B-DNA to zip-DNA: simulating a DNA transition to a novel structure with enhanced charge-transport characteristics

The forced extension of a DNA segment is studied in a series of steered molecular dynamics simulations, employing a broad range of pulling forces. Throughout the entire force range, the formation of a zipper-like (zip-) DNA structure is observed. In that structure, first predicted by Lohikoski et al., the bases of the DNA strands interdigitate with each other and form a single-base aromatic stack. Similar motifs, albeit only a few base pairs in extent, have been observed in experimental crystal structures. Analysis of the dynamics of structural changes in pulled DNA shows that S-form DNA, thought to be adopted by DNA under applied force, serves as an intermediate between B-DNA and zip-DNA. Therefore, the phase transition plateau observed in force-extension curves of DNA is suggested to reflect the B-DNA to zip-DNA structural transition. Electronic structure analysis of purine bases in zip-DNA indicates a several-fold to order of magnitude increase in the π-π electronic coupling among nearest-neighbor nucleobases, compared to B-DNA. We further observe that zip-DNA does not require base pair complementarity between DNA strands, and we predict that the increased electronic coupling in zip-DNA will result in a much higher rate of charge transfer through an all-purine zip-DNA compared to B-DNA of equal length.     

Theoretical investigations of the perylene electronic structure: Monomer,dimers, and excimers

The structural and electronic properties of perylene molecule, dimers, and excimers have been computationally studied. The present work represents the first systematic study of perylene molecule and dimer forms by means of long‐range corrected time‐dependent density functional theory (TDDFT) approaches. Initially, the study explores the photophysical properties of the molecular species. Vertical transitions to many excited singlet states have been computed and rationalized with different exchange‐correlation functionals. Differences between excitation energies are discussed and compared to the absorption spectrum of perylene in gas phase and diluted solution. De‐excitation energy from the relaxed geometry of the lowest excited singlet is in good agreement with the experimental fluorescence emission. Optimization of several coplanar forms of the perylene pair prove that, contrary to generalized gradient approximation (GGA) and hybrid exchange‐correlation functionals, corrected TDDFT is able to bind the perylene dimer in the ground state. Excitation energies from different dimer conformers point to dimer formation prior to photoexcitation. The fully relaxed excimer geometry belongs to the perfectly eclipsed conformation with D_2h symmetry. The excimer equilibrium intermolecular distance is shorter than the separation found for the ground state, which is an indication of stronger interchromophore interaction in the excimer state. Excimer de‐excitation energy is in rather good agreement with the excimer band of perylene in concentrated solution. The study also scans the energy profiles of the ground and lowest excited states along several geometrical distortions. The nature of the interactions responsible for the excimer stabilization is explored in terms of excitonic and charge resonance contributions. © 2015 Wiley Periodicals, Inc.     

Bonded excimer in stacked adenines:Semiclassical simulations

The nonradiative decay of a π-stacked pair of adenine molecules,one of which was excited by an ultrafast laser pulse,is studied by semiclassical dynamics simulations.This simulation investigation is focused on the effect of the formation of bonded excimer in stacked adenines on the mechanism of ultrafast decay.The simulation finds that the formation of the bonded excimer significantly lowers the energy gap between the LUMO and HOMO and consequently facilitates the deactivation of the electronically excited molecule.On the other hand,the formation of the chemical bond between two stacked adenines restricts the deformation vibration of the pyrimidine of the excited molecule due to the steric effect.This slows down the formation of the coupling between the HOMO and LUMO energy levels and therefore delays the deactivation process of the excited adenine molecule to the electronic ground state.     

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.     

Exciton decay mechanism in DNA single strands: back-electron transfer and ultrafast base motions

The photochemistry of DNA systems is characterized by the ultraviolet (UV) absorption of π-stacked nucleobases, resulting in exciton states delocalized over several bases. As their relaxation sensitively depends on local stacking conformations, disentangling the ensuing electronic and structural dynamics has remained an experimental challenge, despite their fundamental role in protecting the genome from potentially harmful UV radiation. Here we use transient absorption and transient absorption anisotropy spectroscopy with broadband femtosecond deep-UV pulses (250–360 nm) to resolve the exciton dynamics of UV-excited adenosine single strands under physiological conditions. Due to the exceptional deep-UV bandwidth and polarization sensitivity of our experimental approach, we simultaneously resolve the population dynamics, charge-transfer (CT) character and conformational changes encoded in the UV transition dipoles of the π-stacked nucleotides. Whilst UV excitation forms fully charge-separated CT excitons in less than 0.3 ps, we find that most decay back to the ground state via a back-electron transfer. Based on the anisotropy measurements, we propose that this mechanism is accompanied by a structural relaxation of the photoexcited base-stack, involving an inter-base rotation of the nucleotides. Our results finally complete the exciton relaxation mechanism for adenosine single strands and offer a direct view into the coupling of electronic and structural dynamics in aggregated photochemical systems.

