Role of monovalent counterions in the ultrafast dynamics of DNA

This paper examines the contribution of counterion motion to the electric-field dynamics in the interior of DNA. The electric field is measured by a coumarin fluorophore that is synthetically incorporated into an oligonucleotide, where it replaces a native base pair. The DNA is a 17-base-pair oligomer with no A- or G-tracts. Time-resolved Stokes-shift measurements on the coumarin are made from 40 ps to 40 ns with each of the alkali ions and or one of several tetraalkylammonium ions as the DNA counterion. With the possible exception of rubidium, there are no indications of site-specific binding of the counterions. For sodium and other ions with a smaller hydrodynamic radius, the dynamics are identical and are fit to a power law. For larger ions, there is a progressive increase in the rate of shifting after 1 ns. This effect correlates with the hydrodynamic radius of the counterion. The lack of change in the spectral shape of the emission shows that neither the broadly distributed power-law relaxation nor the extra nanosecond dynamics are due to heterogeneity in the relaxation rates of different helices.     

Probing the charge-transfer dynamics in DNA at the single-molecule level

Photoinduced charge-transfer fluorescence quenching of a fluorescent dye produces the nonemissive charge-separated state, and subsequent charge recombination makes the reaction reversible. While the information available from the photoinduced charge-transfer process provides the basis for monitoring the microenvironment around the fluorescent dyes and such monitoring is particularly important in live-cell imaging and DNA diagnosis, the information obtainable from the charge recombination process is usually overlooked. When looking at fluorescence emitted from each single fluorescent dye, photoinduced charge-transfer, charge-migration, and charge recombination cause a "blinking" of the fluorescence, in which the charge-recombination rate or the lifetime of the charge-separated state (τ) is supposed to be reflected in the duration of the off time during the single-molecule-level fluorescence measurement. Herein, based on our recently developed method for the direct observation of charge migration in DNA, we utilized DNA as a platform for spectroscopic investigations of charge-recombination dynamics for several fluorescent dyes: TAMRA, ATTO 655, and Alexa 532, which are used in single-molecule fluorescence measurements. Charge recombination dynamics were observed by transient absorption measurements, demonstrating that these fluorescent dyes can be used to monitor the charge-separation and charge-recombination events. Fluorescence correlation spectroscopy (FCS) of ATTO 655 modified DNA allowed the successful measurement of the charge-recombination dynamics in DNA at the single-molecule level. Utilizing the injected charge just like a pulse of sound, such as a "ping" in active sonar systems, information about the DNA sequence surrounding the fluorescent dye was read out by measuring the time it takes for the charge to return.     

Recent developements in charge-transfer theory

In this paper we discuss some recent theoretical developments of importance in the area of charge transfer between atoms and surfaces. Using the complex scaling method we have calculated the energy shift and broadening of atomic levels near metal surfaces. Two novel applications will be discussed. The first concerns the interaction of atomic Rydberg levels with clean metal surfaces. It is shown that as Rydberg atoms approach a surface, strong hybridization occurs that depends sensitively on both the atom-surface separation and the details of the surface potential. The widths of the hybridized states can differ by several orders of magnitude depending on their orientation with respect to the surface. The second application is an investigation of how dielectric overlayers adsorbed on metal surfaces can influence the energy shift and broadening of atomic levels. The calculations show that the energies and widths of atomic levels near metal surfaces can be influenced strongly by thin dielectric films adsorbed on the surface.     

Coumarin base-pair replacement as a fluorescent probe of ultrafast DNA dynamics

The design and synthesis of a novel coumarin C-riboside are described, and is based on the well-known photoprobe Coumarin 102. A diastereofacial selective Heck coupling between a furanoid glycal and a coumarin triflate provided a method for glycoside formation. The coumarin C-glycoside was incorporated synthetically into DNA oligomers, and was used to probe ultrafast dynamics of duplex DNA using time-resolved Stokes shift methods.     

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.     

