Ultrafast excited-state deactivation and energy transfer in guanine-cytosine DNA double helices

The DNA double helix poly(dGdC).poly(dGdC) is studied by fluorescence upconversion spectroscopy with femtosecond resolution. It is shown that the excited-state relaxation of the duplex is faster than that of the monomeric components dGMP and dCMP. This contrasts with the behavior of duplexes composed exclusively of adenine-thymine base pairs, for which an overall lengthening of the fluorescence lifetimes with respect to that of an equimolar mixture of dAMP and TMP was reported previously. Despite the difference in the excited-state deactivation rate between the two types of duplexes, the signature of ultrafast energy transfer is present in both of them. It is attested by the decrease of fluorescence anisotropy decay of the duplexes on the subpicosecond time scale, where molecular motions are inhibited, and is corroborated by the fact that their steady-state fluorescence spectra do not change with the excitation wavelength. Energy transfer involves excited states delocalized over at least two bases, whose existence is revealed by the UV absorption spectrum of the duplex, clearly different from that of an equimolar spectrum of dGMP and dCMP.     

Frenkel exciton model of ultrafast excited state dynamics in AT DNA double helices

Recent ultrafast experiments have implicated intrachain base-stacking rather than base-pairing as the crucial factor in determining the fate and transport of photoexcited species in DNA chains. An important issue that has emerged concerns whether or not a Frenkel excitons is sufficient one needs charge-transfer states to fully account for the dynamics. Here we present an SU(2)  SU(2) lattice model which incorporates both intrachain and interchain electronic interactions to study the quantum mechanical evolution of an initial excitonic state placed on either the adenosine or thymidine side of a model B DNA poly(dA).poly(dT) duplex. Our calculations indicate that over several hundred femtoseconds, the adenosine exciton remains a cohesive excitonic wave packet on the adenosine side of the chain where as the thymidine exciton rapidly decomposes into mobile electron/hole pairs along the thymidine side of the chain. In both cases, the very little transfer to the other chain is seen over the time-scale of our calculations. We attribute the difference in these dynamics to the roughly 4:1 ratio of hole versus electron mobility along the thymidine chain. We also show that this difference is robust even when structural fluctuations are introduced in the form of static off-diagonal disorder.     

Exciton states of dynamic DNA double helices: alternating dCdG sequences

The present communication deals with the excited states of the alternating DNA oligomer (dCdG)5.(dCdG)5 which correspond to the UV absorption band around 260 nm. Their properties are studied in the frame of the exciton theory, combining molecular dynamics simulations and quantum chemistry data. It is shown that the dipolar coupling undergoes important variations with the site and the helix geometry. In contrast, the energy of the monomer transitions within the double helix is not sensitive to the local environment. It is thus considered to be distributed over Gaussian curves whose maximum and width are derived from the experimental absorption spectra of nucleosides in aqueous solution. The influence of the spectral width on the excited state delocalization and the absorption spectra is much stronger than that of the oligomer plasticity. About half of the excited states are delocalized over at least two bases. Many of them result from the mixing of different monomer states and extend on both strands. The trends found in the simulated spectra, when going from non-interacting monomers to the duplex, are in agreement with experimental observations. Conformational changes enhance the diversity of the states which can be populated upon excitation at a given energy. The states with larger spatial extent are located close to the maximum of the absorption spectrum.     

Theoretical analysis of excited states and energy transfer mechanism in conjugated dendrimers

The excited states of the phenylene ethynylene dendrimer are investigated comprehensively by various electronic‐structure methods. Several computational methods, including SCS‐ADC(2), TDHF, TDDFT with different functionals (B3LYP, BH&HLYP, CAM‐B3LYP), and DFT/MRCI, are applied in systematic calculations. The theoretical approach based on the one‐electron transition density matrix is used to understand the electronic characters of excited states, particularly the contributions of local excitations and charge‐transfer excitations within all interacting conjugated branches. Furthermore, the potential energy curves of low‐lying electronic states as the functions of ethynylene bonds are constructed at different theoretical levels. This work provides us theoretical insights on the intramolecular excited‐state energy transfer mechanism of the dendrimers at the state‐of‐the‐art electronic‐structure theories. © 2014 Wiley Periodicals, Inc.     

