The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

Singlet oxygen (1O2) is a biologically relevant reactive oxygen species capable of efficiently reacting with cellular constituents. The resulting oxidatively generated damage to nucleic acids, membrane unsaturated lipids, and protein components has been shown to be implicated in several diseases, including arthritis, cataracts, and skin cancer. Singlet oxygen may be endogenously produced, among various possibilities, by myeloperoxidase, an enzyme implicated in inflammation processes, and also efficiently in skin by the UVA component of solar radiation through photosensitization reactions. Emphasis is placed in this Review on the description of the main oxidation reactions initiated by 1O2 and the resulting modifications within key cellular targets, including guanine for nucleic acids, unsaturated lipids, and targeted amino acids. Most of these reactions give rise to peroxides and dioxetanes, whose formation has been rationalized in terms of [4+2] cycloaddition and 1,2-cycloaddition with dienes + olefins, ...

Singlet Molecular Oxygen Reactions with Nucleic Acids, Lipids, and Proteins.

UV-induced DNA damage plays a key role in the initiation phase of skin cancer. When left unrepaired or when damaged cells are not eliminated by apoptosis, DNA lesions express their mutagneic properties, leading to the activation of proto–oncogene or the inactivation of tumor suppression genes. The chemical nature and the amount of DNA damage strongly depend on the wavelength of the incident photons. The most energetic part of the solar spectrum at the Earth's surface (UVB, 280–320 nm) leads to the formation of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6–4) pyrimidone photoproducts (64PPs). Less energetic but 20–times more intense UVA (320–400 nm) also induces the formation of CPDs together with a wide variety of oxidatively generated lesions such as single strand breaks and oxidized bases. Among those, 8–oxo–7,8–dihydroguanine (8–oxoGua) is the most frequent since it can be produced by several mechanisms. Data available on the respective yield of DNA photoproducts in cells and skin show that exposure to sunlight mostly induces pyrimidine dimers, which explains the mutational signature found in skin tumors, with lower amounts of 8–oxoGua and strand breaks. The present review aims at describing the basic photochemistry of DNA and discussing the quantitative formation of the different UV–induced DNA lesions reported in the literature. Additional information on mutagenesis, repair and photoprotection is briefly provided.

Formation of UV-induced DNA damage contributing to skin cancer development

This is a review of some recent development in femtosecond filamentation science with emphasis on our collective work. Previously reviewed work in the field will not be discussed. We thus start with a very brief description of the fundamental physics of single filamentation of powerful femtosecond laser pulses in air. Intensity clamping is emphasized. One consequence is that the peak intensity inside one or more filaments would not increase significantly even if one focuses the pulse at very high peak power even up to the peta-watt level. Another is that the clamped intensity is independent of pressure. One interesting outcome of the high intensity inside a filament is filament fusion which comes from the nonlinear change of index of refraction inside the filament leading to cross beam focusing. Because of the high intensity inside the filament, one can envisage nonlinear phenomena taking place inside a filament such as a new type of Raman red shift and the generation of very broad band supercontinuum into the infrared through four-wave-mixing. This is what we call by filamentation nonlinear optics. It includes also terahertz generation from inside the filament. The latter is discussed separately because of its special importance to those working in the field of safety and security in recent years. When the filamenting pulse is linearly polarized, the isotropic nature of air becomes birefringent both electronically (instantaneous) and through molecular wave packet rotation and revival (delayed). Such birefringence is discussed in detailed. Because, in principle, a filament can be projected to a long distance in air, applications to pollution measurement as well as other atmospheric science could be earned out. We call this filamentation atmospheric science. Thus, the following subjects are discussed briefly, namely, lightning control, rain making, remote measurement of electric field, microwave guidance and remote sensing of pollutants. A discussion on the higher order Kerr effect on the physics of filamentation is also given. This is a new hot subject of current debate. This review ends on giving our view of the prospect of progress of this field of filamentation in the future. We believe it hinges upon the development of the laser technology based upon the physical understanding of filamentation and on the reduction in price of the laser system.

Advances in intense femtosecond laser filamentation in air

An ‘all-optical’ technique is proposed that can be used to detect broadband terahertz waves by coherently manipulating fluorescence emission from a gas plasma. This technique can be used to measure terahertz pulses at a distance of 10 m with unlimited directionality, even in the presence of water vapour absorption.

Broadband terahertz wave remote sensing using coherent manipulation of fluorescence from asymmetrically ionized gases

We experimentally studied the three-body fragmentation dynamics of CO(2) initiated by intense femtosecond laser pulses. Sequential and nonsequential fragmentations were precisely separated and identified for CO(2)(3+) to break up into O(+) + C(+) + O(+) ions. With accurate measurements of three-dimensional momentum vectors of the correlated atomic ions and calculations of the high-level ab initio potential of CO(2)(3+), we reconstructed the geometric structure of CO(2)(3+) before fragmentation, which turns out to be very close to that of the neutral CO(2) molecule before laser irradiation. Our study indicated that Coulomb explosion is a promising approach for imaging geometric structures of polyatomic molecules if the fragmentation dynamics can be clearly clarified and the appropriate dissociation potential is provided for multiply charged molecular ions.

