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

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.

Electronic relaxation mechanism of 9-methyl-2,6-diaminopurine and 2,6-diaminopurine-2'-deoxyribose in solution

Prolonged ultraviolet exposure results in the formation of cyclobutane pyrimidine dimers (CPDs) in RNA. Consequently, prebiotic photolesion repair mechanisms should have played an important role in the maintenance of the structural integrity of primitive nucleic acids. 2,6-Diaminopurine is a prebiotic nucleobase that repairs CPDs with high efficiency when incorporated into polymers. We investigate the electronic deactivation pathways of 2,6-diaminopurine-2'-deoxyribose and 9-methyl-2,6-diaminopurine in acetonitrile and aqueous solution to shed light on the photophysical and excited state properties of the 2,6-diaminopurine chromophore. Evidence is presented that both are photostable compounds exhibiting similar deactivation mechanisms upon the population of the S1 (ππ* La ) state at 290 nm. The mechanism involves deactivation through the C2- and C6-reaction coordinates and >99% of the excited state population decays through nonradiative pathways involving two conical intersections with the ground state. The radiative and nonradiative lifetimes are longer in aqueous solution compared to acetonitrile. While τ1 is similar in both derivatives, τ2 is ca. 1.5-fold longer in 2,6-diaminopurine-2'-deoxyribose due to a more efficient trapping in the S1 (ππ* La ) minimum. Therefore, 2,6-diaminopurine could have accumulated in significant quantities during prebiotic times to be incorporated into non-canonical RNA and play a significant role in its photoprotection.

Unraveling the ultrafast dynamics of thermal-energy chemical reactions

In this perspective, we discuss how one can initiate, image, and disentangle the ultrafast elementary steps of thermal-energy chemical dynamics, building upon advances in technology and scientific insight. We propose that combinations of ultrashort mid-infrared laser pulses, controlled molecular species in the gas phase, and forefront imaging techniques allow to unravel the elementary steps of general-chemistry reaction processes in real time. We detail, for prototypical first reaction systems, experimental methods enabling these investigations, how to sufficiently prepare and promote gas-phase samples to thermal-energy reactive states with contemporary ultrashort mid-infrared laser systems, and how to image the initiated ultrafast chemical dynamics. The results of such experiments will clearly further our understanding of general-chemistry reaction dynamics.

Rydberg state dynamics and fragmentation mechanism of N,N,N',N'-tetramethylmethylenediamine

The non-adiabatic relaxation processes and the fragmentation dynamics of Rydberg-excited N,N,N',N'-tetramethylmethylenediamine (TMMDA) are investigated using femtosecond time-resolved photoelectron imaging and time-resolved mass spectroscopy. Excitation at 208 nm populates TMMDA in a charge-localized 3p state. Rapid internal conversion (IC) to 3s produces two charge-delocalized conformers with independent time constants and distinct population ratios. As the system explores the 3s potential surface, the structural evolution continues on a 1.55 ps timescale, followed by a slower (12.1 ps) relaxation to the ground state. A thorough comparison of the time-dependent mass and photoelectron spectra suggests that ionization out of the 3p state ends up with the parent ion, the vibrational energy of which is insufficient for the bond cleavage. On the contrary, by virtue of the additional energy acquired by IC from 3p, the internal energy deposited in 3s is available to break the C-N bond, leading to the fragment ion. The fragmentation is found to occur on the ion surface instead of the Rydberg surface.

Structural dynamics upon photoinduced charge transfer in N,N,N',N'-tetramethylmethylenediamine

The ultrafast structural motion linked to the charge transfer process in Rydberg excited N,N,N',N'-tetramethylmethylenediamine (TMMDA) has been monitored in real time using femtosecond time-resolved photoelectron imaging coupled with quantum chemical calculations. Optical excitation to the 3 s Rydberg state initially populates the charge on one of the two amine groups, resulting in a charge-localized structure in the Franck-Condon (FC) region. As the wavepacket evolves on the 3 s potential surface, the molecular geometry changes with time, leading to the corresponding variation in the charge distribution. The ensuing structural evolution yields two distinct conformers GG⁺ and TT⁺ (see text for nomenclature), both with the charge delocalized between the two nitrogen atoms. By virtue of the sensitivity of the Rydberg electron binding energy (BE) on the nuclear geometry, the time-dependent BE spectrum offers an intuitive mapping of the charge transfer reaction that leads from the initially prepared charge-localized GG-FC structure to the fully charge-delocalized GG⁺ and TT⁺ structures. Complementary computations provide evidence that through-space interaction is responsible for the charge delocalization in the GG⁺ and TT⁺ structures.

