DNA double-helix-mediated long-range electron transfer

A theoretical analysis based upon large-scale self-consistent Hartree-Fock calculations at a semiempirical quantum theory level (CNDO/S) is performed to investigate long-range electron transfer in a donor-DNA-acceptor molecule, where the donor and acceptor moieties are tethered to the DNA. The π-stacked base pairs are found to dominate the long-range electronic coupling. Despite the π-electron mediated coupling, the exponential distance decay constant of the electron transfer rate is ∼ 1.2–1.6 Å⁻¹, values typical of electron transfer proteins. The calculated long-range electron transfer rate of the order of 10⁶ s⁻¹ for a metal-to-metal distance of 21 Å is found to be in agreement with kinetic measurements by Meade and Kayyem. Based on the current analysis, the π-electrons dominate the long-range electronic coupling interactions in DNA, but they do not lead to one-dimensional molecular wire-like properties. © 1996 John Wiley & Sons, Inc.     

Energy transfer in polymers—IV. Singlet and triplet energy transfer in polymethylvinylketone films

The efficiency of transfer from the triplet of polymethylvinylketone (PMVK) to naphthalene has been measured at 77°K. The critical distance of transfer according to Hirayama is 11 · 3 Å. This is the usual value of R_o for exchange interaction without migration. Singlet energy transfer from the polymer to benzophenone occurs when donor and acceptor are very close together, at room temperature. In the system PMVK-anthracene, the emission spectrum shows that microcrystals of the additive are formed in the polymer even at low concentration.     

Photoinduced electron transfer and geminate recombination in liquids on short time scales: Experiments and theory

The coupled processes of intermolecular photoinduced forward electron transfer and geminate recombination between the (hole) donor (Rhodamine 3B) and (hole) acceptors (N,N-dimethylaniline) are studied in three molecular liquids: acetonitrile, butyronitrile, and benzonitrile. Two color pump-probe experiments on time scales from approximately 100 fs to hundreds of picoseconds give information about the depletion of the donor excited state due to forward electron transfer and the survival kinetics of the radicals produced by forward electron transfer. The data are analyzed with a model presented previously that includes distance dependent forward and back electron transfer rates, donor and acceptor diffusion, solvent structure, and the hydrodynamic effect in a mean-field theory of through solvent electron transfer. The forward electron transfer is in the normal regime, and the Marcus equation for the distance dependence of the transfer rate is used. The forward electron transfer data for several concentrations in the three solvents are fitted to the theory with a single adjustable parameter, the electronic coupling matrix element Jf at contact. Within experimental error all concentrations in all three solvents are fitted with the same value of Jf. The geminate recombination (back transfer) is in the inverted region, and semiclassical treatment developed by Jortner [J. Chem. Phys. 64, 4860 (1976)] is used to describe the distance dependence of the back electron transfer. The data are fitted with the single adjustable parameter Jb. It is found that the value of Jb decreases as the solvent viscosity increases. Possible explanations are discussed.     

Ultrafast energy transfer of one-dimensional excitons between carbon nanotubes: a femtosecond time-resolved luminescence study

Excitation energy transfer has long been an intriguing subject in the fields of photoscience and materials science. Along with the recent progress of photovoltaics, photocatalysis, and photosensors using nanoscale materials, excitation energy transfer between a donor and an acceptor at a short distance (≤1-10 nm) is of growing importance in both fundamental research and technological applications. This Perspective highlights our recent studies on exciton energy transfer between carbon nanotubes with interwall (surface-to-surface) distances of less than ～1 nm, which are equivalent to or shorter than the size of one-dimensional excitons in carbon nanotubes. We show exciton energy transfer in bundles of single-walled carbon nanotubes with the interwall distances of ～0.34 and 0.9 nm (center-to-center distances ～1.3-1.4 and 1.9 nm). For the interwall distance of ～0.34 nm (center-to-center distance ～1.3-1.4 nm), the transfer rate per tube from a semiconducting tube to adjacent semiconducting tubes is (1.8-1.9) × 10(12) s(-1), and that to adjacent metallic tubes is 1.1 × 10(12) s(-1). For the interwall distance of ～0.9 nm (center-to-center distance ～1.9 nm), the transfer rate per tube from a semiconducting tube to adjacent semiconducting tubes is 2.7 × 10(11) s(-1). These transfer rates are much lower than those predicted by the F?rster model calculation based on a point dipole approximation, indicating the failure of the conventional F?rster model calculations. In double-walled carbon nanotubes, which are equivalent to ideal nanoscale coaxial cylinders, we show exciton energy transfer from the inner to the outer tubes. The transfer rate between the inner and the outer tubes with an interwall distance of ～0.38 nm is 6.6 × 10(12) s(-1). Our findings provide an insight into the energy transfer mechanisms of one-dimensional excitons.     