Structural dynamics of surfaces by ultrafast electron crystallography: experimental and multiple scattering theory

Recent studies in ultrafast electron crystallography (UEC) using a reflection diffraction geometry have enabled the investigation of a wide range of phenomena on the femtosecond and picosecond time scales. In all these studies, the analysis of the diffraction patterns and their temporal change after excitation was performed within the kinematical scattering theory. In this contribution, we address the question, to what extent dynamical scattering effects have to be included in order to obtain quantitative information about structural dynamics. We discuss different scattering regimes and provide diffraction maps that describe all essential features of scatterings and observables. The effects are quantified by dynamical scattering simulations and examined by direct comparison to the results of ultrafast electron diffraction experiments on an in situ prepared Ni(100) surface, for which structural dynamics can be well described by a two-temperature model. We also report calculations for graphite surfaces. The theoretical framework provided here allows for further UEC studies of surfaces especially at larger penetration depths and for those of heavy-atom materials.     

Modeling ultrafast solvated electronic dynamics using time-dependent density functional theory and polarizable continuum model

A first-principles solvated electronic dynamics method is introduced. Solvent electronic degrees of freedom are coupled to the time-dependent electronic density of a solute molecule by means of the implicit reaction field method, and the entire electronic system is propagated in time. This real-time time-dependent approach, incorporating the polarizable continuum solvation model, is shown to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution.     

Unraveling ultrafast dynamics in photoexcited aniline

A combination of ultrafast time-resolved velocity map imaging (TR-VMI) methods and complete active space self-consistent field (CASSCF) ab initio calculations are implemented to investigate the electronic excited-state dynamics in aniline (aminobenzene), with a perspective for modeling (1)πσ* mediated dynamics along the amino moiety in the purine derived DNA bases. This synergy between experiment and theory has enabled a comprehensive picture of the photochemical pathways/conical intersections (CIs), which govern the dynamics in aniline, to be established over a wide range of excitation wavelengths. TR-VMI studies following excitation to the lowest-lying (1)ππ* state (1(1)ππ*) with a broadband femtosecond laser pulse, centered at wavelengths longer than 250 nm (4.97 eV), do not generate any measurable signature for (1)πσ* driven N-H bond fission on the amino group. Between wavelengths of 250 and >240 nm (<5.17 eV), coupling from 1(1)ππ* onto the (1)πσ* state at a 1(1)ππ*/(1)πσ* CI facilitates ultrafast nonadiabatic N-H bond fission through a (1)πσ*/S(0) CI in <1 ps, a notion supported by CASSCF results. For excitation to the higher lying 2(1)ππ* state, calculations reveal a near barrierless pathway for CI coupling between the 2(1)ππ* and 1(1)ππ* states, enabling the excited-state population to evolve through a rapid sequential 2(1)ππ* → 1(1)ππ* → (1)πσ* → N-H fission mechanism, which we observe to take place in 155 ± 30 fs at 240 nm. We also postulate that an analogous cascade of CI couplings facilitates N-H bond scission along the (1)πσ* state in 170 ± 20 fs, following 200 nm (6.21 eV) excitation to the 3(1)ππ* surface. Particularly illuminating is the fact that a number of the CASSCF calculated CI geometries in aniline bear an exceptional resemblance with previously calculated CIs and potential energy profiles along the amino moiety in guanine, strongly suggesting that the results here may act as an excellent grounding for better understanding (1)πσ* driven dynamics in this ubiquitous genetic building block.     

DNA excited-state dynamics: ultrafast internal conversion and vibrational cooling in a series of nucleosides