Femtosecond Time-Resolved Observation of Relaxation and Wave Packet Dynamics of the S1 State in Electronically Excited o-Fluoroaniline

Quantum beat frequency is the basis for understanding interference effects and vibrational wave packet dynamics and has important applications. Using femtosecond time-resolved mass spectrometry and femtosecond time-resolved photoelectron image combined with theoretical calculations, we study the electronic excited-state relaxation of o-fluoraniline molecule and the time-dependent evolution of vibrational wave packets between different eigenstates. After the molecule absorbs a photon of 288.3 nm and is excited to the S₁ state, intramolecular vibrational redistribution first occurs on the time scale τ₁ = 349 fs, and then the transition to the triplet state occurs through the intersystem crossing on the time scale τ₂ = 583 ps, and finally, the triplet state occurs decays slowly through the time scale τ₃ = 2074 ps. We find the intramolecular vibrational redistribution is caused by the 0⁰, 10b¹ and 16a¹ vibrational modes of the S_l state origin. That is, the 288.3 nm femtosecond laser excites the molecule to the S₁ state, and the continuous flow of the vibrational wave packet prepares a coherent superposition state of three vibrational modes. Through extracting the oscillation of different peak intensities in the photoelectron spectrum, we observe reversible changes caused by mutual interference of the S₁ 0⁰, S₁ 10b¹ and S₁ 16a¹ states when the wave packets flow. When the pump pulse is 280 nm, the beat frequency disappears completely. This is explained in terms of increases in the vibrational field density and characteristic period of oscillation, and statistical averaging makes the quantum effect smooth and indistinguishable. In addition, the Rydberg component of the S₁ state is more clearly resolved by combining experiment and theory.

Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT

The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.

A Perspective on Femtosecond Pump-Probe Spectroscopy in the Development of Future Sunscreens

Given the negative impacts of overexposure to ultraviolet radiation (UVR) on humans, sunscreens have become a widely used product. Certain ingredients within sunscreens are responsible for photoprotection and these are known, collectively herein, as ultraviolet (UV) filters. Generally speaking, organic UV filters work by absorbing the potentially harmful UVR and dissipating this energy as harmless heat. This process happens on picosecond time scales and so femtosecond pump–probe spectroscopy (FPPS) is an ideal technique for tracking this energy conversion in real time. Coupling FPPS with complementary techniques, including steady-state spectroscopy and computational methods, can provide a detailed mechanistic picture of how UV filters provide photoprotection. As such, FPPS is crucial in aiding the future design of UV filters. This Perspective sheds light on the advancements made over the past two years on both approved and nature-inspired UV filters. Moreover, we suggest where FPPS can be further utilized within sunscreen applications for future considerations.

Photoelectron Spectroscopy and Theoretical Investigations of Gaseous Doubly Deprotonated 2'-Deoxynucleoside 5'-Monophosphate Dianions

A better understanding of the mechanism of oxidative DNA damage requires obtaining a molecular level description of nucleotides in various charge states. Herein, we report a systematic photoelectron spectroscopy and theoretical investigation of the electronic and geometric structures of four doubly deprotonated 2'-deoxynucleoside 5'-monophosphate dianions, the smallest quintessential DNA building block. These dianions are intrinsically stable with their adiabatic/vertical detachment energies (ADE/VDE) ranging from 0.85/1.07 (A) and 1.05/1.30 (G) to 1.20/1.50 (C) and 1.80/2.10 eV (T). The repulsive Coulomb barrier against electron detachment is 2.0 eV for purines and 2.5 eV for pyrimidines. Dianions are deprotonated at the phosphate group and the amino group of a nucleobase. The π-type HOMO orbital resides on the nucleobase moiety for each dianion. This spatial distribution of HOMO suggests that the most loosely bound electron is detached along the direction perpendicular to the nucleobase. When combined with the previous results, this work makes complete the depiction of basic building blocks of DNA at the molecular level.