Despite its key role in DNA photochemistry, the decay mechanism of excitons in stacked bases has remained difficult to resolve. Ultrafast polarization spectroscopy now reveals a back-electron transfer and ultrafast base motions in adenosine strands.     

UV‐induced DNA Damage: The Role of Electronic Excited States

The knowledge of the fundamental processes induced by the direct absorption of UV radiation by DNA allows extrapolating conclusions drawn from in vitro studies to the in‐vivo DNA photoreactivity. In this respect, the characterization of the DNA electronic excited states plays a key role. For a long time, the mechanisms of DNA lesion formation were discussed in terms of generic “singlet” and “triplet” excited state reactivity. However, since the beginning of the 21^st century, both experimental and theoretical studies revealed the existence of “collective” excited states, i.e. excited states delocalized over at least two bases. Two limiting cases are distinguished: Frenkel excitons (delocalized ππ* states) and charge‐transfer states in which positive and negative charges are located on different bases. The importance of collective excited states in photon absorption (in particular in the UVA spectral domain), the redistribution of the excitation energy within DNA, and the formation of dimeric pyrimidine photoproducts is discussed. The dependence of the behavior of the collective excited states on conformational motions of the nucleic acids is highlighted.     

Theoretical investigation of the mechanism and dynamics of intramolecular coherent resonance energy transfer in soft molecules: a case study of dithia-anthracenophane

A computational study is conducted on dithia-anthracenophane (DTA), for which there is experimental evidence for coherent resonance energy transfer dynamics, and on dimethylanthracene (DMA), a molecule representing the energy donor and the acceptor in DTA. Electronic excitation energies are calculated by configuration interaction singles (CIS) and time-dependent density functional theory (TD-DFT) methods and are compared to experimental ones. Electronic coupling constants are calculated between two DMAs embedded into the ground-state structure of DTA employing methods based on transition densities. The resulting values of electronic coupling provide a more consistent interpretation of experiments than those based on one-half the level spacing of DTA excitation energies. Solvation effects are studied based on the polarizable continuum model (PCM). Solvent-induced polarization and screening effects are shown to make opposite contributions, and the net electronic coupling is little different from the value in a vacuum. The likelihood of coherent population transfer is assessed on the basis of a recently developed theory of coherent resonance energy transfer. The time scale of bath is shown to have an important role in sustaining the quantum coherence. The combination of quantum chemical and dynamical data suggests that the electronic coupling in DTA is in the range of 50-100 cm(-1). The presence of oscillatory excitation population dynamics can be understood from the picture of polaronic excitation moderately dressed with dispersive vibrational modes. The effect of torsional modulation on the excitation energies of DTA and electronic coupling is examined on the basis of optimized structures with the torsional angle constrained. The result suggests that inelastic effect due to torsional motion cannot be disregarded in DTA.     

Intervalence (charge-resonance) transitions in organic mixed-valence systems. Through-space versus through-bond electron transfer between bridged aromatic (redox) centers

Intervalence absorption bands appearing in the diagnostic near-IR region are consistently observed in the electronic spectra of mixed-valence systems containing a pair of aromatic redox centers (Ar(*)(+)/Ar) that are connected by two basically different types of molecular bridges. The through-space pathway for intramolecular electron transfer is dictated by an o-xylylene bridge in the mixed-valence cation radical 3(*)(+) with Ar = 2,5-dimethoxy-p-tolyl (T), in which conformational mobility allows the proximal syn disposition of planar T(*)(+)/T redox centers. Four independent experimental probes indicate the large through-space electronic interaction between such cofacial Ar(*)(+)/Ar redox centers from the measurements of (a) sizable potential splitting in the cyclic voltammogram, (b) quinonoidal distortion of T(*)(+)/T centers by X-ray crystallography, (c) "doubling" of the ESR hyperfine splittings, and (d) a pronounced intervalence charge-resonance band. The through (br)-bond pathway for intramolecular electron transfer is enforced in the mixed-valence cation radical 2a(*)(+) by the p-phenylene bridge which provides the structurally inflexible and linear connection between Ar(*)(+)/Ar redox centers. The direct comparison of intramolecular rates of electron transfer (k(ET)) between identical T(*)(+)/T centers in 3(*)(+) and 2a(*)(+)( )()indicates that through-space and through-bond mechanisms are equally effective, despite widely different separations between their redox centers. The same picture obtains for 3(*)(+) and 2a(*)(+)( )()from theoretical computations of the first-order rate constants for intramolecular electron transfer from Marcus-Hush theory using the electronic coupling elements evaluated from the diagnostic intervalence (charge-transfer) transitions. Such a strong coherence between theory and experiment also applies to the mixed-valence cation radical 7(*)(+), in which the aromatic redox S center is sterically encumbered by annulation.     

