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

Extreme ultraviolet time-resolved photoelectron spectroscopy of adenine, adenosine and adenosine monophosphate in a liquid flat jet

Time-resolved photoelectron spectroscopy using an extreme-ultraviolet (XUV) probe pulse was used to investigate the UV photoinduced dynamics of adenine (Ade), adenosine (Ado), and adenosine-5-monophosphate (AMP) in a liquid water jet. In contrast to previous studies using UV probe pulses, the XUV pulse at 21.7 eV can photoionize all excited states of a molecule, allowing for full relaxation pathways to be addressed after excitation at 4.66 eV. This work was carried out using a gas-dynamic flat liquid jet, resulting in considerably enhanced signal compared to a cylindrical jet. All three species decay on multiple time scales that are assigned based on their decay associated spectra; the fastest decay of ∼100 fs is assigned to ππ* decay to the ground state, while a smaller component with a lifetime of ∼500 fs is attributed to the nπ* state. An additional slower channel in Ade is assigned to the 7H Ade conformer, as seen previously. This work demonstrates the capability of XUV-TRPES to disentangle non-adiabatic dynamics in an aqueous solution in a state-specific manner and represents the first identification of the nπ* state in the relaxation dynamics of adenine and its derivatives.

The tautomer-specific excited state dynamics of 2,6-diaminopurine using resonance-enhanced multiphoton ionization and quantum chemical calculations

2,6-Diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines.

Photodynamics of azaindoles in polar media: the influence of the environment

We have studied the relaxation dynamics of a family of azaindole (AI) structural isomers, 4-, 5-, 6- and 7-AI, by steady-state and time-resolved methods (fs-transient absorption and fluorescence up-conversion), in solvents of different polarity. The measurements in aprotic solvents show distinctive fluorescence yields and excited state lifetimes among the isomers, which are tuned by the polarity of the medium. Guided by simple TD-DFT calculations and based on the behavior observed in the isolated species, it has been possible to address the influence of the environment polarity on the relaxation route. According to the obtained picture, the energy of the nπ* state, which is strongly dependent on the position of the pyridinic nitrogen, controls the rate of the internal conversion channel that accounts for the distinctive photophysical behavior of the isomers. On the other hand, preliminary measurements in protic media (methanol) show a very different photodynamical behavior, in which the anomalous measured fluorescent patterns are very likely the result of reactive channels (proton transfer) triggered by the electronic excitation.

Excited State Deactivation Mechanisms of Protonated Adenine: a Theoretical study

Quantum chemical computational method as well as the adiabatic dynamics simulation have been employed to investigate the non-radiative relaxation mechanism of protonated 9H- and 7H-adenine (AH+). We have located three...

What Leads to Aggregation-Induced Emission?

Aggregation-induced emission (AIE), usually referring to the phenomenon in which molecules emit more strongly in the aggregate state than in the solution state, is intriguing and promising in various optoelectronic and biosensing applications. In this Perspective, the basic principles that can lead to AIE and experimental evidence to reveal the AIE mechanism of tetraphenyl ethylene (TPE)-type molecules are discussed. AIE is the consequence of two factors: (1) the fast energy dissipation by crossing a conical intersection (CI) in solutions but not in solids results in low luminescence efficiencies in the solutions, and (2) the weak intermolecular coupling and thus slow intermolecular energy/charge transfers in the AIE solids effectively prevent quenching and result in relatively high luminescence efficiencies. The key to AIE is that the luminescence efficiency is tuned by controlling molecules to cross or not to cross a CI by changing the phase of molecules. How fast a molecule can cross a CI is dependent on the energy barrier of isomerization, which can be tuned in many ways, including mechanical or electrical stimuli, in addition to changing phases. Barrier-dependent crossing CI also results in a very important consequence: excitation-wavelength-dependent fluorescence yield within one electronic excited state, an anti-Vavilov's rule phenomenon. In principle, there can be an alternative way to tune luminescence efficiency by manipulating the formation of CIs instead of crossing or not crossing them. This approach relies on the fact that the electronic ground state and the excited state have many different properties, e.g., dipole moment. By tuning the environment, e.g., dielectric constant, to favor or disfavor one state, one may be able to lift or lower the potential surface of one state so that the potential surfaces of two states can vary between intersected and not contacted.