Electron Attachment to Isolated Molecules as a Probe to Understand Mitochondrial Reductive Processes

This chapter describes the complementary experimental techniques Electron Transmission Spectroscopy and Dissociative Electron Attachment Spectroscopy, two of the most suitable means for investigating interactions between electrons and gas-phase molecules, resonance formation of temporary molecular negative ions, and their possible decay through the dissociative electron attachment (DEA) mechanism. The latter can be seen as the gas-phase counterpart of the transfer of a solvated electron in solution, accompanied by dissociation of the molecular anion, referred to as dissociative electron transfer (DET). DET takes place in vivo under reductive conditions, for instance, in the intermembrane space of mitochondria under interaction of xenobiotic molecules possessing high electron affinity with electrons "leaked" from the mitochondrial respiratory chain. A likely mechanism of the toxic activity of dichlorodiphenyltrichloroethane based on its DEA properties is briefly outlined, and compared with the well-established harmful effects of the model toxicant carbon tetrachloride ascribed to reductive dechlorination in a cellular ambient. A possible mechanism of the antioxidant activity of polyphenolic compounds present near the main site of superoxide anion production in mitochondria is also briefly discussed.

Ultrafast Photo-ion Probing of the Ring-Opening Process in Trans-Stilbene Oxide

The ultrafast photo‐induced ring opening of the oxirane derivative trans‐stilbene oxide has been studied through the use of ultrafast UV/UV pump‐probe spectroscopy by using photo‐ion detection. Single‐ and multiphoton probe paths and final states were identified through comparisons between UV power studies and synchrotron‐based vacuum ultraviolet (VUV) single‐photon ionization studies. Three major time‐dependent features of the parent ion (sub‐450 fs decay, (1.5±0.2) ps, and >100 ps) were observed. These decays are discussed in conjunction with the primary ring‐opening mechanism of stilbene oxide, which occurs through C−C dissociation in the oxirane ring. The appearance of fragments relating to the masses of dehydrogenated diphenylmethane (167 amu) and dehydrogenated methylbenzene (90 amu) were also investigated. The appearance of the 167 amu fragment could suggest an alternative ultrafast ring‐opening pathway via the dissociation of one of the C−O bonds within the oxirane ring.

Thermal desorption effects on fragment ion production from multi-photon ionized uridine and selected analogues

Experiments on neutral gas-phase nucleosides are often complicated by thermal lability. Previous mass spectrometry studies of nucleosides have identified enhanced relative production of nucleobase ions (e.g. uracil⁺ from uridine) as a function of desorption temperature to be the critical indicator of thermal decomposition. On this basis, the present multi-photon ionization (MPI) experiments demonstrate that laser-based thermal desorption is effective for producing uridine, 5-methyluridine, and 2′-deoxyuridine targets without thermal decomposition. Our experiments also revealed one notable thermal dependence: the relative production of the sugar ion C₅H₉O₄⁺ from intact uridine increased substantially with the desorption laser power and this only occurred at MPI wavelengths below 250 nm (full range studied 222–265 nm). We argue that this effect can only be rationalized plausibly in terms of changing populations of different isomers, tautomers, or conformers in the target as a function of the thermal desorption conditions. Furthermore, the wavelength threshold behavior of this thermally-sensitive MPI channel indicates a critical dependence on neutral excited state dynamics between the absorption of the first and second photons. The experimental results are complemented by density functional theory (DFT) optimizations of the lowest-energy structure of uridine and two further conformers distinguished by different orientations of the hydroxymethyl group on the sugar part of the molecule. The energies of the transitions states between these three conformers are low compared with the energy required for decomposition.

This work reveals the first experimental evidence supporting isomer-dependence in the radiation response of a nucleoside.

Intramolecular Photo-Oxidation as a Potential Source to Probe Biological Electron Damage: A Carboxylated Adenosine Analogue as Case Study

A carboxylated adenosine analog (C-Ado-) has been synthesized and probed via time-resolved photoelectron spectroscopy in order to induce intra-molecular charge transfer from the carboxylic acid moiety to the nucleobase. Intra-molecular charge transfer can be exploited as starting point to probe low-energy electron (LEE) damage in DNA and its derivatives. Time-dependent density functional theory (TD-DFT) calculations at the B3LYP-6311G level of theory have been performed to verify that the highest occupied molecular orbital (HOMO) was located on carboxylic acid and that the lowest occupied molecular orbital (LUMO) was on the nucleobase. Hence, the carboxylic acid could work as electron source, whilst the nucleobase could serve the purpose of electron acceptor. The dynamics following excitation at 4.66 eV (266 nm) were probed using time-resolved photoelectron spectroscopy using probes at 1.55 eV (800 nm) and 3.10 eV (400 nm). The data show rapid decay of the excited state population and, based on the similarity of the overall dynamics to deoxy-adenosine monophosphate (dAMP-), it appears that the dominant decay mechanism is internal conversion following 1ππ* excitation of the nucleobase, rather than charge-transfer from the carboxylic acid to the nucleobase.

