Primary processes underlying the photostability of isolated DNA bases: adenine

The impact of metalation on adsorption geometry, electronic level alignment and UV-stability of organic macrocycles on TiO2(110)

Metal complexes of the tetradentate bipyridine based macrocycle pyrphyrin (Pyr) have recently shown promise as water reduction catalysts in homogeneous photochemical water splitting reactions. In this study, the adsorption and metalation of pyrphyrin on stoichiometric TiO₂(110) is investigated in ultrahigh vacuum by means of scanning tunneling microscopy, photoelectron spectroscopy, low-energy electron diffraction, and density functional theory. In a joint experimental and computational effort, the local adsorption geometry at low coverage, the long-range molecular ordering at higher coverage and the electronic structure have been determined for both the bare ligand and the cobalt-metalated Pyr molecule on TiO₂. The energy level alignment of CoPyr/TiO₂ supports electron injection into TiO₂ upon photoexcitation of the CoPyr complex and thus renders it a potential sensitizer dye. Importantly, Co-incorporation is found to stabilize the Pyr molecule against photo-induced degradation, while the bare ligand is decomposed rapidly under continuous UV-irradiation. This interesting phenomenon is discussed in terms of additional de-excitation channels for electronically highly excited molecular states.

Ultrafast structural dynamics of photoexcited adenine

Ultraviolet Resonance Raman (UVRR) spectroscopy derives distinct electronic properties of adenine in the L_a (260 nm) and B_b (210 nm) excited states.

Time resolved 3D momentum imaging of ultrafast dynamics by coherent VUV-XUV radiation

We present a new experimental setup for measuring ultrafast nuclear and electron dynamics of molecules after photo-excitation and ionization. We combine a high flux femtosecond vacuum ultraviolet (VUV) and extreme ultraviolet (XUV) source with an internally cold molecular beam and a 3D momentum imaging particle spectrometer to measure electrons and ions in coincidence. We describe a variety of tools developed to perform pump-probe studies in the VUV-XUV spectrum and to modify and characterize the photon beam. First benchmark experiments are presented to demonstrate the capabilities of the system.

Ultrafast Relaxation Dynamics of the Ethylene Cation C(2)H(4)+

We present a combined experimental and computational study of the relaxation dynamics of the ethylene cation. In the experiment, we apply an extreme-ultraviolet-pump/infrared-probe scheme that permits us to resolve time scales on the order of 10 fs. The photoionization of ethylene followed by an infrared (IR) probe pulse leads to a rich structure in the fragment ion yields reflecting the fast response of the molecule and its nuclei. The temporal resolution of our setup enables us to pinpoint an upper bound of the previously defined ethylene-ethylidene isomerization time to 30 ± 3 fs. Time-dependent density functional based trajectory surface hopping simulations show that internal relaxation between the first excited states and the ground state occurs via three different conical intersections. This relaxation unfolds on femtosecond time scales and can be probed by ultrashort IR pulses. Through this probe mechanism, we demonstrate a route to optical control of the important dissociation pathways leading to separation of H or H2.

Gas-Phase Femtosecond Particle Spectroscopy: A Bottom-Up Approach to Nucleotide Dynamics

We summarize how gas-phase ultrafast charged-particle spectroscopy has been used to provide an understanding of the photophysics of DNA building blocks. We focus on adenine and discuss how, following UV excitation, specific interactions determine the fates of its excited states. The dynamics can be probed using a systematic bottom-up approach that provides control over these interactions and that allows ever-larger complexes to be studied. Starting from a chromophore in adenine, the excited state decay mechanisms of adenine and chemically substituted or clustered adenine are considered and then extended to adenosine mono-, di-, and trinucleotides. We show that the gas-phase approach can offer exquisite insight into the dynamics observed in aqueous solution, but we also highlight stark differences. An outlook is provided that discusses some of the most promising developments in this bottom-up approach.

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.

