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

The combined results of ab initio electronic-structure calculations and spectroscopic investigations of jet-cooled molecules and clusters provide strong evidence of a surprisingly simple and general mechanistic picture of the nonradiative decay of biomolecules such as nucleic bases and aromatic amino acids. The key role in this picture is played by excited singlet states of πσ* character, which have repulsive potential-energy functions with respect to the stretching of OH or NH bonds. The 1πσ* potential-energy functions intersect not only the bound potential-energy functions of the 1ππ* excited states, but also that of the electronic ground state. Via predissociation of the 1ππ* states and a conical intersection with the ground state, the 1πσ* states trigger an ultrafast internal-conversion process, which is essential for the photostability of biomolecules.
In protic solvents, the 1πσ* states promote a hydrogen-transfer process from the chromophore to the solvent. Calculations for chromophore–water clusters have shown that a spontaneous charge-separation process takes place in the solvent shell, yielding a microsolvated hydronium cation and a microsolvated electron. These results suggest that the basic mechanisms of the complex photochemistry of biomolecules in liquid water can be revealed by experimental and theoretical investigations of relatively small chromophore–water clusters.

Excited-state hydrogen detachment and hydrogen transfer driven by repulsive 1πσ* states: A new paradigm for nonradiative decay in aromatic biomolecules

The development of femtosecond time-resolved methods for the study of gas-phase molecular dynamics is founded upon the seminal studies of Zewail and co-workers, as recognized in 1999 by the Nobel Prize in Chemistry.1 This methodology has been applied to chemical reactions ranging in complexity from bond-breaking in diatomic molecules to dynamics in larger organic and biological molecules, and has led to breakthroughs in our understanding of fundamental chemical processes. Photoexcited polyatomic molecules and anions often exhibit quite complex dynamics involving the redistribution of both charge and energy.2-6 These processes are the primary steps in the photochemistry of many polyatomic systems,7 are important in photobiological processes such as vision and photosynthesis,8 and underlie many concepts in molecular electronics.9 Femtosecond time-resolved methods involve a pump-probe configuration in which an ultrafast pump pulse initiates a reaction or, more generally, creates a nonstationary state or wave packet, the evolution of which is monitored as a function of time by means of a suitable probe pulse. Time-resolved or wave packet methods offer a view complementary to the usual spectroscopic approach and often yield a physically intuitive picture. Wave packets can behave as zeroth-order or even classical-like states and are therefore very helpful in discerning underlying dynamics. The information obtained from these experiments is very much dependent on the nature of the final state chosen in a given probe scheme. Transient absorption and nonlinear wave mixing are often the methods of choice in condensed-phase experiments because of their generality. In studies of molecules and clusters in the gas phase, the most popular methods, laser-induced fluorescence and resonant multiphoton ionization, usually require the probe laser to be resonant with an electronic transition in the species being monitored. However, as a chemical reaction initiated by the pump pulse evolves toward products, one expects that both the electronic and vibrational structures of the species under observation will change. Hence, these probe methods can be * To whom corresondence should be addressed. A.S.: telephone (613) 993-7388, fax (613) 991-3437, E-mail albert.stolow@nrc.ca. D.M.N.: telephone (510) 642-3505, fax (510) 642-3635, E-mail dan@radon.cchem.berkeley.edu. 1719 Chem. Rev. 2004, 104, 1719−1757

/pdf/femtosecond-time-resolved-photoelectron-spectroscopy-1l2aqdijxn.pdf

Femtosecond time-resolved photoelectron spectroscopy.

1.1. Historical Background Hydrogen bonds1,2 are one of the principal intermolecular forces. A special class are ionic hydrogen bonds (IHBs) that form between ions and molecules with bonds strengths of 5-35 kcal/mol, up to a third of the strength of covalent bonds. These strong interactions are critical, for example, in ionic clusters and nucleation, in electrolytes, ion solvation, and acid-base chemistry, in the structures of ionic crystals, surfaces, silicates, and clays, in surface adsorption, and in self-assembly in supramolecular chemistry and molecular crystals.3 IHBs are also important in bioenergetics including protein folding, enzyme active centers, formation of membranes and proton transport, and biomolecular recognition. With such wide-ranging roles, the fundamental properties of IHB interactions need to be understood. The energetics of IHB interactions cannot be isolated and quantified in the condensed phase. However, these interactions can be isolated and studied quantitatively in gas phase. These studies lead to a fundamental understanding of relations between IHB bond strengths and molecular structure, the solvation of ions, especially in the critical inner shells, and acid-based phenomena and bioenergetics. This review will present the basic insights that have been obtained in the past four decades. It will present a comprehensive review of the thermochemistry and its structural implications obtained from ab initio calculations. Relevant recent results from spectroscopy will be also illustrated. The advent of variable temperature high-pressure mass spectrometry (HPMS) introduced by Field and co-workers in the 1960s4 and pulsed high-pressure mass spectrometry (PHPMS) introduced by Kebarle in the late 1960s5 have been particularly significant. These workers realized that at pressures of several torrs and gas densities of 1016-1017 cm-3 in ion sources, ions can undergo 103-106 collisions with neutral molecules during typical residence times of 0.1-10 ms and establish thermal ion populations and * E-mail: m.mautner@solis1.com. 213 Chem. Rev. 2005, 105, 213−284