To better understand DNA photodamage, several nucleosides were studied by femtosecond transient absorption spectroscopy. A 263-nm, 150-fs ultraviolet pump pulse excited each nucleoside in aqueous solution, and the subsequent dynamics were followed by transient absorption of a femtosecond continuum pulse at wavelengths between 270 and 700 nm. A transient absorption band with maximum amplitude near 600 nm was detected in protonated guanosine at pH 2. This band decayed in 191 +/- 4 ps in excellent agreement with the known fluorescence lifetime, indicating that it arises from absorption by the lowest excited singlet state. Excited state absorption for guanosine and the other nucleosides at pH 7 was observed in the same spectral region, but decayed on a subpicosecond time scale by internal conversion to the electronic ground state. The cross section for excited state absorption is very weak for all nucleosides studied, making some amount of two-photon ionization of the solvent unavoidable. The excited state lifetimes of Ado, Guo, Cyd, and Thd were determined to be 290, 460, 720, and 540 fs, respectively (uncertainties are +/-40 fs). The decay times are shorter for the purines than for the pyrimidine bases, consistent with their lower propensity for photochemical damage. Following internal conversion, vibrationally highly excited ground state molecules were detected in experiments on Ado and Cyd by hot ground state absorption at ultraviolet wavelengths. The decays are assigned to intermolecular vibrational energy transfer to the solvent. The longest time constant observed for Ado is approximately 2 ps, and we propose that solute-solvent H-bonds are responsible for this fast rate of vibrational cooling. The results show for the first time that excited singlet state dynamics of the DNA bases can be directly studied at room temperature. Like sunscreens that function by light absorption, the bases rapidly convert dangerous electronic energy into heat, and this property is likely to have played a critical role in life's early evolution on earth.     

The ultrafast charge-transfer-to-solvent dynamics of iodide in tetrahydrofuran. 1. Exploring the roles of solvent and solute electronic structure in condensed-phase charge-transfer reactions

Although they represent the simplest possible charge-transfer reactions, the charge-transfer-to-solvent (CTTS) dynamics of atomic anions exhibit considerable complexity. For example, the CTTS dynamics of iodide in water are very different from those of sodide (Na-) in tetrahydrofuran (THF), leading to the question of the relative importance of the solvent and solute electronic structures in controlling charge-transfer dynamics. In this work, we address this issue by investigating the CTTS spectroscopy and dynamics of I- in THF, allowing us to make detailed comparisons to the previously studied I-/H2O and Na-/THF CTTS systems. Since THF is weakly polar, ion pairing with the counterion can have a substantial impact on the CTTS spectroscopy and dynamics of I- in this solvent. In this study, we have isolated "counterion-free" I- in THF by complexing the Na+ counterion with 18-crown-6 ether. Ultrafast pump-probe experiments reveal that THF-solvated electrons (e-THF) appear 380 +/- 60 fs following the CTTS excitation of "free" I- in THF. The absorption kinetics are identical at all probe wavelengths, indicating that the ejected electrons appear with no significant dynamic solvation but rather with their equilibrium absorption spectrum. After their initial appearance, ejected electrons do not exhibit any additional dynamics on time scales up to approximately 1 ns, indicating that geminate recombination of e-THF with its iodine atom partner does not occur. Competitive electron scavenging measurements demonstrate that the CTTS excited state of I- in THF is quite large and has contact with scavengers that are several nanometers away from the iodide ion. The ejection time and lack of electron solvation observed for I- in THF are similar to what is observed following CTTS excitation of Na- in THF. However, the relatively slow ejection time, the complete lack of dynamic solvation, and the large ejection distance/lack of recombination dynamics are in marked contrast to the CTTS dynamics observed for I- in water, in which fast electron ejection, substantial solvation, and appreciable recombination have been observed. These differences in dynamical behavior can be understood in terms of the presence of preexisting, electropositive cavities in liquid THF that are a natural part of its liquid structure; these cavities provide a mechanism for excited electrons to relocate to places in the liquid that can be nanometers away, explaining the large ejection distance and lack of recombination following the CTTS excitation of I- in THF. We argue that the lack of dynamic solvation observed following CTTS excitation of both I- and Na- in THF is a direct consequence of the fact that little additional relaxation is required once an excited electron nonadiabatically relaxes into one of the preexisting cavities. In contrast, liquid water contains no such cavities, and CTTS excitation of I- in water leads to local electron ejection that involves substantial solvent reorganization.     