Quantum Mechanical Wave Packet Dynamics at a Conical Intersection with Strong Vibrational Dissipation

We derive a reduced model for the nonadiabatic quantum dynamics of an electronic wave packet moving through a conical intersection in the presence of strong vibrational damping. Starting from the dissipative two-state two-model model, we transform the tuning and the coupling mode to the bath. The resulting quantum two-state model with two highly structured environments is solved numerically exactly in the regime of strong vibrational damping. We find negative cross peaks in the ultrafast optical 2D spectra as clear signatures of the conical intersection. They arise from secondary excitations of the wave packet after having passed through the photophysical energy funnel. This feature is in agreement with recent transient absorption measurements of rhodopsin.

XUV excitation followed by ultrafast non-adiabatic relaxation in PAH molecules as a femto-astrochemistry experiment

Highly excited molecular species are at play in the chemistry of interstellar media and are involved in the creation of radiation damage in a biological tissue. Recently developed ultrashort extreme ultraviolet light sources offer the high excitation energies and ultrafast time-resolution required for probing the dynamics of highly excited molecular states on femtosecond (fs) (1 fs=10⁻¹⁵s) and even attosecond (as) (1 as=10⁻¹⁸ s) timescales. Here we show that polycyclic aromatic hydrocarbons (PAHs) undergo ultrafast relaxation on a few tens of femtoseconds timescales, involving an interplay between the electronic and vibrational degrees of freedom. Our work reveals a general property of excited radical PAHs that can help to elucidate the assignment of diffuse interstellar absorption bands in astrochemistry, and provides a benchmark for the manner in which coupled electronic and nuclear dynamics determines reaction pathways in large molecules following extreme ultraviolet excitation.

Extreme UV light sources allow us to study the dynamics of excited molecular stets over remarkably short timeframes. Here, the authors probe polyaromatic hydrocarbons—large organic molecules—and show their electronic excitation and subsequent ultrafast relaxation.

Time-Resolved Photoelectron Spectroscopy of Dissociating 1,2-Butadiene Molecules by High Harmonic Pulses

Using 42 nm high harmonic pulses, the dissociation dynamics of 1,2-butadiene was investigated by time-resolved photoelectron spectroscopy (TRPES), enabling us to observe dynamical changes of multiple molecular orbitals (MOs) with higher temporal resolution than conventional light sources. Because each lower-lying occupied MO has particular spatial electron distribution, the structural dynamics of photochemical reaction can be revealed. On the femtosecond time scale, a short-lived excited state with a lifetime of 37 ± 15 fs and the coherent oscillation of the photoelectron yield stimulated by Hertzberg-Teller coupling were observed. Ab initio molecular dynamics simulations in the electronically excited state find three relaxation pathways from the vertically excited structure in S1 to the ground state, and one of them is the dominant relaxation pathway, observed as the short-lived excited state. On the picosecond time scale, the photoelectron yields related to the C-C bond decreased upon photoexcitation, indicating C-C bond cleavage.

Computational modeling of photoexcitation in DNA single and double strands

The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.

Excited-state relaxation of hydrated thymine and thymidine measured by liquid-jet photoelectron spectroscopy: experiment and simulation

Time-resolved photoelectron spectroscopy is performed on thymine and thymidine in aqueous solution to study the excited-state relaxation dynamics of these molecules. We find two contributions with sub-ps lifetimes in line with recent excited-state QM/MM molecular dynamics simulations (J. Chem. Phys. 2013, 139, 214304). The temporal evolution of ionization energies for the excited ππ* state along the QM/MM molecular dynamics trajectories were calculated and are compatible with experimental results, where the two contributions correspond to the relaxation paths in the ππ* state involving different conical intersections with the ground state. Theoretical calculations also show that ionization from the nπ* state is possible at the given photon energies, but we have not found any experimental indication for signal from the nπ* state. In contrast to currently accepted relaxation mechanisms, we suggest that the nπ* state is not involved in the relaxation process of thymine in aqueous solution.