Kinetic analyses of photosensitized reactions involving energy transfer from two distinct excited states

This paper presents general equations for treating sensitized reactions when two different excited states of the sensitizer both contribute to sensitization. Specific equations are presented for common limiting conditions, including cases where the two excited states are and are not interconvertible.     

Singlet-triplet energy splitting and excited states of phenylnitrene

The vertical and adiabatic singlet-triplet energy splittings (Delta E ST) of phenylnitrene were computed by a variety of multireference configuration interaction and perturbation theory methods employing basis sets of up to quadruple-xi quality and extrapolation to the complete basis set limit. The vertical and adiabatic energy gaps are 18.9 and 15.9 kcal mol (-1), respectively, the latter in reasonable agreement with the revised experimental value of 15.1 +/- 0.2 kcal mol (-1). The energy difference between both states at the geometry of the a (1)A 2 singlet state was also considered and amounts to 13.8 kcal mol (-1). In obtaining accurate state energy splittings, basis set completeness turns out to be a more important issue than the level of dynamical electron correlation treatment. Density functional theory that is frequently employed to investigate phenylnitrenes and their rearrangements yields varying results and, depending on the functional, gives adiabatic energy differences between 9 and 16 kcal mol (-1). The b (1)A 1 state has a similar geometry as the ground state of 1 and is 31 kcal mol (-1) higher in energy. According to best estimates, the next higher singlet states, c (1)A 1 and d (1)B 1, are 57 and 72 kcal mol (-1) above the ground state. In the triplet manifold, vertical excitation energies to the A (3)B 1 and B (3)A 2 states are 71 and 77 kcal mol (-1), respectively.     

Collisional energy transfer in the intermediate states used for optical-optical double resonance excitation of ion-pair states in I2

The optical-optical double resonance spectra of I(2) and I(2)-Xe mixtures at room temperature reported in the literature using a fixed-wavelength, broad band pump laser have now been recorded using a tuneable, narrow band source. We show that during the time of the overlapped laser pulses ( approximately 10 ns) and with 10-20 Torr of Xe there is widespread collisional energy transfer in the intermediate state and that this phenomenon offers an alternative explanation for the broad bands in the excitation spectrum, assigned to XeI(2) complexes by the authors of the earlier study (M. E. Akopyan, I. Y. Novikova, S. A. Poretsky and A. M. Pravilov, Chem. Phys., 2005, 310, 287). Dispersed emission bands, previously attributed to direct fluorescence from the ion-pair state(s) of the complexes, are re-assigned to emission from ion-pair states of the parent I(2) that are populated by collisional energy transfer out of the initially excited state.     

Intermode energy transfer in vibrationally excited O3

The laser excited fluorescence method has been employed to determine the rate constants for vibrational relaxation of the O₃ (010), O₃ (100) and O₃ (001) levels at 298 K. The fluorescence observations from the O₃ (010) level provide direct measurements of the rate for intermode vibrational energy transfer from the coupled ν₁ and ν₃ modes to the ν₂ mode. The slowness of this process indicates the likelihood that the ν₁ and/or ν₃ modes (rather than the ν₂ mode) play a predominant role in the laser enhanced reaction between O₃² and NO at 298 K.     