Revisiting the spectroscopy of xanthine derivatives: theobromine and theophylline

We explore the influence of the relative position of the methyl substituent on the photophysics of theophylline and theobromine, two molecules that are structurally related to the DNA bases. Using a combination of spectroscopic techniques and quantum mechanical calculations, we show that moving the methyl group from N1 in theophylline to N7 in theobromine causes significant differences in their excited state properties, i.e., it produces pyramidalization of N7 in the excited state of the latter. Paradoxically, this modification seems to have little effect on the structural properties of the cation and the ionization process. It is suggested that similar effects may exist in the excited state properties of DNA bases.

Unveiling the complex vibronic structure of the canonical adenine cation

Adenine, a DNA base, exists as several tautomers and isomers that are closely lying in energy and that may form a mixture upon vaporization of solid adenine. Indeed, it is challenging to bring adenine into the gas phase, especially as a unique tautomer. The experimental conditions were tuned to prepare a jet-cooled canonical adenine (9H-adenine). This isolated DNA base was ionized by single VUV photons from a synchrotron beamline and the corresponding slow photoelectron spectrum was compared to ab initio computations of the neutral and ionic species. We report the vibronic structure of the X+ 2A'' (D0), A+ 2A' (D1) and B+ 2A'' (D2) electronic states of the 9H adenine cation, from the adiabatic ionization energy (AIE) up to AIE + 1.8 eV. Accurate AIEs are derived for the 9H-adenine (X[combining tilde] 1A') + hν → 9H-adenine+ (X+ 2A'', A+ 2A', B+ 2A'') + e- transitions. Close to the AIE, we fully assign the rich vibronic structure solely to the 9H-adenine (X 1A') + hν → 9H-adenine+ (X+ 2A'') transition. Importantly, we show that the lowest cationic electronic states of canonical adenine are coupled vibronically. The present findings are important for understanding the effects of ionizing radiation and the charge distribution on this elementary building block of life, at ultrafast, short, and long timescales.

A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs

The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs.

TDDFT Study of the Optical Excitation of Nucleic Acid Bases-C60 Complexes

The potential of C₆₀ as a nucleic acid base (NAB) optical sensor is theoretically explored. We investigate the adsorption of four NABs, namely, adenine, cytosine, guanine, and thymine, on C₆₀ in the gas phase. For the optimal NAB@C₆₀ adsorption configurations, obtained using a dispersion-corrected density functional, we calculate the vis-near-ultraviolet optical response using time-dependent density functional theory. While the isolated C₆₀ and NAB molecules do not exhibit visible optical excitation, we find that C₆₀/NAB conjugation gives rise to distinct spectral features in the visible range. These results suggest that C₆₀ conjugation can be applied for photodetection of individual NABs.

Role of Electron-Driven Proton-Transfer Processes in the Ultrafast Deactivation of Photoexcited Anionic 8-oxoGuanine-Adenine and 8-oxoGuanine-Cytosine Base Pairs