Photosynthesis and photo-stability of nucleic acids in prebiotic extraterrestrial environments

Laboratory experiments have shown that the UV photo-irradiation of low-temperature ices of astrophysical interest leads to the formation of organic molecules, including molecules important for biology such as amino acids, quinones, and amphiphiles. When pyrimidine is introduced into these ices, the products of irradiation include the nucleobases uracil, cytosine, and thymine, the informational sub-units of DNA and RNA, as well as some of their isomers. The formation of these compounds, which has been studied both experimentally and theoretically, requires a succession of additions of OH, NH₂, and CH₃groups to pyrimidine. Results show that H₂O ice plays key roles in the formation of the nucleobases, as an oxidant, as a matrix in which reactions can take place, and as a catalyst that assists proton abstraction from intermediate compounds. As H₂O is also the most abundant icy component in most cold astrophysical environments, it probably plays the same roles in space in the formation of biologically relevant compounds. Results also show that although the formation of uracil and cytosine from pyrimidine in ices is fairly straightforward, the formation of thymine is not. This is mostly due to the fact that methylation is a limiting step for its formation, particularly in H₂O-rich ices, where methylation must compete with oxidation. The relative inefficiency of the abiotic formation of thymine to that of uracil and cytosine, together with the fact that thymine has not been detected in meteorites, are not inconsistent with the RNA world hypothesis. Indeed, a lack of abiotically produced thymine delivered to the early Earth may have forced the choice for an RNA world, in which only uracil and cytosine are needed, but not thymine.

Ultrafast non-radiative decay of gas-phase nucleosides

De-excitation of DNA nucleosides on picosecond timescales was measured and found to be twice as fast as the equivalent nucleobases.

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.

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.

Surface Hopping Dynamics with Correlated Single-Reference Methods: 9H-Adenine as a Case Study

Surface hopping dynamics methods using the coupled cluster to approximated second order (CC2), the algebraic diagrammatic construction scheme to second order (ADC(2)), and the time-dependent density functional theory (TDDFT) were developed and implemented into the program system Newton-X. These procedures are especially well-suited to simulate nonadiabatic processes involving various excited states of the same multiplicity and the dynamics in the first excited state toward an energetic minimum or up to the region where a crossing with the ground state is found. 9H-adenine in the gas phase was selected as the test case. The results showed that dynamics with ADC(2) is very stable, whereas CC2 dynamics fails within 100 fs, because of numerical instabilities present in the case of quasi-degenerate excited states. ADC(2) dynamics correctly predicts the ultrafast character of the deactivation process. It predicts that C2-puckered conical intersections should be the preferential pathway for internal conversion for low-energy excitation. C6-puckered conical intersection also contributes appreciably to internal conversion, becoming as important as C2-puckered for high-energy excitations. In any case, H-elimination plays only a minor role. TDDFT based on a long-range corrected functional fails to predict the ultrafast deactivation. In the comparison with several other methods previously used for dynamics simulations of adenine, ADC(2) has the best performance, providing the most consistent results so far.

Mapping the Ultrafast Dynamics of Adenine onto Its Nucleotide and Oligonucleotides by Time-Resolved Photoelectron Imaging

The intrinsic photophysics of nucleobases and nucleotides following UV absorption presents a key reductionist step toward understanding the complex photodamage mechanisms occurring in DNA. The decay mechanism of adenine in particular has been the focus of intense investigation, as has how these correlate to those of its more biologically relevant nucleotide and oligonucleotides in aqueous solution. Here, we report on time-resolved photoelectron imaging of the deprotonated 3'-deoxy-adenosine-5'-monophosphate nucleotide and the adenosine di- and trinucleotides. Through a comparison of gas- and solution-phase experiments and available theoretical studies, the dynamics of the base are shown to be relatively insensitive to the surrounding environment. The decay mechanism primarily involves internal conversion from the initially populated (1)ππ* states to the ground state. The relaxation dynamics of the adenosine oligonucleotides are similar to those of the nucleobase, in contrast to the aqueous oligonucleotides, where a fraction of the ensemble forms long-lived excimer states.