Exciton-induced lattice distortion and excimer formation

The considerations necessary for the development of a complete theory of excimer formation in crystals are analysed. A simple model which incorporates exciton-generated lattice distortion into the travelling exciton is presented, a distortion type related to excimer formation defined and the role it plays in establishing a route for excimer formation discussed. The consequences of a large change in pair molecule separation in going from crystal to excimer are emphasised and possible competition with photodimerization as an alternative end result mentioned. Referring to experimental evidence for a travelling excimer in 9-cyanoanthracene, it is shown here that a strong exciton-phonon coupling term peculiar to this crystal would be favourable. Mechanisms suggested elsewhere for migration of excimer excitation in pyrene are discussed in terms of the ideas developed here.     

Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems

Two-dimensional photon-echo experiments indicate that excitation energy transfer between chromophores near the reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides occurs coherently with decoherence times of hundreds of femtoseconds, comparable to the energy transfer time scale in these systems. The original explanation of this observation suggested that correlated fluctuations in chromophore excitation energies, driven by large scale protein motions could result in long lived coherent energy transfer dynamics. However, no significant site energy correlation has been found in recent molecular dynamics simulations of several model light harvesting systems. Instead, there is evidence of correlated fluctuations in site energy-electronic coupling and electronic coupling-electronic coupling. The roles of these different types of correlations in excitation energy transfer dynamics are not yet thoroughly understood, though the effects of site energy correlations have been well studied. In this paper, we introduce several general models that can realistically describe the effects of various types of correlated fluctuations in chromophore properties and systematically study the behavior of these models using general methods for treating dissipative quantum dynamics in complex multi-chromophore systems. The effects of correlation between site energy and inter-site electronic couplings are explored in a two state model of excitation energy transfer between the accessory bacteriochlorophyll and bacteriopheophytin in a reaction center system and we find that these types of correlated fluctuations can enhance or suppress coherence and transfer rate simultaneously. In contrast, models for correlated fluctuations in chromophore excitation energies show enhanced coherent dynamics but necessarily show decrease in excitation energy transfer rate accompanying such coherence enhancement. Finally, for a three state model of the Fenna-Matthews-Olsen light harvesting complex, we explore the influence of including correlations in inter-chromophore couplings between different chromophore dimers that share a common chromophore. We find that the relative sign of the different correlations can have profound influence on decoherence time and energy transfer rate and can provide sensitive control of relaxation in these complex quantum dynamical open systems.     

The excitation spectrum of pure liquid mesitylene in the energy range 4.5–21 eV

The fluorescence of pure liquid mesitylene at -50°C is investigated as function of excitation energy in the range 4.5–21 eV when the open surface of the liquid is excited. The normalized intensity is constant for excitation in the first two electronic absorption bands and increases significantly for excitation in the third absorption band. This increase in fluorescent quantum yield is explained as a result of reduced non-radiative transitions due to a decrease in the van der Waals interactions between the molecules at the surface of the liquid, and also by a decrease in the efficiency of excimer formation there. With increasing energy of the exciting photon photoelectrons are released which produce secondary excitations and hence cause the observed increase in fluorescent yield.     

Excimer formation dynamics in the isolated tetracene dimer

The understanding of excimer formation and its interplay with the singlet-correlated triplet pair state ¹(TT) is of high significance for the development of efficient organic electronics. Here, we study the photoinduced dynamics of the tetracene dimer in the gas phase by time-resolved photoionisation and photoion imaging experiments as well as nonadiabatic dynamics simulations in order to obtain mechanistic insight into the excimer formation dynamics. The experiments are performed using a picosecond laser system for excitation into the S₂ state and reveal a biexponential time dependence. The time constants, obtained as a function of excess energy, lie in the range between ≈10 ps and 100 ps and are assigned to the relaxation of the excimer on the S₁ surface and to its deactivation to the ground state. Simulations of the quantum-classical photodynamics are carried out in the frame of the semi-empirical CISD and TD-lc-DFTB methods. Both theoretical approaches reveal a dominating relaxation pathway that is characterised by the formation of a perfectly stacked excimer. TD-lc-DFTB simulations have also uncovered a second relaxation channel into a less stable dimer conformation in the S₁ state. Both methods have consistently shown that the electronic and geometric relaxation to the excimer state is completed in less than 10 ps. The inclusion of doubly excited states in the CISD dynamics and their diabatisation further allowed to observe a transient population of the ¹(TT) state, which, however, gets depopulated on a timescale of 8 ps, leading finally to the trapping in the excimer minimum.

