Estimates of electronic coupling for excess electron transfer in DNA

Electronic coupling V(da) is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of V(da) for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a pi stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of V(da) are obtained with the standard 6-31G(*) and extended 6-31+ +G(**) basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of V(da) are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements V(da) for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack.     

Diphenylnitrenium ion: cyclization, electron transfer, and polymerization reactions

Reactions of diphenylnitrenium ion were examined using laser flash photolysis (LFP), product analysis, and computational modeling using density functional theory (DFT). In the absence of trapping agents, diphenylnitrenium ion cyclizes to form carbazole. On the basis of laser flash photolysis experiments and DFT calculations it is argued that this process is a concerted cyclization/proton transfer that forms the H-4a tautomer of carbazole. Additional LFP experiments and product studies show that diphenylnitrenium ion reacts with electron-rich arenes (e.g., N,N-dimethylaniline, diphenylamine, and carbazole) through an initial one-electron transfer. The radical intermediates formed in this step then couple to form dimeric products. Secondary reactions between the diphenylnitrenium ion and these dimers results in the formation of oligomeric materials.     

Synthesis,electronic structure,and electron transfer dynamics of (Aryl)ethynyl-bridged donor-acceptor systems

The ET dynamics of a series of donor-spacer-acceptor (D-Sp-A) systems featuring (porphinato)zinc(II), (aryl)ethynyl bridge, and arene diimide units were investigated by pump-probe transient absorption spectroscopy. Analysis of these data within the context of the Marcus-Levich-Jortner equation suggests that the pi-conjugated (aryl)ethynyl bridge plays an active role in the charge recombination (CR) reactions of these species by augmenting the extent of (porphinato)zinc(II) cation radical electronic delocalization; this increase in cation radical size decreases the reorganization energy associated with the CR reaction and thereby attenuates the extent to which the magnitudes of the CR rate constants are solvent dependent. The symmetries of porphyrin-localized HOMO and HOMO-1, the energy gap between these two orbitals, and D-A distance appear to play key roles in determining whether the (aryl)ethynyl bridge simply mediates electronic superexchange or functions as an integral component of the D and A units.     

Chromophore/DNA interactions: femto- to nanosecond spectroscopy, NMR structure, and electron transfer theory

The mechanism of photoinduced hole injection into DNA has been studied using an integrated approach that combines NMR structural analysis, time-resolved spectroscopy, and quantum-chemical calculations. A covalently linked acridinium derivative, the protonated 9-amino-6-chloro-2-methoxyacridine (X+), is replacing a thymine and separated from either guanine (G) or the easier to oxidize 7-deazaguanine (Z) by one adenine.thymine (A.T) base pair. The key features of this donor/acceptor system are the following: (i) In more than 95% of the duplexes, X+ is located in a central, coplanar position between the neighboring A.T base pairs with its long axis in parallel showing minimal twist and tilt angles (<15 degrees). The complementary adenine base is turned out into the extrahelical space. In a minority of less than 5%, X+ is found to be still attached to the duplex. X+ is most probably associated with one of the phosphates, since it is neither intercalated between more remote base pairs nor bound to sugars or grooves. This minority characterized by an excited state lifetime >10 ns gives rise to a small background signal in time-resolved measurements and contributes predominantly to steady-state fluorescence spectra. (ii) Although the intercalation mode of X+ is well defined, the NMR structure reveals that there are two conformations of X+ with respect to the arrangement of its methoxy substituent. In one conformation, the methoxy group is in the plane of the chromophore, while, in the other extraplanar conformation, the methoxy group forms an angle of 70 degrees with the acridinium ring. The fluorescence decay of 5'-ZAX and 5'-GAX tracts can be fitted to a biexponential function with similar amplitudes, reflecting the oxidation dynamics of G and Z, with the slower rate being determined by larger thermal activation energy. The attribution of biexponential electron transfer (ET) dynamics to the bimodal orientation of the methoxy group at the acridinium is supported by quantum-chemical calculations. These predict a larger free energy change for hole transfer in the nonplanar conformation as compared to the planar one, whereas the difference in the electronic couplings is negligible. (iii) Kinetic studies of the directionality of the 1(X+)* induced hole injection reveal similarly fast decay components in both directions of the duplex, that is, in 5'-ZAX and 5'-XAZ, with the amplitude of the fast component being significantly reduced in 5'-XAZ. The NMR structure shows that local structural deviations from B-DNA are much more pronounced in the 3'-5' direction than in the 5'-3' direction. According to quantum-chemical calculations, the directionality of charge injection is not a universal feature of the DNA duplex but depends critically on the rotation angle of the aromatic plane of the acridinium within the pi stack. The arrangement of X+ in 5'-ZAX and 5'-XAZ corresponds to a conformation with weak directionality of the electronic couplings. The increased disorder in the 3'-5'direction favors slow hole transfer components at the expense of the fast ones. (iv) A comparison of the hole transfer in 5'-GAX and 5'-ZAG shows that classical Marcus theory can explain the ratio of the charge shift rates of more than 2 orders of magnitude on the basis of a free energy difference between G and Z of 0.3 eV. Both NMR structures and quantum-chemical calculations justify the appreciable neglect of differences of electronic couplings as well as in the reorganization energy in 5'-GAX and 5'-ZAG. Despite the attractive concept for the behavior of floppy DNA oligonucleotides, in this acridinium/DNA system, there is no evidence for conformational gating, that is, for fluctuations in the electronic couplings that permit the ET to occur.     