The dynamics of the B-A transition of natural DNA double helices

The dynamics of the B-A transition of DNA double helices with different GC contents and various chain lengths has been characterized by an electric field pulse technique. The field-induced B-A reaction is separated from orientation effects using the magic angle technique. Amplitudes reflecting the B-A reaction are observed selectively in the limited range of ethanol contents, where CD spectra demonstrate the B-A transition. The maximum amplitude appears at 1-2% higher ethanol content than the center of the B-A transition observed by CD because electric field pulses induce a relatively large perturbation from the A- toward the B-form. The relaxation curves measured after pulse termination reflect a spectrum of up to three relaxation processes. For DNA's with approximately 50% GC, the main part of the amplitude ( approximately 75%) is associated with time constants of approximately 2 micros, and another major component appears with time constants of 50-100 micros. These relaxation effects have been observed for DNA samples with 859, 2629, 7160, and 48501 bp. The time constant associated with the main amplitude increases with decreasing GC content from approximately 2 micros at 50% GC to approximately 3 mus at 41% GC and approximately 10 micros at 0% GC at the center of the B-A transition. Model calculations on the kinetics of cooperative linear Ising lattices predict the appearance of a distinct maximum of the mean relaxation time at the center of the transition. The absence of such maximum in our experimental data indicates a low cooperativity of the B-A transition with a nucleation parameter of approximately 0.1. The rate of the B-A transition is lower by approximately 3 orders of magnitude than that predicted by molecular dynamics simulations.     

Rigid medium stabilization of metal-to-ligand charge transfer excited states

The salts [Ru(bpy)3](PF6)2, cis-[Ru(bpy)2(py)2](PF6)2, trans-[Ru(bpy)2(4-Etpy)2](PF6)2, [Ru(tpy)2](PF6)2, and [Re(bpy)(CO)3(4-Etpy)](PF6) (bpy=2,2'-bipyridine, py=pyridine, 4-Etpy=4-ethylpyridine, and tpy=2,2':6',2-terpyridine) have been incorporated into poly(methyl methacrylate) (PMMA) films and their photophysical properties examined by both steady-state and time-resolved absorption and emission measurements. Excited-state lifetimes for the metal salts incorporated in PMMA are longer and emission energies enhanced due to a rigid medium effect when compared to fluid CH3CN solution. In PMMA part of the fluid medium reorganization energy, lambdaoo, contributes to the energy gap with lambdaoo approximately 700 cm-1 for [Ru(bpy)3](PF6)2 from emission measurements. Enhanced lifetimes can be explained by the energy gap law and the influence of the excited-to-ground state energy gap, Eo, on nonradiative decay. From the results of emission spectral fitting on [Ru(bpy)3](PF6)2* in PMMA, Eo is temperature dependent above 200 K with partial differentialEo/ partial differentialT=2.8 cm-1/deg. cis-[Ru(bpy)2(py)2](PF6)2 and trans-[Ru(bpy)2(4-Etpy)2](PF6)2 are nonemissive in CH3CN and undergo photochemical ligand loss. Both emit in PMMA and are stable toward ligand loss even for extended photolysis periods. The lifetime of cis-[Ru(bpy)2(py)2](PF6)2* in PMMA is temperature dependent, consistent with a contribution to excited-state decay from thermal population and decay through a low-lying dd state or states. At temperatures above 190 K, coinciding with the onset of the temperature dependence of Eo for [Ru(bpy)3](PF6)2*, lifetimes become significantly nonexponential. The nonexponential behavior is attributed to dynamic coupling between MLCT and dd states, with the lifetime of the latter greatly enhanced in PMMA with tau approximately 3 ns. On the basis of these data and data in 4:1 (v/v) EtOH/MeOH, the energy gap between the MLCT and dd states is decreased by approximately 700 cm-1 in PMMA with the dd state at higher energy by DeltaH0 approximately 1000 cm-1. The "rigid medium stabilization effect" for cis-[Ru(bpy)2(py)2](PF6)2* in PMMA is attributed to inhibition of metal-ligand bond breaking and a photochemical cage effect.     

Supercollisions and energy transfer of highly vibrationally excited molecules

Collisional energy-transfer probability distribution functions of highly vibrationally excited molecules and the existence of supercollisions remain as the outstanding questions in the field of intermolecular energy transfer. In this investigation, collisional interactions between ground state Kr atoms and highly vibrationally excited azulene molecules (4.66 eV internal energy) were examined at a collision energy of 410 cm-1 using a crossed molecular beam apparatus and time-sliced ion imaging techniques. A large amount of energy transfer (1000-5000 cm-1) in the backward direction was observed. We report the experimental measurement for the shape of the energy-transfer probability distribution function along with a direct observation of supercollisions.     