Probing the Conical Intersection Dynamics of the RNA Base Uracil by UV-Pump Stimulated-Raman-Probe Signals; Ab Initio Simulations

Nonadiabatic electron and nuclear dynamics of photoexcited molecules involving conical intersections is of fundamental importance in many reactions such as the self-protection mechanism of DNA and RNA bases against UV irradiation. Nonlinear vibrational spectroscopy can provide an ultrafast sensitive probe for these processes. We employ a simulation protocol that combines nonadiabatic on-the-fly molecular dynamics with a mode-tracking algorithm for the simulation of femtosecond stimulated Raman spectroscopy (SRS) signals of the high frequency C–H- and N–H-stretch vibrations of the photoexcited RNA base uracil. The simulations rely on a microscopically derived expression that takes into account the path integral of the excited state evolution and the pulse shapes. Analysis of the joint time/frequency resolution of the technique reveals a matter chirp contribution that limits the inherent temporal resolution. Characteristic signatures of relaxation dynamics mediated in the vicinity of conical intersection are predicted. The C–H and N–H spectator modes provide high sensitivity to their local environment and act as local probes with submolecular and high temporal resolution.

Time-resolved photoelectron imaging of the isolated deprotonated nucleotides

Time-resolved photoelectron spectroscopy of deprotonated nucleotides provides new insights into their relaxation dynamics.

Photoinduced processes in nucleic acids

Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.

Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond

In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach.

State-specific heavy-atom effect on intersystem crossing processes in 2-thiothymine: a potential photodynamic therapy photosensitizer

Thiothymidine has a potential application as a photosensitizer in cancer photodynamic therapy (PDT). As the chromophore of thiothymidine, 2-thiothymine exhibits ultrahigh quantum yield of intersystem crossing to the lowest triplet state T(1) (ca. 100%), which contrasts with the excited-state behavior of the natural thymine that dissipates excess electronic energy via ultrafast internal conversion to the ground state. In this work, we employed high-level complete-active space self-consistent field and its second-order perturbation methods to explore the photophysical mechanism of a 2-thiothymine model. We have optimized the minimum energy structures in the low-lying seven electronic states, as well as ten intersection points. On the basis of the computed potential energy profiles and spin-orbit couplings, we proposed three competitive, efficient nonadiabatic pathways to the lowest triplet state T(1) from the initially populated singlet state S(2). The suggested mechanistic scenario explains well the recent experimental phenomena. The origin responsible for the distinct photophysical behaviors between thymine and 2-thiothymine is ascribed to the heavy-atom effect, which is significantly enhanced in the latter. Additionally, this heavy-atom effect is found to be state-specific, which could in principle be used to tune the photophysics of 2-thiothymine. The present high-level electronic structure calculations also contribute to understand the working mechanism of thiothymidine in PDT.

Ultrafast dynamics of aniline following 269-238 nm excitation and the role of the S2(pi3s/pi sigma) state

Femtosecond time-resolved photoelectron imaging is employed to investigate ultrafast electronic relaxation in aniline, a prototypical aromatic amine. The molecule is excited at wavelengths between 269 and 238 nm. We observe that the S2(pi3s/pi sigma*) state is populated directly during the excitation process at all wavelengths and that the population bifurcates to two decay pathways. One of these involves ultrafast relaxation from the Rydberg component of S2(pi3s/pi sigma*) to the S1(Pi Pi)* state, from which it relaxes back to the electronic ground state on a much longer timescale. The other appears to involve motion along the pi sigma* dissociative potential energy surface. At higher excitation energies, the dominant excitation is to the S3(pi pi*) state, which undergoes extremely efficient electronic relaxation back to the ground state. Our study supports some conclusions reached from H-atom photofragment translational spectroscopy measurements and pump-probe photoionization measurements and contradicts some others.

