The scope of this review is the nature and dynamics of the singlet excited electronic states created in nucleic acids and their constituents by UV light. Interest in the UV photochemistry of nucleic acids has long been the motivation for photophysical studies of the excited states, because these states are at the beginning of the complex chain of events that culminates in photodamage. UV-induced damage to DNA has profound biological consequences, including photocarcinogenesis, a growing human health problem.1-3 Sunlight, which is essential for life on earth, contains significant amounts of harmful UV (λ < 400 nm) radiation. These solar UV photons constitute one of the most ubiquitous and potent environmental carcinogens. This extraterrestrial threat is impressive for its long history; photodamage is as old as life itself. The genomic information encoded by these biopolymers has been under photochemical attack for billions of years. It is not surprising then that the excited states of the nucleic acid bases (see Chart 1), the most important UV chromophores of nucleic acids, are highly stable to photochemical decay, perhaps as a result of selection pressure during a long period of molecular evolution. This photostability is due to remarkably rapid decay pathways for electronic energy, which are only now coming into focus through femtosecond laser spectroscopy. The recently completed map of the human genome and the ever-expanding crystallographic database of nucleic acid structures are two examples that illustrate the richly detailed information currently available about the static properties of nucleic acids. In contrast, much less is known about the dynamics of these macromolecules. This is particularly true of the dynamics of the excited states that play a critical role in DNA photodamage. Efforts to study nucleic acids by time-resolved spectroscopy have been stymied by the apparent lack of suitable fluorophores. In contrast, dynamical spectroscopy of proteins has flourished thanks to intrinsically fluorescent amino acids such as tryptophan, tyrosine, and phenylalanine.4 The primary UVabsorbing constituents of nucleic acids, the nucleic acid bases, have vanishingly small fluorescence quantum yields under physiological conditions of temperature and pH.5 In fact, the bases were frequently described as “nonfluorescent” in the early literature. * To whom correspondence should be addressed. E-mail: kohler@ chemistry.ohio-state.edu. Phone: (614) 688-3944. Fax: (614) 2921685. 1977 Chem. Rev. 2004, 104, 1977−2019

Ultrafast Excited-State Dynamics in Nucleic Acids

Plasma–liquid interactions represent a growing interdisciplinary area of research involving plasma science, fluid dynamics, heat and mass transfer, photolysis, multiphase chemistry and aerosol science. This review provides an assessment of the state-of-the-art of this multidisciplinary area and identifies the key research challenges. The developments in diagnostics, modeling and further extensions of cross section and reaction rate databases that are necessary to address these challenges are discussed. The review focusses on non-equilibrium plasmas.

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Plasma-liquid interactions: A review and roadmap

Since the discovery of the hydrated electron more than 40 years ago, a general consensus has emerged that the hydrated electron occupies a quasispherical cavity in liquid water. We simulated the electronic structure and dynamics of the hydrated electron using a rigorously derived pseudopotential to treat the electron-water interaction, which incorporates attractive oxygen and repulsive hydrogen features that have not been included in previous pseudopotentials. What emerged was a hydrated electron that did not reside in a cavity but instead occupied a ~1-nanometer-diameter region of enhanced water density. Both the calculated ground-state absorption spectrum and the excited-state spectral dynamics after simulated photoexcitation of this noncavity hydrated electron showed excellent agreement with experiment. The relaxation pathway involves a rapid internal conversion followed by slow ground-state cooling, the opposite of the mechanism implicated by simulations in which the hydrated electron occupies a cavity.

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Does the Hydrated Electron Occupy a Cavity

For mixed quantum‐classical molecular dynamics simulations of solvated excess charges a novel and efficient method to expand the solute electronic wave function in a distributed Gaussian basis with a shell structure is presented. The aggregate of Gaussian orbitals is capable of mimicking the shape fluctuation of the excess charge distribution and its diffusion through the solvent. This approach also offers an easy pathway to treat the solvent electronic polarization in an explicit and self‐consistent fashion. As applications, the results of adiabatic molecular dynamics simulations for the hydrated electron and the aqueous chloride are reported. For e−/H2O the computed ground state absorption spectrum is discussed. Adiabatic relaxation as well as nonadiabatic transition rates are evaluated—the latter by means of an original Golden Rule formula—and compared to experimental results. In the case of Cl−/H2O the charge transfer to solvent spectra are analyzed. The ability of the mobile basis set method to descr...

Molecular dynamics simulation of an excess charge in water using mobile Gaussian orbitals

An excess electron in a sample of classical water molecules at room temperature has been simulated using path integral techniques. The electron–water interaction is modeled by a pseudopotential with effective core repulsion and further terms for the Coulomb interaction and polarization effects. Various discretizations of the electron path, up to 1000 points, are examined. The charge distribution of the electron is found to be compact and to occupy a cavity in the water, in agreement with the conventional picture. The solvation shell structure is similar to that of relatively large solvated atomic anions, but the radial electron‐solvent correlations are largely smeared out due to fluctuations of the electronic density distribution. In parts of the simulation the structure of the first solvation shell corresponds on the average to the structure proposed for hydrated electrons by Kevan. The computed solvation energy and the estimated energy of the first optical excitation agree reasonably well with experimental data.