A cubic arrangement of DNA double helices based on nickel-guanine interactions

DNA oligonucleotides can be used in order to assemble highly structured materials. Oligonucleotides with sticky ends can form long linear structures, whereas branching is required to form two- and three-dimensional nanostructures. In this paper, we show that when Ni(2+) is attached to the N7 atom of guanine, it can also act as a branching point. Thus, we have found that the heptanucleotide d(GAATTCG) can assemble into long linear duplex structures, which cross in space to generate a cubic structure. The three-dimensional arrays are stabilized by phosphate-Ni(2+)-guanine interactions. For the first time, the crystallization of a B form DNA oligonucleotide in a cubic system is reported, space group I23. Large solvent cavities are found among the DNA duplexes.     

Structural arrangement of two DNA double helices using cross-linked oligonucleotide connectors

Disulfide cross-linked oligonucleotides, which connect two different sequences of DNA strands, have been synthesized and characterized. Two double helices connected by two different cross-linked oligonucleotides can be arranged in both parallel and antiparallel orientations by addition of the specific complementary strands.     

Application of the energy gap law to the decay of charge transfer excited states,solvent effects

Values of non-radiative decay rate constants (k_nr) and emission energies (E_cm) have been obtained for Os(Phen₃)²⁺ in a series of solvents and the results are consistent with the energy gap law. For hydroxylic solvents like water or methanol related studies suggest the existence of strong, specific contributions to the vibrational trapping energy of the solvent.     

Intra- and intermolecular energy transfer in highly excited ozone complexes

The energy transfer of highly excited ozone molecules is investigated by means of classical trajectories. Both intramolecular energy redistribution and the intermolecular energy transfer in collisions with argon atoms are considered. The sign and magnitude of the intramolecular energy flow between the vibrational and the rotational degrees of freedom crucially depend on the projection K(a) of the total angular momentum of ozone on the body-fixed a axis. The intermolecular energy transfer in single collisions between O(3) and Ar is dominated by transfer of the rotational energy. In accordance with previous theoretical predictions, the direct vibrational de-excitation is exceedingly small. Vibration-rotation relaxation in multiple Ar+O(3) collisions is also studied. It is found that the relaxation proceeds in two clearly distinguishable steps: (1) During the time between collisions, the vibrational degrees of freedom are "cooled" by transfer of energy to rotation; even at low pressure equilibration of the internal energy is slow compared to the time between collisions. (2) In collisions, mainly the rotational modes are "cool" by energy transfer to argon.     

DNA double helices recognize mutual sequence homology in a protein free environment

The structure and biological function of the DNA double helix are based on interactions recognizing sequence complementarity between two single strands of DNA. A single DNA strand can also recognize the double helix sequence by binding in its groove and forming a triplex. We now find that sequence recognition occurs between intact DNA duplexes without any single-stranded elements as well. We have imaged a mixture of two fluorescently tagged, double helical DNA molecules that have identical nucleotide composition and length (50% GC; 294 base pairs) but different sequences. In electrolytic solution at minor osmotic stress, these DNAs form discrete liquid-crystalline aggregates (spherulites). We have observed spontaneous segregation of the two kinds of DNA within each spherulite, which reveals that nucleotide sequence recognition occurs between double helices separated by water in the absence of proteins, consistent with our earlier theoretical hypothesis. We thus report experimental evidence and discuss possible mechanisms for the recognition of homologous DNAs from a distance.     

Pseudo cage effect in double energy transfer

In some systems, the donor of a triplet—triplet energy transfer can be sensitized in its singlet state through a singlet—singlet energy transfer (Dexter mechanism), where the donor is the acceptor of the triplet transfer itself. As a consequence an extra acceptor molecule in the triplet energy transfer is present in the vicinity of the donor, thus enhancing the efficiency of the transfer process. Experiments show clearly this effect and a diffusional model gives semi-quantitative agreement with the experimental data.