http://www.astro-ecology.com/PDFTheIonicHydrogenBondChemicalReviews2005Paper.pdf

The Ionic Hydrogen Bond

Radiationless deactivation pathways of excited gas phase nucleobases were investigated using mass-selected femtosecond resolved pump-probe resonant ionization. By comparison between nucleobases and methylated species, in which tautomerism cannot occur, we can access intrinsic mechanisms at a time resolution never reported so far (80 fs). At this time resolution, and using appropriate substitution, real nuclear motion corresponding to active vibrational modes along deactivation coordinates can actually be probed. We provide evidence for the existence of a two-step decay mechanism, following a 267 nm excitation of the nucleobases. The time resolution achieved together with a careful zero time-delay calibration between lasers allow us to show that the first step does correspond to intrinsic dynamics rather than to a laser cross correlation. For adenine and 9-methyladenine a first decay component of about 100 fs has been measured. This first step is radically increased to 200 fs when the amino group hydrogen atoms of adenine are substituted by methyl groups. Our results could be rationalized according to the effect of the highly localized nature of the excitation combined to the presence of efficient deactivation pathway along both pyrimidine ring and amino group out-of-plane vibrational modes. These nuclear motions play a key role in the vibronic coupling between the initially excited pipi(*) and the dark npi(*) states. This seems to be the common mechanism that opens up the earlier phase of the internal conversion pathway which then, in consideration of the rather fast relaxation times observed, would probably proceed via conical intersection between the npi(*) relay state and high vibrational levels of the ground state.

Excited states dynamics of DNA and RNA bases: characterization of a stepwise deactivation pathway in the gas phase.

Electronic spectra of the jet-cooled DNA base adenine were obtained by the resonant two-photon ionization (R2PI) and the laser induced fluorescence (LIF) techniques. The 0–0 band to the lowest electronically excited state was found to be located at 35 503 cm−1. Well-resolved vibronic structures were observed up to 1100 cm−1 above the 0–0 level, followed by a slow rise of broad structureless absorption. The lowest electronic state was proposed to be of nπ* character, which lies ∼600 cm−1 below the onset of the ππ* state. The broad absorption was attributed to the extensive vibronic mixing between the nπ* state and the high-lying ππ* state.

Resonant two-photon ionization and laser induced fluorescence spectroscopy of jet-cooled adenine

A recognition method includes receiving an input image; and recognizing a plurality of elements associated with the input image using a single recognizer pre-trained to recognize a plurality of elements simultaneously.

Method and apparatus for recognizing object, and method and apparatus for training recognizer

A multiphoton ionization study was carried out on hydrated clusters of DNA base adenine in supersonic molecular beams. Resonant two-photon ionization at 266 nm showed that the relative ion intensity between the hydrated clusters Am(H2O)n and the unhydrated ones was anomalously small, particularly for m = 1, in contrast to the case of electron impact ionization. The ratio was of the order of 10-2 for m = 1, 10-1 for m = 2, but about 1 for m ≥ 3. One-photon excitation to the first electronically excited state was found to be responsible for the extensive fragmentation of adenine monomer hydrates A1(H2O)n. The water acts as a proton-donating solvent whose hydrogen bonding with the solute becomes weakened in the nπ* excited state, thereby giving the excited state its repulsive nature. Hydrates of adenine complex Am(H2O)n (m ≥ 2) tend to better survive the rupture of the water cage at higher m, probably because the energy transfer between adenine molecules is not sufficiently fast. The fragmentation was found ...

Anomalous Fragmentation of Hydrated Clusters of DNA Base Adenine in UV Photoionization

Hydration of DNA base cations in the gas phase

Binary motion estimation algorithms reduce the computational complexity of motion estimation, but, sometimes generate an inaccurate motion vector. This paper proposes a novel two-bit representation, called twobit transform-second derivatives (2BT-SD) which improves the efficiency of image binarization and the accuracy of motion estimation by making use of the positive and negative second derivatives independently in the derivation of the second bit plane. The second derivatives are also used to detect flat or background regions, avoiding expensive motion vector search operations for macroblocks in these areas, and deriving the motion vectors by prediction from neighboring blocks. In applying the proposed 2BT-SD in the H.264/AVC standard, a further reduction of motion estimation complexity with a minor accuracy reduction is achieved by using 2BT-SD representation for secondary motion estimation while using the full resolution representation for the primary motion estimation. A hardware cost analysis shows that about 209 K gates of hardware logics and 2.7 K bytes of memory are reduced by 2BT-SD for motion estimation of 1280times720 size videos when compared with the full resolution motion estimation. Experiments show that the proposed 2BT-SD achieves better motion estimation accuracy than other binary motion estimations and provides faster processing time in flat or background regions with an acceptable bit-rate increase.

Namjoon Kim

Papers

Resonant two-photon ionization and laser induced fluorescence spectroscopy of jet-cooled adenine

Method and apparatus for recognizing object, and method and apparatus for training recognizer

Anomalous Fragmentation of Hydrated Clusters of DNA Base Adenine in UV Photoionization

Hydration of DNA base cations in the gas phase

Two-bit transform based block motion estimation using second derivatives