Quantum simulation study of the hydrated electron

The optical absorption spectra of solvated electrons in H/sub 2/O and D/sub 2/O have been measured at 274, 298, 340, and 380 K. All the spectra were fitted very well with the Gaussian and Lorentzian shape functions at the low- and high-energy sides of the absorption maximum, respectively, excluding the high-energy tail. The spectrum does not shift uniformly with temperature. The temperature coefficient of absorption decreases rapidly with increasing energy on the low-energy side of the absorption maximum, while it changes only slightly on the high-energy side. When the temperature increases the Lorentzian width remains constant, the Gaussian width varies proportionally to T/sup 1/2/, and the spectrum becomes more symmetrical. On going from H/sub 2/O to D/sub 2/O we found that the spectrum at a given A/A/sub max/ shows a shift of +0.05 eV in the low-energy wing. The shift decreases with increasing energy, reaching 0.03 eV at the absorption maximum. On the high-energy side of the band the shift becomes negative at h..nu.. > 2.2 eV. The shift on the low-energy side seems to be related to the difference of the zero-point energies of the inter- and intramolecular vibrations. The wavelength dependence of the temperature and isotope effects ismore » consistent with the model that different types of excitation occur on the low- and high-energy sides of the absorption band. The temperature and isotopic dependence of the low-energy side are consistent with its width being due to phonon interactions.« less

Temperature and isotope effects on the shape of the optical absorption spectrum of solvated electrons in water

Shapes of optical spectra of solvated electrons. Effect of pressure

The optical absorption spectra of solvated electrons in water, alcohols, and tetrahydrofuran are empirically resolved into two Gaussian bands and a continuum tail. The first Gaussian band covers most of the low energy side of the spectrum. The second Gaussian band lies at an energy slightly above that of the absorption maximum of the total spectrum. With the exception of tert-butyl alcohol, in water and alcohols the following were observed: (a) the first Gaussian bands have the same half-width, but the oscillator strength in water is about double that in an alcohol;(b) the second Gaussian bands have similar half-widths and oscillator strengths; (c) the continuum tails have similar half-widths, yet that in water possesses only about one third as much oscillator strength as one in an alcohol. In tert-butyl alcohol and tetrahydrofuran the first Gaussian band and the continuum tail each carry nearly half of the total oscillator strength.

Band resolution of optical spectra of solvated electrons in water, alcohols, and tetrahydrofuran

Substitution of D and H in ammonia increases the energy of the optical absorption maximum E/sub ..cap alpha../sub max// of solvated electrons by 0.04 eV at 200 to 240 K. The temperature dependence of E/sub ..cap alpha../sub max// may also be slightly larger in ND/sub 3/ (-2.6 MeV/K) than in NH/sub 3/ (-2.4 MeV/K). The bandwidth at half-height W/sub 1/2/ is unaltered by isotopic substitution. The low-energy side of the absorption band has a Gaussian shape. The width parameter of the Gaussian increased slightly with temperature, being g/sub 1/ = 0.010 T/sup 1/2/ eV in both NH/sub 3/ and ND/sub 3/. The high-energy side of the absorption band is neither a Lorentzian nor a single power function of E. If it is expressed by A/A/sub max/ varies as E/sup -..cap alpha../, the value of ..cap alpha.. decreases from 6 in the vicinity of A/A/sub max/ = 0.4 to 3 near A/A/sub max/ = 0.03. The band asymmetry parameter is W/sub b//W/sub r/ approximately equal to 1.35 at 200 to 240 K, similar to that for electrons in water at 300 K. The temperature coefficient -(delta E/delta T)/sub A/A/sub max// of the low-energy side of the band is greater than thatmore » of the high-energy side in ND/sub 3/ and water, and probably also in NH/sub 3/. The optical absorption transitions are different on the two sides of the band.« less

Isotope and temperature effects on the optical absorption spectrum of solvated electrons in liquid ammonia

The optical absorption band of electrons solvated in ethers has an approximately Gaussian shape on the low energy side of the absorption maximum. The high energy side is wider and has an approximately Lorentzian shape down to A/Amax ≈ 0.3, then extends into a long tail to high energies. The energy at the absorption maximum EAmax and the Gaussian and Lorentzian dispersion parameters g and l are reported as functions of temperature for electrons in diethyl ether (DEE), di-n-propyl ether (DPE), di-n-butyl ether (DBE), and tetrahydrofuran (THF). The values in eV of the parameters at 180 K are: EAmax = 0.76 in THF, 0.67 in DEE, 0.65 in DPE and DBE; l = 0.32 in THF, DEE, and DPE, 0.39 in DBE; g = 0.19 in all the ethers. The temperature coefficients of EAmax are ∼ −2 × 10−3 eV/K, those of l are −(1 ± 1)10−4 eV/K, and those of g are +4 × 10−4 eV/K. The band becomes less asymmetrical as the temperature increases. To make progress in the theoretical treatment of solvated electron spectra attention should be focusse...

Fang-Yuan Jou

Papers

Temperature and isotope effects on the shape of the optical absorption spectrum of solvated electrons in water

Shapes of optical spectra of solvated electrons. Effect of pressure

Band resolution of optical spectra of solvated electrons in water, alcohols, and tetrahydrofuran

Isotope and temperature effects on the optical absorption spectrum of solvated electrons in liquid ammonia

Optical spectra of electrons solvated in liquid ethers: temperature effects