Charge transfer excitations in cofacial fullerene-porphyrin complexes

Porphyrin and fullerene donor-acceptor complexes have been extensively studied for their photo-induced charge transfer characteristics. We present the electronic structure of ground states and a few charge transfer excited states of four cofacial porphyrin-fullerene molecular constructs studied using density functional theory at the all-electron level using large polarized basis sets. The donors are base and Zn-tetraphenyl porphyrins and the acceptor molecules are C(60) and C(70). The complexes reported here are non-bonded with a face-to-face distance between the porphyrin and the fullerene of 2.7 to 3.0 A?. The energies of the low lying excited states including charge transfer states calculated using our recent excited state method are in good agreement with available experimental values. We find that replacing C(60) by C(70) in a given dyad may increase the lowest charge transfer excitation energy by about 0.27 eV. Variation of donor in these complexes has marginal effect on the lowest charge transfer excitation energy. The interfacial dipole moments and lowest charge transfer states are studied as a function of face-to-face distance.     

Direct chemical evidence for charge transfer between photoexcited 2-aminopurine and guanine in duplex DNA

Photoexcited 2-aminopurine (Ap*) is extensively exploited as a fluorescent base analogue in the study of DNA structure and dynamics. Quenching of Ap* in DNA is often attributed to stacking interactions between Ap* and DNA bases, despite compelling evidence indicating that charge transfer (CT) between Ap* and DNA bases contributes to quenching. Here we present direct chemical evidence that Ap* undergoes CT with guanine residues in duplex DNA, generating oxidative damage at a distance. Irradiation of Ap in DNA containing the modified guanine, cyclopropylguanosine (CPG), initiates hole transfer from Ap* followed by rapid ring opening of the CPG radical cation. Ring opening accelerates hole trapping to a much shorter time regime than for guanine radicals in DNA; consequently, trapping effectively competes with back electron transfer (BET) leading to permanent CT chemistry. Significantly, BET remains competitive, even with this much faster trapping reaction, consistent with measured kinetics of DNA-mediated CT. The distance dependence of BET is sharper than that of forward CT, leading to an inverted dependence of product yield on distance; at short distances product yield is inhibited by BET, while at longer distances trapping dominates, leading to permanent products. The distance dependence of product yield is distinct from forward CT, or charge injection. As with photoinduced charge transfer in other chemical and biological systems, rapid kinetics for charge injection into DNA need not be associated with a high yield of DNA damage products.     

Charge Transfer in 1,8-Naphthalimide: A Combined Theoretical and Experimental Approach

Photophysics of 1,8-naphthalimide (NAPMD) in different solvents has been delineated in this paper. Theoretically calculated bond distance of N–H and C=O groups rule out any intramolecular proton transfer in the excited state. Concomitant increase in negative charge on O atom compared to N atom and dipole moment hints at possible intramolecular charge transfer. Progressive redshift with polarity of solvents in emission and absorption spectra also confirms the theoretical prediction. Weakening of N–H bond helps hydrogen abstraction and anion formation in water with decay time of 2.54 ns through intermolecular proton transfer. This was corroborated from the ground state photoexcitation of laboratory synthesized anion of NAPMD. Amide hydrolysis in higher pH and excess proton availability at low pH are responsible for anion emission quenching. A possible electron transfer diminishes phosphorescence at 77 K with changing pH.     