The understanding of excimer formation and its interplay with the singlet-correlated triplet pair state ¹(TT) is of high significance for the development of efficient organic electronics.     

Initial excited-state structural dynamics of 2'-deoxyguanosine determined via UV resonance Raman spectroscopy

The resonance Raman spectra of 2'-deoxyguanosine, a DNA nucleoside, were measured in aqueous solution at wavelengths throughout its 260 nm absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism with two electronic states yielded the initial excited-state structural dynamics in both states. The vibrational modes containing the N(7)═C(8) stretching and C(8)-H bending internal coordinates were found to exhibit significant initial structural dynamics upon photoexcitation to either state and are coincident with the photochemical reaction coordinate involving the formation of the 2'-deoxyguanosine cation radical.     

Theoretical studies toward understanding the excited state dynamics of a bichromophoric molecule

By means of the time-dependent density functional theory, the authors study the torsional dynamics of the lowest singlet electronic excited state (S1) of a bichromophoric molecule, 2-(9-anthryl)-1H-imidazo [4,5-f]-phenanthroline (AIP). The intramolecular dynamical relaxation process, the S1 potential energy surface, and the vibrationally resolved electronic absorption and fluorescence spectra are estimated. The results reveal that the strong electron-nuclear coupling leads to a dynamic structural distortion in S1 state so that the mirror-image symmetry of absorption and fluorescence spectra of AIP breaks down. The torsional motion between the donor and acceptor moieties in AIP favors the intramolecular electronic energy transfer process. The transfer rate is dominated by the relaxation time along S1 low-frequency torsional motion.     

A reduced density-matrix theory of absorption line shape of molecular aggregate

A theory for the absorption line shape of molecular aggregates in condensed phase is formulated based on a reduced density-matrix approach. Intermolecular couplings in the aggregates are assumed to be weak (F?rster type of energy transfer mechanism). The spin-Boson model is employed to include the effect of electron-phonon coupling. Using the projection operator technique, we derive kinetic equations for the reduced electronic density matrix associated with the absorption spectrum. General expressions of time-dependent rate constants in the kinetic equations are derived by using the cumulant expansion technique. The resulting time-dependent kinetic equations are solved numerically. We illustrate the applicability of the present theory by calculating the line shape of a dimer (a pair of donor and acceptor of energy transfer). For a J-aggregate type of molecular pair (with excitonic redshift), a tail appears on the blue side of the absorption spectrum due to the existence of inhomogeneity in electronic state mixing which is originated from the electron-phonon coupling.     

Primary processes in plant photosynthesis: photosystem I reaction center

The photosystem I (PSI) pigment-protein complex of plants converts light energy into a transmembrane charge separation, which ultimately leads to the reduction of carbon dioxide. Recent studies on the dynamics of primary energy transfer, charge separation, and following electron transfer of the reaction center (RC) of the PSI prepared from spinach are reviewed. The main results of femtosecond transient absorption and fluorescence spectroscopies as applied to the P700-enchied PSI RC are summarized. This specially prepared material contains only 12–14 chlorophylls per P700, which is a special pair of chlorophyll a and has a significant role in primary charge separation. The P700-enriched particles are useful to study dynamics of cofactors, since about 100 light-harvesting chlorophylls are associated with wild PSI RC and prevent one from observing the elementary steps of the charge separation. In PSI RC energy and electron transfer were found to be strongly coupled and an ultrafast up-hill energy equilibration and charge separation were observed upon preferential excitation of P700. The secondary electron-transfer dynamics from the reduced primary electron acceptor chlorophyll a to quinone are described. With creating free energy differences (ΔG₀) for the reaction by reconstituting various artificial quinones and quinoids, the rate of electron transfer was measured. Analysis of rates versus ΔG₀ according to the quantum theory of electron transfer gave the reorganization energy, electronic coupling energy and other factors. It was shown that the natural quinones are optimized in the photosynthetic protein complexes. The above results were compared with those of photosynthetic purple bacteria, of which the structure and functions have been studied most.     