Ultrafast Dynamics of the Isolated Adenosine-5'-triphosphate Dianion Probed by Time-Resolved Photoelectron Imaging

The excited state dynamics of the doubly deprotonated dianion of adenosine-5'-triphosphate, [ATP-H₂]^2-, has been spectroscopically explored by time-resolved photoelectron spectroscopy following excitation at 4.66 eV. Time-resolved photoelectron spectra show that two competing processes occur for the initially populated ¹ππ* state. The first is rapid electron emission by tunneling through a repulsive Coulomb barrier as the ¹ππ* state is a resonance. The second is nuclear motion on the ¹ππ* state surface leading to an intermediate that no longer tunnels and subsequently decays by internal conversion to the ground electronic state. The spectral signatures of the features are similar to those observed for other adenine-derivatives, suggesting that this nucleobase is quite insensitive to the nearby negative charges localized on the phosphates, except of course for the appearance of the additional electron tunneling channel, which is open in the dianion.

Simulation of UV absorption spectra and relaxation dynamics of uracil and uracil-water clusters

Despite many studies, the mechanisms of nonradiative relaxation of uracil in the gas phase and in aqueous solution are still not fully resolved. Here we combine theoretical UV absorption spectroscopy with nonadiabatic dynamics simulations to identify the photophysical mechanisms that can give rise to experimentally observed decay time constants. We first compute and theoretically assign the electronic spectra of uracil using the second-order algebraic-diagrammatic-construction (ADC(2)) method. The obtained electronic states, their energy differences and state-specific solvation effects are the prerequisites for understanding the photodynamics. We then use nonadiabatic trajectory-surface-hopping dynamics simulations to investigate the photoinduced dynamics of uracil and uracil-water clusters. In contrast to previous studies, we found that a single mechanism - the ethylenic twist around the C[double bond, length as m-dash]C bond - is responsible for the ultrafast component of the nonradiative decay, both in the gas phase and in solution. Very good agreement with the experimentally determined ultrashort decay time constants is obtained.

Ultraviolet-light-triggered isomerization of Rydberg-excited propanal: Real-time capture of ultrafast structural evolution and dynamics investigation

Structure rearrangement processes, such as isomerization, are attracting extensive interest as a potential carrier in molecular scale electronics design. UV-light-triggered isomerization of Rydberg-excited propanal with two UV photons has been investigated with time-resolved photoelectron spectroscopy. By following the photoionization from 3s Rydberg states in the time domain, the ultrafast structural evolution and the corresponding photoisomerization dynamics are observed and tracked in real-time. The conversion barrier for isomerization from cis-propanal to gauche isomer is estimated to be about 1500 ± 100 cm^-1 experimentally. Both the photoisomerization yield and the conversion rate have shown strong dependence on the excitation energy. It is observed that whether vibration modes are selectively excited or not, cis-to-gauche photoisomerization of propanal in 3s Rydberg state occurs once the excitation energy is higher than the conversion barrier without any vibrational excitation specificity. This yields a powerful approach to studying structural evolution dynamics in large molecules, which may have applications in molecular devices.

Site-Specific Photo-oxidation of the Isolated Adenosine-5'-triphosphate Dianion Determined by Photoelectron Imaging

Photoelectron imaging of the isolated adenosine-5'-triphosphate dianion excited to the ¹ππ* states reveals that electron emission is predominantly parallel to the polarization axis of the light and arises from subpicosecond electron tunneling through the repulsive Coulomb barrier (RCB). The computed RCB shows that the most probable electron emission site is on the amino group of adenine. This is consistent with the photoelectron imaging: excitation to the ¹ππ* states leads to an aligned ensemble distributed predominantly parallel to the long axis of adenine; the subsequent electron tunneling site is along this axis; and the negatively charged phosphate groups guide the outgoing electron mostly along this axis at long range. Imaging of electron tunneling from polyanions combined with computational chemistry may offer a general route for probing the intrinsic photo-oxidation site and dynamics as well as the overall structure of complex isolated species.

On the Origin of the Photostability of DNA and RNA Monomers: Excited State Relaxation Mechanism of the Pyrimidine Chromophore

Today's genetic composition is the result of continual refinement processes on primordial heterocycles present in prebiotic Earth and at least partially regulated by ultraviolet radiation. Femtosecond transient absorption spectroscopy and state-of-the-art ab initio calculations are combined to unravel the electronic relaxation mechanism of pyrimidine, the common chromophore of the nucleobases. The excitation of pyrimidine at 268 nm populates the S₁(nπ*) state directly. A fraction of the population intersystem crosses to the triplet manifold within 7.8 ps, partially decaying within 1.5 ns, while another fraction recovers the ground state in >3 ns. The pyrimidine chromophore is not responsible for the photostability of the nucleobases. Instead, C2 and C4 amino and/or carbonyl functionalization is essential for shaping the topography of pyrimidine's potential energy surfaces and results in accessible conical intersections between the initially populated electronic excited state and the ground state.