Nonsequential and sequential fragmentation of CO2(3+) in intense laser fields

A new type of molecular fragmentation induced by femtosecond intense laser at the intensity of 2 x 10(14) W/cm2 is reported. For the parent molecule of methane, ethylene, n-butane, and 1-butene, fluorescence from H (n = 3-->2), CH (A 2Delta, B 2Sigma-, and C 2Sigma+-->X 2Pi), or C2 (d 3Pi g-->a 3Pi u) is observed in the spectrum. It shows that the fragmentation is a universal property of neutral molecule in the intense laser field. Unlike breaking only one or two chemical bonds in conventional UV photodissociation, the fragmentation caused by the intense laser undergoes vigorous changes, breaking most of the bonds in the molecule, like an explosion. The fragments are neutral species and cannot be produced through Coulomb explosion of multiply charged ion. The laser power dependence of CH (A-->X) emission of methane on a log-log scale has a slope of 10 +/- 1. The fragmentation is thus explained as multiple channel dissociation of the superexcited state of parent molecule, which is created by multiphoton excitation.

Explosive photodissociation of methane induced by ultrafast intense laser

Although numerous studies have been devoted to the charge transfer through double-stranded DNA (dsDNA), one of the major problems that hinder their potential applications in molecular electronics is the fast deprotonation of guanine cation (G+•) to form a neutral radical that can cause the termination of hole transfer. It is thus of critical importance to explore other DNA structures, among which G-quadruplexes are an emerging topic. By nanosecond laser flash photolysis, we report here the direct observation and findings of the unusual deprotonation behavior (loss of amino proton N2–H instead of imino proton N1–H) and slower (1–2 orders of magnitude) deprotonation rate of G+• within G-quadruplexes, compared to the case in the free base dG or dsDNA. Four G-quadruplexes AG3(T2AG3)3, (G4T4G4)2, (TG4T)4, and G2T2G2TGTG2T2G2 (TBA) are measured systematically to examine the relationship of deprotonation with the hydrogen-bonding surroundings. Combined with in depth kinetic isotope experiments and pKa analysis, ...

Direct Observation of Guanine Radical Cation Deprotonation in G-Quadruplex DNA

Intensified research interests are posed with the thionucleobase 4- thiouracil (4-TU), due to its important biological function as site-specific photoprobe to detect RNA structures and nucleic acid−nucleic acid contacts. By means of time-resolved IR spectroscopy and density functional theory (DFT) studies, we have examined the unique photophysical and photochemical properties of 4-TU. It is shown that 4-TU absorbs UVA light and results in the triplet formation with a high quantum yield (0.9). Under N2-saturated anaerobic conditions, the reactive triplet undergoes mainly cross-linking, leading to the (5− 4)/(6−4) pyrimidine−pyrimidone product. In the presence of O2 under aerobic conditions, the triplet 4-TU acts as an energy donor to produce singlet oxygen 1 O2 by triplet−triplet energy transfer. The highly reactive oxygen species 1 O2 then reacts readily with 4-TU, leading to the products of uracil (U) with a yield of 0.2 and uracil-6-sulfonate (U SO3 ) that is fluorescent at ∼390 nm. The product formation pathways and product distribution are well rationalized by the joint B3LYP/6- 311+G(d,p) calculations. From dynamics and mechanistic point of views, these results enable a further understanding for 4-TU acting as reactive precursors for photochemical reactions relevant to 1 O2, which has profound implications for photo cross- linking, DNA photodamage, as well as photodynamic therapy studies.

Photophysical and photochemical properties of 4-thiouracil: time-resolved IR spectroscopy and DFT studies.

We report, for the first time, a direct observation of the super-excited states of CH4 in femtosecond intense laser fields using a pump (800 nm)–probe (1338 nm) technique. An unambiguous depletion of the CH (A 2 � → X 2 �) fluorescence signal as a function of the delay time is attributed to the de-excitation of the super-excited states by the probe laser pulse. The lifetime of the super-excited state is measured to be about 160 fs. (Some figures in this article are in colour only in the electronic version)

https://iopscience.iop.org/article/10.1088/0953-4075/41/22/225601/pdf

Di Song

Papers

Nonsequential and sequential fragmentation of CO2(3+) in intense laser fields

Explosive photodissociation of methane induced by ultrafast intense laser

Direct Observation of Guanine Radical Cation Deprotonation in G-Quadruplex DNA

Photophysical and photochemical properties of 4-thiouracil: time-resolved IR spectroscopy and DFT studies.

Direct observation of super-excited states in methane created by a femtosecond intense laser field