Ultrafast charge-transfer dynamics of donor-substituted truxenones

The photophysics of two donor-substituted truxenone derivatives has been studied by femtosecond time-resolved transient absorption spectroscopy. The systems consist of a central truxenone acceptor with three triarylamine (TARA) branches which act as electron donors. Upon excitation in the visible regime an electron is transferred from the donor to the acceptor, generating a charge-separated state. This state can be probed via the characteristic absorption of the TARA radical cation around 700 nm. A second absorption band around 420 nm exhibits the same kinetics and is assigned to an absorption of the radical anion of the truxenone moiety. The back electron transfer and the recovery of the ground state can be interpreted within the framework of Marcus theory. To study the dependence of the back electron transfer on the electronic coupling, the distance between the donor and the acceptor was adjusted. Two solvents were employed, dimethylsulfoxide and dichloroethane. A biexponential decay of the bands assigned to the charge-separated state was observed, with time constants in the picosecond range. Surprisingly, the rates for electron back transfer do not follow the simple picture of the donor-acceptor distance being the determining factor. The observations are explained within a model that additionally takes steric interactions between the donor and the acceptor into account.     

Lattice dynamical approach to the phase transition in A-TCNB charge-transfer crystals

Lattice dynamical calculations have been performed for the charge-transfer complex crystal of anthracene with 1,2,4,5-tetracyanobenzene. Application is made to the orientational phase transition observed in this system. The results suggest that the high temperature phase is dynamically disordered and that the phase transition is driven by a librational phonon mode exhibiting soft mode behavior.     

Intramolecular charge-transfer dynamics in covalently linked perylene-dimethylaniline and cyanoperylene-dimethylaniline

The excited-state dynamics of covalently linked electron donor-acceptor systems consisting of N, N-dimethylaniline (DMA) as electron donor and either perylene (Pe) or cyanoperylene (CNPe) as acceptor has been investigated in a large variety of solvents, including a room-temperature ionic liquid, by using femtosecond time-resolved fluorescence and absorption spectroscopy. The negligibly small solvent dependence of the absorption spectrum of both compounds and the strong solvatochromism of the fluorescence are interpreted by a model where optical excitation results in the population of a locally excited state (LES) and emission takes place from a charge-separated state (CSS). This interpretation is supported by the fluorescence up-conversion and the transient absorption measurements that reveal substantial spectral dynamics in polar solvents only, occurring on time scales going from a few hundreds of femtoseconds in acetonitrile to several tens of picoseconds in the ionic liquid. The early transient absorption spectra are similar to those found in nonpolar solvents and are ascribed to the LES absorption. The late spectra due to CSS absorption show bands that are red-shifted relative to those of the radical anion of the acceptor moiety by an amount that depends on solvent polarity, pointing to partial charge separation. Global analysis of the time-resolved data indicates that the charge separation dynamics in PeDMA is essentially solvent controlled, whereas that in CNPeDMA is faster than diffusive solvation, this difference being accounted for by a larger driving force for charge separation in the latter. On the other hand, the CSS lifetime of PeDMA is of the order of a few nanoseconds independently of the solvent, whereas that of CNPeDMA decreases with increasing solvent polarity from a few nanoseconds to a few hundreds of picoseconds. Comparison of these results with previously published data on the fluorescence quenching of Pe and CNPe in pure DMA shows that the charge separation and the ensuing charge recombination occur on similar time scales independently of whether these processes are intra- or intermolecular.     

Environment-dependent ultrafast photoisomerization dynamics in azo dye

Azoaromatic dyes have been extensively investigated over the past decade due to their potential use in a variety of optical devices that exploit their ultrafast photoisomerization processes. Among the azoaromatic dyes, Disperse Red 19 is a commercially available azobenzene nonlinear optical chromophore with a relatively high ground-state dipole moment. In the present study, we used ultrafast time-resolved spectroscopy to clarify the dynamics of a push-pull substituted azobenzene dye. Solution and film samples exhibited different ultrafast dynamics, indicating that the molecular environment affects the photoisomerization dynamics of the dye.     

Lattice dynamics of tetracyanoethylene

Lattice dynamics calculations for both crystalline forms of tetracyanoethylene are presented. The comparison of the calculated static and dynamical properties with the experimental data, leads us to suggest an improved parameter set for the “6-exp” potential function for crystals with cyano groups.     