基于电子结构理论的能量转移速率计算

以高精度的完全活化空间自洽场及二级微扰能量校正(CASPT2//CASSCF)电子结构计算为基础, 利用Förster和Dexter 2种模型, 建立了能量转移速率的数值模拟方案, 并将其用于2种典型的有机发光二极管发光分子Pt-4和FPt的光物理过程的计算, 结果发现, 蓝光态到红光态的能量转移和蓝光态到基态的辐射跃迁之间的竞争决定了发光颜色的浓度依赖性, 阐明了2个配合物溶液体系发射白光的微观机制. 通过比较2个配合物单体和双体不同电子态的结构和性质的差异, 对发光颜色与溶液浓度依赖性的微观本质给出了新的理论. 此外, 本文建立的能量转移速率模拟方案, 同时适用于其它激发态电子结构方法, 因此具有普适性.     

Energy gap law of electron transfer in nonpolar solvents

We investigate the energy gap law of electron transfer in nonpolar solvents for charge separation and charge recombination reactions. In polar solvents, the reaction coordinate is given in terms of the electrostatic potentials from solvent permanent dipoles at solutes. In nonpolar solvents, the energy fluctuation due to solvent polarization is absent, but the energy of the ion pair state changes significantly with the distance between the ions as a result of the unscreened strong Coulomb potential. The electron transfer occurs when the final state energy coincides with the initial state energy. For charge separation reactions, the initial state is a neutral pair state, and its energy changes little with the distance between the reactants, whereas the final state is an ion pair state and its energy changes significantly with the mutual distance; for charge recombination reactions, vice versa. We show that the energy gap law of electron-transfer rates in nonpolar solvents significantly depends on the type of electron transfer.     

Fluorescence spectroscopic studies on binding of a flavonoid antioxidant quercetin to serum albumins

Binding of quercetin to human serum albumin (HSA) was studied and the binding constant measured by following the red-shifted absorption spectrum of quercetin in the presence of HSA and the quenching of the intrinsic protein fluorescence in the presence of different concentrations of quercetin. Fluorescence lifetime measurements of HSA showed decrease in the average lifetimes indicating binding at a location, near the tryptophan moiety, and the possibility of fluorescence energy transfer between excited tryptophan and quercetin. Critical transfer distance (R _o ) was determined, from which the mean distance between tryptophan-214 in HSA and quercetin was calculated. The above studies were also carried out with bovine serum albumin (BSA).     

Theoretical prediction of the contact distance dependence of the electron transfer reactivity of the ClO/ClO− coupling system

On the basis of the structures and properties of the ClO/ClO^? system obtained at the density functional theory (DFT) (UB3LYP) level, employing the 6‐311+G(3df) standard basis set, the electron transfer reactivity of this system is investigated. The results indicate that there are five possible stable coupling complexes that correspond to the generous minima on the global potential energy surfaces (PES). The most stable coupling complex is planar EC4, in which there is a O? O linkage with two trans‐Cl atoms. Their stabilization energies are calculated to be 20.57 (EC1: C₁), 20.54 (EC2: C₂, ²B), 20.69 (EC3: C₁), 20.70 (EC4: C_s, ²A′), and 20.69 (EC.5: C_2h, ²B_u) kcal/mol at the B3LYP/6‐311+G(3df) level; with the correction of the basis set superposition error (BSSE), the stability order of these encounter complexes is EC4 > EC.5 > EC3 > EC1 > EC2. Based on the five encounter complexes, five coupling modes are designed for the study of the electron transfer reactivity of this system. The dissociation energy curves at the activated states and the corresponding activation energies of these five coupling modes are obtained and are compared at the B3LYP/6‐311+G(3df) and MP2/6‐311+G* levels. The inapplicability of DFT methods has also been discussed in this article in predicting the energy curves, especially with a long contact distance, in which DFT methods give the abnormal behavior for the dissociations of the complexes caused by the “inverse symmetry breaking” problem. On the basis of the golden rule of the time‐dependent perturbation theory, the electron transfer reactivity and the contact distance dependence of the various electron transfer kinetics parameters (e.g., activation energy, coupling matrix element) have been analyzed at the UMP2(full)/6‐311+G* level. The electron transfer can take place over a range of contact distances, but the most effective coupling distance corresponds to only a small range. The coupling orientation analyses also indicate that the most favorable coupling mode to the electron transfer does not always correspond to the most stable encounter complex mechanism. Some highly energetic coupling modes are more favorable for the electron transfer. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Energy Transfer between Flavin and Cytochrome c