From Neutral Aniline to Aniline Trication: A Computational and Experimental Study

We report density functional theory computations and photoionization mass spectrometry measurements of aniline and its positively charged ions. The geometrical structures and properties of the neutral and singly, doubly, and triply positively charged aniline are computed using density functional theory with the generalized gradient approximation. At each charge, there are multiple isomers closely spaced in total energy. Whereas the lowest energy states of both neutral and cation have the same topology C₆H₅-NH₂, the dication and trication have the C₅NH₅-CH₂ topology with the nitrogen atom in the meta- and para-positions, respectively. We compute the dissociation pathways of all four charge states to NH or NH⁺ and NH₂ or NH₂⁺, depending on the initial charge of the aniline precursor. Dissociation leading to the formation of NH (from the neutral and cation) and NH⁺ (from the dication and trication) proceeds through multiple transition states. On the contrary, the dissociation of NH₂ (from the neutral and cation) and NH₂⁺ (from the dication and trication) is found to proceed without an activation energy barrier. The trication was found to be stable toward abstraction on NH⁺ and NH₂⁺ by 0.96 and 0.18 eV, respectively, whereas the proton affinity of the trication is substantially higher, 1.98 eV. The mass spectra of aniline were recorded with 1300 nm, 20 fs pulses over the peak intensity range of 1 × 10¹³ to 3 × 10¹⁴ W cm^-2. The analysis of the mass spectra suggests high stability of both dication and trication to fragmentation. The formation of the fragment NH⁺ and NH₂⁺ ions is found to proceed via Coulomb explosion.

Ultrafast valence to non-valence excited state dynamics in a common anionic chromophore

Non-valence states in neutral molecules (Rydberg states) have well-established roles and importance in photochemistry, however, considerably less is known about the role of non-valence states in photo-induced processes in anions. Here, femtosecond time-resolved photoelectron imaging is used to show that photoexcitation of the S₁(ππ*) state of the methyl ester of deprotonated para-coumaric acid – a model chromophore for photoactive yellow protein (PYP) – leads to a bifurcation of the excited state wavepacket. One part remains on the S₁(ππ*) state forming a twisted intermediate, whilst a second part leads to the formation of a non-valence (dipole-bound) state. Both populations eventually decay independently by vibrational autodetachment. Valence-to-non-valence internal conversion has hitherto not been observed in the intramolecular photophysics of an isolated anion, raising questions into how common such processes might be, given that many anionic chromophores have bright valence states near the detachment threshold.

Photoactive biomolecules rely on chromophores whose photochemistry depends on the environment. Here, the excited state dynamics of a model for the anionic biochromophore in photoactive yellow protein is investigated by time-resolved photoelectron spectroscopy showing involvement of a non-valence state, and lack of E-Z isomerisation in the gas phase.

Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy

The relaxation dynamics of thymine and its derivatives thymidine and thymidine monophosphate are studied using time-resolved photoelectron spectroscopy applied to a water microjet. Two absorption bands are studied; the first is a bright ππ* state which is populated using tunable-ultraviolet light in the range 4.74-5.17 eV and probed using a 6.20 eV probe pulse. By reversing the order of these pulses, a band containing multiple ππ* states is populated by the 6.20 eV pulse and the lower energy pulse serves as the probe. The lower lying ππ* state is found to decay in ∼400 fs in both thymine and thymidine independent of pump photon energy, while thymidine monophosphate decays vary from 670 to 840 fs with some pump energy dependence. The application of a computational quantum mechanical/molecular mechanical scheme at the XMS-CASPT2//CASSCF/AMBER level of theory suggests that conformational differences existing between thymidine and thymidine monophosphate in solution account for this difference. The higher lying ππ* band is found to decay in ∼600 fs in all three cases, but it is only able to be characterized when the 5.17 eV probe pulse is used. Notably, no long-lived signal from an nπ* state can be identified in either experiment on any of the three molecules.