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.     

Photoluminescence of europium(III) dithiocarbamate complexes: electronic structure, charge transfer and energy transfer

For the first time, we observed photoluminescence in Eu(III) dithiocarbamate complexes at room temperature -- more specifically in [Eu(Et(2)NCS(2))(3)phen], [Eu(Et(2)NCS(2))(3)bpy] and the novel [Eu(Ph(2)NCS(2))(3)phen], where phen stands for 1,10-phenanthroline and bpy for 2,2'-bipyridine. Correlations between the electronic structure of the dithiocarbamate ligands on one hand, and covalency, intensity, and ligand field spectroscopic parameters on the other, could be established. Moreover, the relative values of the emission quantum efficiencies obtained for these complexes, as well as their dependence with temperature, could be satisfactorily described by a theoretical methodology recently developed.     

Excess electron transfer in flavin-capped,thymine dimer-containing DNA hairpins

The transfer of an excess electron through DNA was investigated with DNA hairpins, which contain a flavin cap functioning as an electron donor. A thymine dimer with an open backbone acts as the electron acceptor. The dimer translates the electron capture into a strand break, which is readily detectable by HPLC. Analysis of four hairpins, in which the distance between the flavin donor and the dimer acceptor was systematically increased, revealed a flat distance dependence of the repair efficiency supporting the view that excess electrons hop through DNA using intermediate A-T base pairs as temporary charge carriers.     

Hole and excess electron transfer dynamics in DNA

Charge transfer in DNA attracts substantial attention from researchers in a wide group of fields such as bioscience, nanotechnology and physical chemistry. It is well known that both positive and negative charges, which are holes and excess electrons, respectively, contribute to the charge transfer in DNA. In the case of hole transfer in DNA, detailed mechanisms and dynamical parameters have been estimated by means of time-resolved spectroscopic methods and product analysis. On the other hand, detailed dynamics of excess electron transfer have not been established yet, although several aspects have been revealed by the continuous efforts of various research groups. In the present Perspective, studies on the charge transfer dynamics in DNA are summarized.     

Rydberg electron transfer to SF6: product ion lifetimes

The lifetimes of SF6- ions produced by Rydberg electron transfer in K(np)SF6 collisions at high n, n greater or similar to 30, are examined using a Penning ion trap. The data point to the formation of ions with a range of lifetimes that extends from approximately 1 to greater or similar to 10 ms. Sizable numbers of ions remain in the trap even 40 ms after initial injection and at least part of this signal can be attributed to radiative stabilization. Measurements of free low-energy electron attachment to SF6 in the trap show that the product ions have lifetimes similar to those of SF6- ions formed by electron transfer in high-n collisions.     

Efficient interstrand excess electron transfer in PNA:DNA hybrids

PNA:DNA strands were prepared containing a flavin electron donor and a thymine dimer acceptor, which gives a strand break upon single electron reduction. With these constructs, it was confirmed that an excess electron transfer through the base stack can be efficient in an interstrand fashion. The effect of an increased distance, a changed sequence, and stacking was explored.     