Calculations of the exciton coupling elements between the DNA bases using the transition density cube method

Excited states of the double-stranded DNA model (A)12.(T)12 were calculated in the framework of the Frenkel exciton theory. The off-diagonal elements of the exciton matrix were calculated using the transition densities and ideal dipole approximation associated with the lowest energy pipi* excitations of the individual nucleobases as obtained from time-dependent density functional theory calculations. The values of the coupling calculated with the transition density cubes (TDC) and ideal dipole approximation (IDA) methods were found to be significantly different for the small interchromophore distances. It was shown that the IDA overestimates the coupling significantly. The effects of structural fluctuations of the DNA chain on the magnitude of dipolar coupling were also found to be very significant. The difference between the maximum and minimum values was as large as 1000 and 300 cm(-1) for the IDA and TDC methods, respectively. To account for these effects, the properties of the excited states were averaged over a large number of conformations obtained from the molecular dynamics simulations. Our calculations using the TDC method indicate that the absorption of the UV light creates exciton states carrying the majority of the oscillator strength that are delocalized over at least six DNA bases. Upon relaxation, the excitation states localize over at least four contiguous bases.     

Detailed mechanism for photoinduced cytosine dimerization: a semiclassical dynamics simulation

Semiclassical dynamics simulation is used to study dimerization of two stacked cytosine molecules following excitation by ultrashort laser pulses (25 fs fwhm, Gaussian, 4.1 eV photon energy). The initial excited state was found to form an ultrashort exciton state, which eventually leads to the formation of an excimer state by charge transfer. When the interbase distance, defined as an average value of C(5)-C(5)' and C(6)-C(6)', becomes less than 3 ?, charge recombination occurs due to strong intermolecular interaction, eventually leading to an avoided crossing within 20-30 fs. Geometries at the avoided crossing, with average intermolecular distance of about 2.1 ?, are in accord with CASSCF/CASPT2 calculations. Results indicate that the C(2)-N(1)-C(6)-C(5) and C(2)'-N(1)'-C(6)'-C(5)' dihedral angles' bending vibrations play a significant role in the vibronic coupling between the HOMO and LUMO, which leads to a nonadiabatic transition to the electronic ground state.     

Charge Transfer through the DNA Base Stack

Whether the DNA base pair stack might serve as a medium for efficient, long-range charge transfer has been debated almost since the first proposal of the double-helical structure of DNA. The consequences of long-range radical migration through DNA are important with respect to understanding carcinogenesis and mutagenesis. Double-helical DNA has in its core a stacked array of aromatic heterocyclic base pairs, and this molecular π stack represents a unique system in which to explore the chemistry of electron transfer. We designed a family of metal complexes which bind to DNA by intercalative stacking within the helix; these metallointercalators may be usefully applied in probing DNA-mediated electron transfer. Here we describe a range of electron transfer reactions we carried out which are mediated by the DNA base paired stack. In some cases, DNA serves as a bridge, and spectroscopic analyses permit us to probe how the π stack couples DNA-bound donors and acceptors. These studies point to the sensitivity of coupling to DNA intercalation. However, if the DNA π stack effectively bridges donors and acceptors, the base-pair stack itself might serve not only as a conduit for electron transfer in DNA, but also in reactions initiated from a remote position. We carried out a series of reactions involving oxidative damage to DNA arising from the remotely positioned oxidant on the helix. The implications of long-range charge migration through DNA to effect damage are substantial. As in other DNA-mediated charge transfers, these reactions are highly dependent on DNA intercalation and the integrity of the intervening base-pair stack, but not on molecular distance. Furthermore, a physiologically important DNA lesion, the thymine dimers, can be reversed in a reaction initiated by electron transfer. This repair reaction can also be promoted from a distance as a result of long-range charge migration through the DNA base pair stack.     

Ab initio study of exciton transfer dynamics from a core–shell semiconductor quantum dot to a porphyrin-sensitizer

The observed resonance energy transfer in nanoassemblies of CdSe/ZnS quantum dots and pyridyl-substituted free-base porphyrin molecules [Zenkevich et al., J. Phys. Chem. B 109 (2005) 8679] is studied computationally by ab initio electronic structure and quantum dynamics approaches. The system harvests light in a broad energy range and can transfer the excitation from the dot through the porphyrin to oxygen, generating singlet oxygen for medical applications. The geometric structure, electronic energies, and transition dipole moments are derived by density functional theory and are utilized for calculating the Förster coupling between the excitons residing on the quantum dot and the porphyrin. The direction and rate of the irreversible exciton transfer is determined by the initial photoexcitation of the dot, the dot–porphyrin coupling and the interaction to the electronic subsystem with the vibrational environment. The simulated electronic structure and dynamics are in good agreement with the experimental data and provide real-time atomistic details of the energy transfer mechanism.