UV absorption spectra of DNA bases in the 350-190 nm range: assignment and state specific analysis of solvation effects

The theoretical assignment of electronic spectra of polyatomic molecules is a challenging problem that requires the specification of the character of a large number of electronic states. We propose a procedure for automatically determining the character of electronic transitions and apply it to the study of UV spectra of DNA bases in the gas phase and in the aqueous environment. The procedure is based on the computation of electronic wave function overlaps and accounts for an extensive sampling of nuclear geometries. Novelties of this work are the theoretical assignment of the electronic spectra of DNA bases up to 190 nm and a state specific analysis of solvation effects. By accounting for different effects contributing to the total solvent shift we obtained a good agreement between the computed and experimental spectra. Effects of vibrational averaging, temperature and solvent-induced structural changes shift excitation energies to lower values. Solvent-solute electrostatic interactions are state specific and strongly destabilize nRyd states, and to lesser extent nπ* and πRyd states. Altogether, this results in the stabilization of ππ* states and destabilization of nπ*, πRyd and nRyd states in solution.

Femtosecond real-time probing of the excited-state intramolecular proton transfer reaction in methyl salicylate

The excited-state intramolecular proton transfer (ESIPT) process and subsequent electronic relaxation dynamics in methyl salicylate have been investigated using femtosecond time-resolved ion yield spectroscopy combined with time-resolved photoelectron imaging. Excitation with a tunable pump pulse populates the keto tautomer in the first excited electronic state S₁(ππ^*). As a hydrogen atom transfers from the phenolic group to the carbonyl group within 100 fs, the molecular geometry changes gradually, leading to a variation in the electronic photoionization channel. By virtue of the accidental resonance with some intermediate Rydberg states, the time-dependent photoelectron spectra provide a direct mapping of the ESIPT reaction from the initially populated keto tautomer to the proton-transferred enol tautomer. Subsequently, the population around the enol configuration undergoes intramolecular vibrational redistribution on a subpicosecond time scale, followed by internal conversion to the ground state with a wavelength-dependent lifetime in the picosecond range. Furthermore, the excitation energies of several Rydberg states in methyl salicylate are determined experimentally.

Design and characterization of a recirculating liquid-microjet photoelectron spectrometer for multiphoton ultraviolet photoelectron spectroscopy

A new recirculating liquid-microjet photoelectron spectrometer for multiphoton ultraviolet photoelectron spectroscopy is described. A recirculating system is essential for studying samples that are only available in relatively small quantities. The reduction in background pressure when using the recirculating system compared to a liquid-nitrogen cold-trap results in a significant improvement in the quality of the photoelectron spectra. Moreover, the recirculating system results in a negligible streaming potential. The instrument design, operation, and characterization are described in detail, and its performance is illustrated by comparing a photoelectron spectrum of aqueous phenol recorded using the recirculating system with one recorded using a liquid nitrogen cold-trap.

Initial excited-state structural dynamics of 2′-deoxyadenosine

Purine nucleobases (adenosine and guanosine) are prone to spontaneous breaking of the nucleosidic bond to form abasic sites in both DNA and RNA. However, the purines also undergo photochemical reactions, including oxidation and cycloaddition, to form damage sites, albeit at lower photochemical quantum yields than the pyrimidines. In this study, we use ultraviolet resonance Raman spectroscopy to measure the initial excited-state structural dynamics in the nucleoside, 2′-deoxyadenosine. The resonance Raman-derived initial excited-state structural dynamics throughout the 260 nm La excited electronic state of adenine are found to be smaller in the nucleoside than in the previously reported 9-methyladenine nucleobase derivative, consistent with what is found for the pyrimidines thymine and uracil. Interestingly, resonance-enhanced vibrational modes in this electronic state also contain internal coordinates localized on the sugar, which may represent a different energy dissipation mechanism than in the pyrimidine nucleosides. The results will be discussed in terms of the initial excited-state photophysics and photochemistry of DNA and RNA.

Excited-State Dynamics in the RNA Nucleotide Uridine 5'-Monophosphate Investigated Using Femtosecond Broadband Transient Absorption Spectroscopy

Damage to RNA from ultraviolet radiation induces chemical modifications to the nucleobases. Unraveling the excited states involved in these reactions is essential; however, investigations aimed at understanding the electronic-energy relaxation pathways of the RNA nucleotide uridine 5'-monophosphate (UMP) have not received enough attention. In this Letter, the excited-state dynamics of UMP is investigated in aqueous solution. Excitation at 267 nm results in a trifurcation event that leads to the simultaneous population of the vibrationally excited ground state, a long-lived ¹nπ* state, and a receiver triplet state within 200 fs. The receiver state internally converts to the long-lived ³ππ* state in an ultrafast time scale. The results elucidate the electronic relaxation pathways and clarify earlier transient absorption experiments performed for uracil derivatives in solution. This mechanistic information is important because long-lived nπ* and ππ* excited states of both singlet and triplet multiplicities are thought to lead to the formation of harmful photoproducts.