Intermolecular vs. intramolecular photoinduced electron transfer from nucleotides in DNA to acridinium ion derivatives in relation with DNA cleavage

Photoirradiation of various 10-methylacridinium ions (AcrR⁺, R = H, ⁱPr, and Ph) intercalated in DNA results in ultrafast intramolecular electron transfer, followed by rapid back electron transfer between AcrR⁺ and nucleotides in DNA. The electron-transfer dynamics in DNA were monitored by femtosecond time-resolved transient absorption spectroscopy. Both acridinyl radical and nucleotide radical cations, formed in the photoinduced electron transfer in DNA, were successfully detected in an aqueous solution. These transient absorption spectra were assigned by the comparison with those of DNA nucleotide radical cations, which were obtained by the intermolecular electron-transfer oxidation of nucleotides with the electron-transfer state of 9-mesityl-10-methylacridinium ion (Acr–Mes⁺) produced upon photoexcitation of Acr⁺–Mes. Photoinduced cleavage of DNA with various acridinium ions (AcrR⁺, R = H, ⁱPr, Ph, and Mes) has also been examined by agarose gel electrophoresis, which indicates that the rapid intramolecular back electron transfer between acridinyl radical and nucleotide radical cation in DNA suppresses the DNA cleavage as compared with the intermolecular electron-transfer oxidation of nucleotides with Acr–Mes⁺.     

Probing molecular wires: synthesis, structural, and electronic study of donor-acceptor assemblies exhibiting long-range electron transfer

A series of donor-acceptor arrays (C60-oligo-PPV-exTTF; 16-20) incorporating pi-conjugated oligo(phenylenevinylene) wires (oligo-PPV) of different length between pi-extended tetrathiafulvalene (exTTF) as electron donor and C60 as electron acceptor has been prepared by multistep convergent synthetic approaches. The electronic interactions between the three electroactive species present in 16-20 were investigated by UV-visible spectroscopy and cyclic voltammetry (CV). Our studies clearly show that, although the C60 units are connected to the exTTF donors through a pi-conjugated oligo-PPV framework, no significant electronic interactions are observed in the ground state. Interestingly, photoinduced electron-transfer processes over distances of up to 50 Angstroms afford highly stabilized radical ion pairs. The measured lifetimes for the photogenerated charge-separated states are in the range of hundreds of nanoseconds (approximately 500 ns) in benzonitrile, regardless of the oligomer length (i.e., from the monomer to the pentamer). A different lifetime (4.35 micros) is observed for the heptamer-containing array. This difference in lifetime has been accounted for by the loss of planarity of the oPPV moiety that increases with the wire length, as established by semi-empirical (PM3) theoretical calculations carried out with 19 and 20. The charge recombination dynamics reveal a very low attenuation factor (beta = 0.01 +/- 0.005 Angstroms(-1)). This beta value, as well as the strong electron coupling (V approximately 5.5 cm(-1)) between the donor and the acceptor units, clearly reveals a nanowire behavior for the pi-conjugated oligomer, which paves the way for applications in nanotechnology.     

Conformational studies of small ring derivatives by x-ray crystallography—I: The crystal structure of p-nitrostyrene oxide

The crystal structure of p-nitrostyrene oxide has been determined at room temperature from three-dimensional X-ray diffractometer data, and refined by full-matrix least-squares to a final R = 0·045. The crystals are monoclinic, space group P2₁/c with unit-cell dimensions a = 7·8244(2), b = 7·1277(2), c = 14·2059(4) Å, β = 104·193(3)°. The value of the dihedral angle formed by the phenyl ring and the oxirane ring (80·2°) can be rationalised on the basis of pseudoconjugation between the two rings, and of non-bonding interactions of one of the ortho-hydrogens of the phenyl ring with the hydrogens of the oxirane ring. The oxirane ring contains a short CC bond of length 1·448(4) Å.     

Possible mechanisms of intermolecular charge transfer and electron transfer processes in the excited electronic state

Mechanisms of intermolecular charge transfer and electron transfer processes in the electronically excited states of solute molecules have been discussed in relation to the exciplex formation and fluorescence quenching reactions in solution. A new model for the electron transfer process has been proposed and studied by the quantum mechanical method. Some naive and intuitive concepts of the electron transfer process have been given a more rigorous theoretical basis. An experiment which can test this model has been suggested. Furthermore, the possible connections among the very weak CT complex formation, exciplex formation and the electron transfer reaction have been discussed in general on the basis of the theoretical considerations.