Confined ultrafast torsional dynamics of Thioflavin-T in a nanocavity

The influence of confinement in the supramolecular β-cyclodextrin nanocavity on the excited state torsional dynamics of the amyloid fibril sensor, Thioflavin-T, is explored using subpicosecond fluorescence up-conversion spectroscopy. In the presence of β-cyclodextrin, the emission intensity and the fluorescence lifetime of Thioflavin-T significantly increases, indicating the confinement effect of the nanocage on the photophysical behaviour of the dye. Detailed time-resolved fluorescence studies show an appreciable dynamic Stokes' shift for the dye in the β-cyclodextrin nanocavity. Analysis of the time-resolved area normalized emission spectra (TRANES) indicates the formation of an emissive TICT state. The rate of formation of the TICT state, as calculated from the time dependent changes in the peak frequency and the width of the emission spectra, is found to be substantially slower in the β-cyclodextrin nanocavity compared to that in bulk water. Present results indicate that ultrafast torsional motion in Thioflavin-T is significantly retarded due to confinement by the β-cyclodextrin nanocavity.     

Lattice dynamics of cuprous iodide

The lattice dynamics of cuprous iodide have been investigated on the basis of an ‘11-parameter’ rigid-ion model (RIM). The reported neutron scattering data of CuI are reasonably well decribed by the model, especially when an optimized procedure for the selection of parameters is used. Results are presented for the phonon dispersion curves of CuI. The critical point phonon (CPP) frequencies inferred from the model are shown to provide satisfactory assignments of the observed two-phonon features in the available Raman spectrum.     

Distance dependent coherence variation in DNA charge-transfer processes

We explore distance dependent variation of the coherence length relevant to DNA charge-transfer processes within 5'-GAnG3-3' DNA sequences. Recently developed on-the-fly filtered propagator functional path integral approach was employed to sort out transport trajectories with significant contribution and to analyze correlation between electronic states. In particular, the coherence length was quantitatively determined through characteristics of off-diagonal quantum trajectories. Simulated coherence lengths and experimentally observed rate constants [Nature 2001, 412, 318] were found to be consistent such that, up to n = 2, the exponential decrease of the rate constants is associated with the donor-acceptor coherence driven charge transfer. In contrast, the rate constants become insensitive to the distance for n > or = 3 in which donor and acceptor are no longer significantly correlated. It was also found that the coherence within a collective state governs the overall charge transfer, which is composed of a part of a sequence within the coherence length from the donor.     

Novel lanthanide-based polymeric chains and corresponding ultrafast dynamics in solution

Two types of structurally related one-dimensional coordination polymers were prepared by reacting lanthanide trichloride hydrates [LnCl(3)·(H(2)O)(m)] with dibenzoylmethane (Ph(2)acacH) and a base. Using cesium carbonate (Cs(2)CO(3)) and praseodymium, neodymium, samarium, or dysprosium salts yielded [Cs{Ln(Ph(2)acac)(4)}](n) (Ln = Pr (1), Nd (2), Sm (3), Dy (4)) in considerable yields. Reaction of potassium tert-butoxide (KOtBu) and the neodymium salt [NdCl(3)·(H(2)O)(6)] with Ph(2)acacH resulted in [K{Nd(Ph(2)acac)(4)}](n) (5). All polymers exhibit a heterobimetallic backbone composed of alternating lanthanide and alkali metal atoms which are bridged by the Ph(2)acac ligands in a linear fashion. ESI-MS investigations on DMF solutions of 1-5 revealed a dissociation of all the five compounds upon dissolution, irrespective of the individual lanthanide and alkali metal present. Temporal profiles of changes in optical density were acquired performing pump/probe experiments with DMF solutions of 1-5 via femtosecond laser spectroscopy, highlighting a lanthanide-specific relaxation dynamic. The corresponding relaxation times ranging from seven picoseconds to a few hundred picoseconds are strongly dependent on the central lanthanide atom, indicating an intramolecular energy transfer from ligands to lanthanides. This interpretation also demands efficient intersystem crossing within one to two picoseconds from the S(1) to T(1) level of the ligands. Magnetic studies show that [Cs{Dy(Ph(2)acac)(4)}](n) (4) has slow relaxation of the magnetization arising from the single Dy(3+) ions and can be described as a single-ion single molecule magnet (SMM). Below 0.5 K, hysteresis loops of the magnetization are observed, which show weak single chain magnet (SCM) behavior.