Time-resolved radiation chemistry: femtosecond photoelectron spectroscopy of electron attachment and photodissociation dynamics in iodide-nucleobase clusters

Iodide-nucleobase (I-·N) clusters studied by time-resolved photoelectron spectroscopy (TRPES) are an opportune model system for examining radiative damage of DNA induced by low-energy electrons. By initiating charge transfer from iodide to the nucleobase and following the dynamics of the resulting transient negative ions (TNIs) with femtosecond time resolution, TRPES provides a novel window into the chemistry triggered by the attachment of low-energy electrons to nucleobases. In this Perspective, we examine and compare the dynamics of electron attachment, autodetachment, and photodissociation in a variety of I-·N clusters, including iodide-uracil (I-·U), iodide-thymine (I-·T), iodide-uracil-water (I-·U·H2O), and iodide-adenine (I-·A), to develop a more unified representation of our understanding of nucleobase TNIs. The experiments probe whether dipole-bound or valence-bound TNIs are formed initially and the subsequent time evolution of these species. We also provide an outlook for forthcoming applications of TRPES to larger iodide-containing complexes to enable the further investigation of microhydration dynamics in nucleobases, as well as electron attachment and photodissociation in more complex nucleic acid constituents.

Probing Coherent Vibrations of Organic Phosphonate Radical Cations with Femtosecond Time-Resolved Mass Spectrometry

Organic phosphates and phosphonates are present in a number of cellular components that can be damaged by exposure to ionizing radiation. This work reports femtosecond time-resolved mass spectrometry (FTRMS) studies of three organic phosphonate radical cations that model the DNA sugar-phosphate backbone: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), and diisopropyl methylphosphonate (DIMP). Upon ionization, each molecular radical cation exhibits unique oscillatory dynamics in its ion yields resulting from coherent vibrational excitation. DMMP has particularly well-resolved 45 fs ( 732 ± 28 cm - 1 ) oscillations with a weak feature at 610⁻650 cm - 1 , while DIMP exhibits bimodal oscillations with a period of ∼55 fs and two frequency features at 554 ± 28 and 670⁻720 cm - 1 . In contrast, the oscillations in DEMP decay too rapidly for effective resolution. The low- and high-frequency oscillations in DMMP and DIMP are assigned to coherent excitation of the symmetric O⁻P⁻O bend and P⁻C stretch, respectively. The observation of the same ionization-induced coherently excited vibrations in related molecules suggests a possible common excitation pathway in ionized organophosphorus compounds of biological relevance, while the distinct oscillatory dynamics in each molecule points to the potential use of FTRMS to distinguish among fragment ions produced by related molecules.

New insights into the dissociation dynamics of methylated anilines

Combined time-resolved photoelectron spectroscopy and photofragment imaging supports a possible valence-to-Rydberg decay mechanism in methylated anilines.

Imaging Reversible and Irreversible Structural Evolution in Photoexcited 2,4-Difluoroaniline

Here, we demonstrate the capability of femtosecond time-resolved photoelectron imaging to visualize the reversible and irreversible structural evolution in electronically excited 2,4-difluoroaniline. As a coherent superposition of out-of-plane vibrational motions is created following 299.8 nm excitation, the molecular geometry alters periodically, thus modulating the photoionization channel. The reversible nuclear motion between distinct geometries is directly observed as the reverse beats in the time-dependent photoelectron spectra. Moreover, with the molecule highly vibrationally excited at 289.0 nm, the exponential decrease/increase changes in photoelectron signal provide a physically intuitive and complete picture of the irreversible geometry rearrangement away from a nonplanar geometry in the vertical Franck-Condon region toward the planar minimum.

Coherent two-dimensional electronic mass spectrometry

Coherent two-dimensional (2D) optical spectroscopy has revolutionized our ability to probe many types of couplings and ultrafast dynamics in complex quantum systems. The dynamics and function of any quantum system strongly depend on couplings to the environment. Thus, studying coherent interactions for different environments remains a topic of tremendous interest. Here we introduce coherent 2D electronic mass spectrometry that allows 2D measurements on effusive molecular beams and thus on quantum systems with minimum system–bath interaction and employ this to identify the major ionization pathway of 3d Rydberg states in NO₂. Furthermore, we present 2D spectra of multiphoton ionization, disclosing distinct differences in the nonlinear response functions leading to the ionization products. We also realize the equivalent of spectrally resolved transient-absorption measurements without the necessity for acquiring weak absorption changes. Using time-of-flight detection introduces cations as an observable, enabling the 2D spectroscopic study on isolated systems of photophysical and photochemical reactions.