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Zusammenfassung Mechanismen für den intermolekularen Ladungs- und Elektronenübergang bei gelösten Molekülen in elektronisch angeregten Zuständen werden im Zusammenhang mit der Bildung von Exiplexen und der Fluoreszenzlöschung diskutiert. Für den Elektronenübergang wird ein neues Modell vorgeschlagen, das quantenmechanisch untersucht wird. Dadurch wird einigen einfachen und intuitiven Vorstellungen zum Elektronenübergang eine breitere theoretische Grundlage gegeben. Zur Überprüfung des Modells wird ein Experiment vorgeschlagen. Ferner werden auf der Grundlage theoretischer Überlegungen mögliche Zusammenhänge zwischen der Bildung eines sehr schwachen charge transfef-Komplexes, der Bildung eines Exiplexes und dem Elektronenübergang diskutiert.

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Résumé Les mécanismes de transfert de charge intermoléculaire et de transfert d'électrons dans les états électroniques excités de molécules solutées sont discutés en relation avec la formation d'exciplex et les réactions d'extinction de fluorescence en solution. On propose et on étudie quantiquement un nouveau modèle pour les processus de transfert d'électrons. Il donne une base théorique plus rigoureuse à certains représentations naïves et intuitives du transfert d'électron. On suggère une expérience pour étudier la validité de ce modèle. Enfin les rapports possibles entre la formation de complexes CT très faibles, la formation d'exciplex et la réaction de transfert d'électrons a été discutée de façon générale sur la base de considérations théoriques.

     

Ligand migration in myoglobin: a combined study of computer simulation and x-ray crystallography

A ligand-migration mechanism of myoglobin was studied by a multidisciplinary approach that used x-ray crystallography and molecular dynamics simulation. The former revealed the structural changes of the protein along with the ligand migration, and the latter provided the statistical ensemble of protein conformations around the thermal average. We developed a novel computational method, homogeneous ensemble displacement, and generated the conformational ensemble of ligand-detached species from that of ligand-bound species. The thermally averaged ligand-protein interaction was illustrated in terms of the potential of mean force. Although the structural changes were small, the presence of the ligand molecule in the protein matrix significantly affected the 3D scalar field of the potential of mean force, in accordance with the self-opening model proposed in the previous x-ray study.     

Photoinduced electron transfer in ion pairs of cation-anion polymethine dyes

Photoinduced electron transfer in ion pairs of cation-anion polymethine dyes was studied by flash photolysis. The formation of radicals, which are the products of photoinduced transfer of an electron from an anion to a cation in the ion pairs, was observed during photoexcitation of a number of cation-anion dyes in nonpolar and some weakly polar solvents (in particular, in toluene and chloroform). Photoinduced electron transfer is also observed during triplet sensitization of ion pairs of the cation-anion dyes. The redox potentials of the cations and anions constituting the dyes were measured; the radical yields were compared with the free energies of photoinduced electron transfer. Photoinduced electron transfer in the systems under study was compared with similar process in cyanineborate ion pairs.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 878–884, May, 1995.The authors thank I. Ya. Levitin for help in measuring redox potentials.This work was financially supported by the Russian Foundation for Basic Research (Project No. 93-03-4217).     

Spectroscopy and electronic structure of electron deficient zinc phthalocyanines

The effect of introduction of perfluoro alkyl groups into phthalocyanines, as evidenced by the spectroscopic properties of 1,4,8,11,15,18,22,25-octa-fluoro-2,3,9,10,16,17,23,24-octa-perfluoro isopropyl zinc phthalocyanine, ZnF(64)Pc(-2) and its ring-reduced radical anion species, [ZnF(64)Pc(-3)](-), are reported. A combination of UV-visible absorption and magnetic circular dichroism (MCD) spectroscopy, ESI and MALDI-TOF mass spectrometry, cyclic and differential pulse voltammetry, and complete theoretical calculations using INDO/S and DFT techniques reveals that the substitution of all sixteen hydrogen atoms in protio ZnPc(-2) by eight F and eight i-C(3)F(7) groups red shifts the Q and pi --> pi transitions and narrows the HOMO-LUMO gap while simultaneously preventing ring photooxidation and stabilizing the radical anion. The [ZnF(64)Pc(-3)](-) species, which is in equilibrium in solution with the neutral complex when a reducing agent is present, is unusually stable. The above effects are attributed to the strong electron withdrawing properties of the peripheral substituents, which render ZnF(64)Pc extremely electron deficient.     

Molecular structure effects in intramolecular electronic energy transfer

A study of intramolecular energy transfer (intra-ET) in a series of bichromophoric molecules composed of cyclic α-diketones and para substituted benzene ring is reported. Preliminary results show that the transfer efficiency is strongly structure dependent suggesting that Dexter-type exchange interaction is responsible for intra-ET between close chromophores in a bichromophoric molecule.