Energy transfer between photoexcited flavin and cytochrome c has been investigated in order to estimate intermolecular forces between flavin and cytochrome c. The quenching of the fluorescence of flavin by cytochrome c excited at 372 nm was found to be much greater than that excited at 465 nm. This dependence of the quenching on the exciting wavelength is considered to be due to the “prerelaxational” fast energy transfer. From the analysis of the quenching of the fluorescence of FMN and lumiflavin by cytochrome c excited at 465 nm, it was concluded that 1) the quenching is mainly controlled by resonance energy transfer, and 2) the heterogeneous dispersion state of molecules due to electrostatic forces makes the critical transfer distance, R ₀, of the resonance process longer than the real distance. For the quenching of the fluorescence of flavodoxin by cytochrome c, it was found that complex formation is a dominant process and is controlled to a great extent by electrostatic forces. Furthermore, fluorescence decay curves were measured by a single-photon counting method in order to estimate the dynamic processes of flavin fluorescence. The results also showed that the resonance process exists in the energy transfer between flavin and cytochrome c.     

Photoinduced electron transfer in hydrogen bonded donor--acceptor systems. Free energy and distance dependence studies and an analysis of the role of diffusion.

The free energy dependence of electron transfer in a few small-molecule donor--acceptor systems having hydrogen-bonding appendages was studied to evaluate the role of diffusion in masking the inverted region in bimolecular PET reactions. A small fraction of the probe molecules associate and this led to the simultaneous observation of unimolecular and diffusion-mediated quenching of the probe fluorescence. Free energy dependence studies showed that the unimolecular electron transfer obeys Marcus behavior and the diffusion-mediated electron transfer obeys Rehm--Weller behavior. The absence of an inverted region in bimolecular PET reactions is thus attributed to diffusion. The results of the free energy dependence studies suggest that distance dependence of electron transfer plays a role in masking the inverted region. To ascertain this aspect we have carried out a study of the distance dependence of electron transfer in the hydrogen-bonded donor--acceptor systems. For a system in the normal region an exponential rate decrease was observed. For a system in the inverted region it was observed that the rate depends very feebly on distance. Thus distance dependence studies did not confirm the prediction of enhanced rates at larger distances in the inverted region.     

Study on the binding of puerarin to bovine serum albumin by isothermal titration calorimetry and spectroscopic approaches

The interaction of a flavonoid molecule (puerarin) with bovine serum albumin (BSA) was characterized by isothermal titration calorimetry (ITC), optical spectroscopic technique, and molecular modeling method under physiological conditions. The binding parameters for the reaction were calculated according to ITC experiments at different temperatures. The thermodynamic parameters, negative enthalpy changes (ΔH), and positive entropy (ΔS) indicated that the binding processes were entropically driven. The alterations of protein secondary structure in the presence of puerarin in aqueous solution were estimated by the evidences from FT-IR and CD spectroscopy with reductions of α-helices. On the basis of fluorescence resonance energy transfer (FRET) between excited tryptophan in BSA and BSA bound puerarin, the critical transfer distance and mean distance between tryptophan in BSA and puerarin were estimated.     

吲哚-9,10-二甲氧基蒽体系分子内能量转移反应的研究

本文分别用亚甲基和甾体雌二醇刚性链将吲哚与9,10-二甲氧基蒽连接起来,合成了两个分子内能量转移体系,研究了分子內吲哚的激发能向9,10-二甲氧基蒽的传递过程与距离及溶剂环境的关系;发现在两个体系中激发吲哚都可以发生从吲哚到9,10-二甲氧基蒽的单重态-单重态能量转移,在远距离的条件下,能量转移按偶极子-偶极子共振机制进行,由实验结果,根据Forster公式计算得到的给体与受体之间的距离与用分子模型测量得到的距离是一样的,并研究了溶剂极性对能量转移过程的影响。     

