaron formation through dissociation of delocalized excitons is significantly enhanced by adding Si as an electron acceptor, revealing ultrafast electron transfer from P3HT to Si. P3HT/Si films with aggregated RR-P3HT are found to provide free charge carriers in planar as well as in bulk heterojunctions, and losses are due to nongeminate recombination. In contrast for RRa-P3HT/Si, geminate recombination of bound carriers is observed as the dominant loss mechanism. Site-selective excitation by variation of pump wavelength uncovers an energy transfer from P3HT coils to aggregates with a 1/e transfer time of 3 ps and reveals a factor of 2 more efficient polaron formation using aggregated RR-P3HT compared to disordered RRa-P3HT. Therefore, we find that polymer structural order rather than excess energy is the key criterion for free charge generation in hybrid P3HT/Si solar cells.