Monitoring Non-Adiabatic Dynamics of the RNA Base Uracil by UV-Pump-IR-Probe Spectroscopy

Resolving the excited state dynamics of DNA- and RNA- nucleobases has attracted considerably attention. UV irradiation of the isolated nucleobases leads to the population of an electronic excited state which is quenched by internal conversion mediated by conical intersections on an ultrafast timescale. We present non-adiabatic on-the-fly molecular dynamics simulations of the UV-pump-IR-probe signal of the pyrimidine nucleobase uracil using a novel semiclassical protocol which takes into account the path integral over the excited state vibrational dynamics and properly describes the joint temporal and spectral resolution of the technique. Simulations of vibrational motions of carbonyl fingerprint modes in the electronically excited states reveal clear signatures of different relaxation pathways on a timescale of hundreds of femtoseconds which arise from an ultrafast branching in the excited state. We show that the inherent temporal and spectral resolution of the technique is not purely instrumental but also depends on the vibrational fluctuation timescale.

ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization

Non-adiabatic on-the-fly molecular dynamics (NA-O-MD) simulations require the electronic wavefunction, energy gradients, and derivative coupling vectors in every timestep. Thus, they are commonly restricted to the excited state dynamics of molecules with up to ≈20 atoms. We discuss an approximation that combines the ONIOM(QM:QM) method with NA-O-MD simulations to allow calculations for larger molecules. As a proof of principle we present the excited state dynamics of a (6-4)-lesion containing dinucleotide (63 atoms), and especially the importance to include the confinement effects of the DNA backbone. The method is able to include electron correlation on a high level of theory and offers an attractive alternative to QM:MM approaches for moderate sized systems with unknown force fields.

Interplay between vibrational energy transfer and excited state deactivation in DNA components

Femtosecond laser spectroscopies are used to examine a thymine family of systems chosen to expose the interplay between excited state deactivation and two distinct vibrational energy transfer (VET) pathways: (i) VET from the base to the deoxyribose ring; (ii) VET between neighboring units in a dinucleotide. We find that relaxation in the ground electronic state accelerates markedly as the molecular sizes increase from the nucleobase to the dinucleotide. This behavior directly reflects growth in the density of vibrational quantum states on the substituent of the base. Excited state lifetimes are studied at temperatures ranging from 100 to 300 K to characterize the thermal fluctuations that connect the Franck-Condon geometries and the conical intersections leading back to the ground state. An Arrhenius analysis yields an approximate excited state energy barrier of 13 meV in the thymine dinucleotide. In addition, we find that the transfer of vibrational energy from the base to the substituent suppresses thermal fluctuations across this energy barrier. The possibility that the solvent viscosity imposes friction on the reaction coordinate is examined by comparing thymine and adenine systems. Experiments suggest that the solvent viscosity has little effect on barrier crossing dynamics in thymine because the conical intersection is accessed through relatively small out-of-plane atomic displacements. Overall, we conclude that the transfer of vibrational quanta from thymine to the deoxyribose ring couples significantly to the internal conversion rate, whereas the neighboring unit in the dinucleotide serves as a secondary heat bath. In natural DNA, it follows that (local) thermal fluctuations in the geometries of subunits involving the base and deoxyribose ring are most important to this subpicosecond relaxation process.

Shedding new light on the role of the Rydberg state in the photochemistry of aniline

Efficient electronic relaxation following the absorption of ultraviolet light is crucial for the photostability of biological chromophores, so understanding the microscopic details of the decay pathways is of considerable interest. Here, we employ femtosecond time-resolved photoelectron imaging to investigate the ultrafast intramolecular dynamics of aniline, a prototypical aromatic amine, following excitation just below the second absorption maximum. We find that both the second ππ* state and the Rydberg state are populated during the excitation process. Surprisingly, the dominant non-radiative decay pathway is an ultrafast relaxation mechanism that transfers population straight back to the electronic ground-state. The vibrational energy resolution and photoelectron angular distributions obtained in our experiments reveal an interesting bifurcation of the Rydberg population to two non-radiative decay channels. The existence of these competing non-radiative relaxation channels in aniline illustrates how its photostability arises from a subtle balance between dynamics on different electronically excited states and importantly between Rydberg and valence states.