Sequence, structure and energy transfer in DNA

Excitation energy transfer in DNA has similarities to charge transfer, but the transport is of an excited state, not of mass or charge. Use of the fluorescent, modified adenine base 2‐aminopurine (2AP) as an energy trap in short (3‐ to 20‐base) single‐ and double‐stranded DNA oligomers is reviewed. Variation of 2AP’s neighboring sequence shows (1) relatively efficient transfer from adenine compared to that from cytosine and thymine, (2) efficient transfer from guanine, but only when 2AP is at the 3′ end, (3) approximate equality of efficiencies for 3′ to 5′ and 5′ to 3′ directional transfer in adenine tracks. The overall, average transfer distance at room temperature is about four adenine bases or less before de‐excitation. The transfer fluorescence excitation spectral shape is similar to that of the absorption spectrum of the neighboring normal bases, confirming that initial excitation of the normal bases, followed by emission from 2AP (i.e. energy transfer), is occurring. Transfer apparently may take place both along one strand and cross‐strand, depending on the oligomer sequence. Efficiency increases when the temperature is decreased, rising above 50% (overall efficiency) in decamers of adenine below ?60°C (frozen media). Modeling of the efficiencies of transfer from the nearest several adenine neighbors of 2AP in these oligomers suggests that the nearest two neighbors transfer with near 100% efficiency. As bases in B DNA, as well as in single‐stranded DNA, are separated by less than 5 Å (less than the size of a base), standard Förster transfer theory should not apply. Indeed, while both theory and experiment show efficiency decreasing with donor–acceptor distance, the experimental dependence clearly disagrees with Förster 1/r⁶ dependence. It is not yet clear what the best theoretical approach is, but any calculation must deal accurately with the excited states of bases, including strong base–base interactions and structural fluctuations, and should reflect the increase of efficiency with temperature decrease and the relative insensitivity to strandedness (single, double). Attempts to use DNA as a molecular “fiber optic” face three primary challenges. First, reasonable efficiency over more than a base or two occurs only in adenine stretches at temperatures well below freezing. Second, transfer in these adenine tracks is efficient in both directions. Third, absorption of UV light occurs randomly, making excitation at a specific site on this “fiber optic” a challenge.     

Fluorescence resonance energy transfer (FRET) in chemistry and biology: Non-F?rster distance dependence of the FRET rate

Fluorescence resonance energy transfer (FRET) is a popular tool to study equilibrium and dynamical properties of polymers and biopolymers in condensed phases and is now widely used in conjunction with single molecule spectroscopy. In the data analysis, one usually employs the F?rster expression which predicts (l/R ⁶) distance dependence of the energy transfer rate. However, critical analysis shows that this e_xpression can be of rather limited validity in many cases. We demonstrate this by explicitly considering a donor-acceptor system, polyfluorene (PF₆)-tetraphenylporphyrin (TPP), where the size of both donor and acceptor is comparable to the distance separating them. In such cases, one may expect much weaker distance (as l/R ² or even weaker) dependence. We have also considered the case of energy transfer from a dye to a nanoparticle. Here we find l/R ⁴ distance dependence at large separations, completely different from F?rster. We also discuss recent application of FRET to study polymer conformational dynamics. Dedicated to Prof J Gopalakrishnan on his 62nd birthday.     

Energy transfer in polymers—VII: Triplet energy migration and transfer in copolymers styrene-vinylbenzophenone

The efficiency of triplet energy transfer from the benzophenone group to naphthalene has been studied in a series of copolymers styrene-vinylbenzophenone, either as films or in glassy solutions at 77 K. Energy migration has been shown to be efficient in both cases. For a given copolymer, Hirayama's critical distance is larger in films than in glassy solutions. In both cases, it decreases with decreasing vinylbenzophenone content. The number of jumps between identical molecules during the life-time of the excited state has been calculated according to the hopping model and Voltz theory on energy migration. The results show that energy migration in these solid polymers is not the consequence of exchange interactions decreasing exponentially with the mean distance between the chromophores. Organized regions, characterized by a higher efficiency of transfer, have to be taken into account.