It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the 8-oxo-G nucleoside may have been a primordial precursor of present-day flavins in DNA or RNA repair. Because the electron transfer leading to the splitting of a thymine-thymine pair in a CPD lesion occurs in the photoexcited state, a reasonably long excited-state lifetime of 8-oxo-G is required. The neutral (protonated) form of 8-oxo-G exhibits a very short (sub-picosecond) intrinsic excited-state lifetime which is unfavorable for repair. It has therefore been argued that the anionic (deprotonated) form of 8-oxo-G, which exhibits a much longer excited-state lifetime, is more likely to be a suitable cofactor for DNA repair. Herein, we have investigated the exited-state quenching mechanisms in the hydrogen-bonded complexes of deprotonated 8-oxo-G^- with adenine (A) and cytosine (C) using ab initio wave-function-based electronic-structure calculations. The calculated reaction paths and potential-energy profiles reveal the existence of barrierless electron-driven inter-base proton-transfer reactions which lead to low-lying S₁/S₀ conical intersections. The latter can promote ultrafast excited-state deactivation of the anionic base pairs. While the isolated deprotonated 8-oxo-G^- nucleoside may have been an efficient primordial repair cofactor, the excited states of the 8-oxo-G^--A and 8-oxo-G^--C base pairs are likely too short-lived to be efficient electron-transfer repair agents.

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

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.

Gas-Phase IR Spectroscopy of Nucleobases

IR spectroscopy of nucleobases in the gas phase reflects simultaneous advances in both experimental and computational techniques. Important properties, such as excited state dynamics, depend in subtle ways on structure variations, which can be followed by their infrared signatures. Isomer specific spectroscopy is a particularly powerful tool for studying the effects of nucleobase tautomeric form and base pair hydrogen-bonding patterns.

Electronic excitations in Guanine quadruplexes

Guanine rich DNA strands, such as those encountered at the extremities of human chromosomes, have the ability to form four-stranded structures (G-quadruplexes) whose building blocks are guanine tetrads. G-quadruplex structures are intensively studied in respect of their biological role, as targets for anticancer therapy and, more recently, of their potential applications in the field of molecular electronics. Here we focus on their electronic excited states which are compared to those of non-interacting mono-nucleotides and those of single and double stranded structures. Particular emphasis is given to excited state relaxation processes studied by time-resolved fluorescence spectroscopy from femtosecond to nanosecond time scales. They include ultrafast energy transfer and trapping of ππ* excitations by charge transfer states. The effect of various structural parameters, such as the nature of the metal cations located in the central cavity of G-quadruplexes, the number of tetrads or the conformation of the constitutive single strands, are examined.

Proton irradiation of DNA nucleosides in the gas phase

Charge localization within nucleosides after proton irradiation is strongly influenced by the ionization energy of the base.

Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back

L_a and excimer state population exchange, along the common puckering decay coordinate, explains the longest DNA lifetime component.

Geometric and energetic consequences of prototropy for adenine and its structural models – a review

Prototropy for adenine and its convenient models causes parallel changes of geometric (HOMED) and energetic (ΔE) parameters for neutral tautomers.

New Method for Double-Resonance Spectroscopy in a Cold Quadrupole Ion Trap and Its Application to UV-UV Hole-Burning Spectroscopy of Protonated Adenine Dimer

A novel method for double-resonance spectroscopy in a cold quadrupole ion trap is presented, which utilizes dipolar resonant excitation of fragment ions in the quadrupole ion trap. Photofragments by a burn laser are removed by applying an auxiliary RF to the trap, and a probe laser detects the depletion of photofragments by the burn laser. By scanning the wavelength of the burn laser, conformation-specific UV spectrum of a cold ion is obtained. This simple and powerful method is applicable to any type of double-resonance spectroscopy in a cold quadrupole ion trap and was applied to UV-UV hole-burning spectroscopy of protonated adenine dimer. It was found that protonated adenine dimer has multiple conformers/tautomers, each with multiple excited states with drastically different excited state dynamics.