Multidimensional spectroscopy is a powerful tool in exploring photo-induced dynamics and electron coupling processes in molecules. Here the authors demonstrate coherent two-dimensional electronic mass spectrometry on molecular beams and its application to photoionization studies of the NO₂ molecule.

Photoprotection: extending lessons learned from studying natural sunscreens to the design of artificial sunscreen constituents

Evolution has ensured that plants and animals have developed effective protection mechanisms against the potentially harmful effects of incident ultraviolet radiation (UVR). Tanning is one such mechanism in humans, but tanning only occurs post-exposure to UVR. Hence, there is ever growing use of commercial sunscreens to pre-empt overexposure to UVR. Key requirements for any chemical filter molecule used in such a photoprotective capacity include a large absorption cross-section in the UV-A and UV-B spectral regions and the availability of one or more mechanisms whereby the absorbed photon energy can be dissipated without loss of the molecular integrity of the chemical filter. Here we summarise recent experimental (mostly ultrafast pump-probe spectroscopy studies) and computational progress towards unravelling various excited state decay mechanisms that afford the necessary photostability in chemical filters found in nature and those used in commercial sunscreens. We also outline ways in which a better understanding of the photophysics and photochemistry of sunscreen molecules selected by nature could aid the design of new and improved commercial sunscreen formulations.

How nature covers its bases

The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.

Femtosecond time-resolved observation of butterfly vibration in electronically excited o-fluorophenol

The butterfly vibration during the hydrogen tunneling process in electronically excited o-fluorophenol has been visualized in real time by femtosecond time-resolved ion yield spectroscopy coupled with time-resolved photoelectron imaging technique. A coherent superposition of out-of-plane C–F butterfly motions is prepared in the first excited electronic state (S₁). As the C–F bond vibrates with respect to the aromatic ring, the nuclear geometry varies periodically, leading to the corresponding variation in the photoionization channel. By virtue of the more favorable ionization probability from the nonplanar minimum via resonance with the Rydberg states, the evolution of the vibrational wave packet is manifested as a superimposed beat in the parent-ion transient. Moreover, time-resolved photoelectron spectra offer a direct mapping of the oscillating butterfly vibration between the planar geometry and nonplanar minimum. The beats for the photoelectron peaks originating from the planar geometry are out of phase with those from the nonplanar minimum. Our results provide a physically intuitive and complete picture of the oscillatory flow of energy responsible for the coherent vibrational motion on the excited state surface.

Cluster Model Studies of Anion and Molecular Specificities via Electrospray Ionization Photoelectron Spectroscopy

Ion specificity, a widely observed macroscopic phenomenon in condensed phases and at interfaces, is a fundamental chemical physics issue. Herein we report our recent studies of such effects using cluster models in an "atom-by-atom" and "molecule-by-molecule" fashion not possible with the condensed-phase methods. We use electrospray ionization (ESI) to generate molecular and ionic clusters to simulate key molecular entities involved in local binding regions and characterize them by employing negative ion photoelectron spectroscopy (NIPES). Inter- and intramolecular interactions and binding configurations are directly obtained as functions of the cluster size and composition, providing molecular-level descriptions and characterization over the local active sites that play crucial roles in determining the solution chemistry and condensed-phase phenomena. The topics covered in this article are relevant to a wide range of research fields from ion specific effects in electrolyte solutions, ion selectivity/recognition in normal functioning of life, to molecular specificity in aerosol particle formation, as well as in rational material design and synthesis.

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.

Ultrafast dynamics in the DNA building blocks thymidine and thymine initiated by ionizing radiation

Ultrafast dynamics and fragmentation of thymidine and thymine after ionization by attosecond extreme ultraviolet radiation studied in the time-domain.

Dynamics of π*-resonances in anionic clusters of para-toluquinone

Frequency-resolved photoelectron spectroscopy applied to mass-selected cluster anions is an insightful approach to characterise the dynamics of π*-resonances with microsolvation.

A Perspective on the Ultrafast Photochemistry of Solution-Phase Sunscreen Molecules

Sunscreens are one of the most common ways of providing on-demand additional photoprotection to the skin. Ultrafast transient absorption spectroscopy has recently proven to be an invaluable tool in understanding how the components of commercial sunscreen products display efficient photoprotection. Important examples of how this technique has unravelled the photodynamics of common components are given in this Perspective, and some of the remaining unanswered questions are discussed.