Geometric consequences of electron delocalization for adenine tautomers in aqueous solution

Geometric consequences of electron delocalization were studied for all possible adenine tautomers in aqueous solution by means of ab initio methods {PCM(water)//DFT(B3LYP)/6-311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6-311+G(d,p)}. To measure the consequences of any type of resonance conjugation (π-π, n-π, and σ-π), the geometry-based harmonic oscillator model of electron delocalization (HOMED) index, recently extended to the isolated (DFT) and hydrated (PCM//DFT) molecules, was applied to the molecular fragments (imidazole, pyrimidine, 4-aminopyrimidine, and purine) and also to the whole tautomeric system. For individual tautomers, the resonance conjugations and consequently the bond lengths strongly depend on the position of the labile protons. The HOMED indices are larger for tautomers (or their fragments) possessing the labile proton(s) at the N rather than C atom. Solvent interactions with adenine tautomers slightly increase the resonance conjugations. Consequently, they slightly shorten the single bonds and lengthen the double bonds. When going from the gas phase to water solution, the HOMED indices increase (by less than 0.15 units). There is a good relation between the HOMED indices estimated in water solution and those in the gas phase for the neutral and ionized forms of adenine. Subtle effects, being a consequence of intramolecular interactions between the neighboring groups, are so strongly reduced by solvent that the relation between the HOMED indices and the relative energies for the neutral adenine tautomers seems to be better in water solution than in the gas phase.

Excited states of protonated DNA/RNA bases

The excited state lifetime of protonated DNA/RNA bases is strongly dependent on the tautomeric form.

Coupled-cluster and density functional theory studies of the electronic 0–0 transitions of the DNA bases

The 0–0 transitions of the electronic excitation spectra of the lowest tautomers of the four nucleotide (DNA) bases have been studied using linear-response approximate coupled-cluster singles and doubles (CC2) calculations.

Computational study on the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O

Deamination of adenine is one of several forms of premutagenic lesions occurring in DNA. In the present study, mechanisms for the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O were investigated. HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), and B3LYP/6-31+G(d) levels of theory were employed to search for and optimize all geometries. Energies were calculated at the G3MP2B3 and CBS-QB3 levels of theory. The effect of solvent (water) was computed using the polarizable continuum model (PCM). Intrinsic reaction coordinate (IRC) calculations were performed for all transition states. Five pathways were investigated for the deamination reaction of adenine with OH−/nH2O and 3H2O. The first four pathways (A–D) are initiated by deprotonation at the amino group of adenine by OH−, while pathway E is initiated by tautomerization of adenine. For all pathways the next two steps involve formation of a tetrahedral intermediate followed by dissociation to products via a 1,3-proton shift. Deamination with a single OH− has a high activation barrier (190 kJ mol−1 using the G3MP2B3 level) for the rate-determining step. The addition of one water molecule reduces this barrier by 68 kJ mol−1 at the G3MP2B3 level. Adding additional water molecules decreases the overall activation energy of the reaction, but the effect becomes smaller with each additional water molecule. The most plausible mechanism is pathway E, the deamination reaction of adenine with 3H2O, with an overall G3MP2B3 activation energy of 139 and 137 kJ mol−1 for the gas phase and PCM, respectively. This barrier is lower than that for the deamination with OH−/3H2O by 6 and 2 kJ mol−1 for the gas phase and PCM, respectively.

The spectroscopy of jet-cooled porphyrins: an insight into the vibronic structure of the Q band

We will present resonant two-photon ionization spectra for meso-tetraphenylporphyrin, H 2 TPP , measured under isolated conditions. The polycrystalline compound was vaporized, in vacuo, using both thermal and laser desorption, and seeded into a supersonic expansion of an inert-carrier gas. The molecules remain largely intact in the gaseous phase. However, the two techniques for vaporizing H 2 TPP give different internal temperatures for the isolated substrate, with greater vibrational cooling achieved using laser desorption. A comparison of the peak positions and intensities in the resonant two-photon ionization spectra of thermal- and laser-desorbed molecules provides an insight into the vibrational structure of the Q band. In particular, the greater contribution made by electronic transitions originating from higher vibrational levels in the ground state of H 2 TPP is emphasized. We conclude that vibronic coupling in the ground electronic state plays an important role in a quantum-mechanical interpretation of the Q band.

Wavelength dependence of electronic relaxation in isolated adenine using UV femtosecond time-resolved photoelectron spectroscopy

Electronic relaxation pathways in photoexcited nucleobases have received much theoretical and experimental attention due to their underlying importance to the UV photostability of these biomolecules. Multiple mechanisms with different energetic onsets have been proposed by ab initio calculations yet the majority of experiments to date have only probed the photophysics at a few selected excitation energies. We present femtosecond time-resolved photoelectron spectra (TRPES) of the DNA base adenine in a molecular beam at multiple excitation energies between 4.7-6.2 eV. The two-dimensional TRPES data is fit globally to extract lifetimes and decay associated spectra for unambiguous identification of states participating in the relaxation. Furthermore, the corresponding amplitude ratios are indicative of the relative importance of competing pathways. We adopt the following mechanism for the electronic relaxation of isolated adenine; initially the S(2)(ππ*) state is populated by all excitation wavelengths and decays quickly within 100 fs. For excitation energies below ∼5.2 eV, the S(2)(ππ*)→S(1)(nπ*)→S(0) pathway dominates the deactivation process. The S(1)(nπ*)→S(0) lifetime (1032-700 fs) displays a trend toward shorter time constants with increasing excitation energy. On the basis of relative amplitude ratios, an additional relaxation channel is identified at excitation energies above 5.2 eV.

Sub-microsecond photodissociation pathways of gas phase adenosine 5'-monophosphate nucleotide ions

The sub-microsecond dissociation pathways for the protonated and deprotonated forms of adenosine 5'-monophosphate were probed in the gas phase using a linear time of flight spectrometer. The studies show two dissociation pathways for the AMP ions indicating dominant ergodic pathways in the photodissociation of these species. The photofragmentation was determined to be a single photon process for the AMP ions. Photodetachment of the AMP anion excited at 266 nm was not observed, leaving dissociation as the prominent pathway for relaxation of the excess energy in the biomolecule. The photofragments were analysed at the electrostatic ion storage ring (ELISA) and found to be similar to collision induced fragments in the case of anions but different in the case of cations.

A modified four-state model for the "dual fluorescence" of N(6),N(6)-dimethyladenine derived from femtosecond fluorescence spectroscopy

The radiationless deactivation of the excited electronic states of the dual fluorescence molecule N(6),N(6)-dimethyladenine (DMAde) was investigated using femtosecond time-resolved fluorescence up-conversion spectroscopy. The molecules were studied in solution in water and in dioxane. Fluorescence-time profiles were recorded in the wide wavelength range of 290 <or= lambda(fl) <or= 650 nm. The excitation wavelengths in the region of the first UV absorption band were tuned from close to the electronic origin (lambda(pump) = 294 nm) to excess energies of approximately 5400 cm(-1) above (lambda(pump) = 258 nm). Global fits to the measured curves turned out to reflect distinctive molecular relaxation processes on five well-defined time scales. Sub-100 fs and 0.52(3) ps lifetimes were found to predominate at the shortest UV and blue emission wavelengths in water, 1.5(1) and 3.0(2) ps components at intermediate wavelengths and a 62(1) ps value in the red region of the spectrum (2sigma error limits of the last digits in parentheses). In dioxane, these lifetimes changed to <or=0.27 and 0.63(4) ps in the UV, 1.5(1) and 10.9(10) ps in a wide range of intermediate, and 1.40(4) ns at the longest wavelengths. However, little dependence of the respective time constants on lambda(pump) was observed, indicating that the ensuing relaxation processes proceed via practically barrierless pathways through conical intersections. Building on the knowledge for the parent molecule adenine (Ade), the observations were rationalized with the help of a modified four-state model for the electronic dynamics in DMAde with the pipi*(L(a)), pipi*(L(b)), and npi* states similar to those in Ade and an intramolecular charge-transfer (ICT) state, which has no counterpart in Ade, responsible for the long-wavelength fluorescence.