Ultraviolet relaxation dynamics in uracil: Time-resolved photoion yield studies using a laser-based thermal desorption source

Time-resolved x-ray spectroscopy of nucleobases and their thionated analogs

The photoinduced relaxation dynamics of nucleobases and their thionated analogs have been investigated extensively over the past decades motivated by their crucial role in organisms and their application in medical and biochemical research and treatment. Most of these studies focused on the spectroscopy of valence electrons and fragmentation. The advent of ultrashort x-ray laser sources such as free-electron lasers, however, opens new opportunities for studying the ultrafast molecular relaxation dynamics utilizing the site- and element-selectivity of x-rays. In this review, we want to summarize ultrafast experiments on thymine and 2-thiouracil performed at free-electron lasers. We performed time-resolved x-ray absorption spectroscopy at the oxygen K-edge after UV excitation of thymine. In addition, we investigated the excited state dynamics of 2-tUra via x-ray photoelectron spectroscopy at sulfur. For these methods, we show a strong sensitivity to the electronic state or charge distribution, respectively. We also performed time-resolved Auger-Meitner spectroscopy, which shows spectral shifts associated with internuclear distances close to the probed site. We discuss the complementary aspects of time-resolved x-ray spectroscopy techniques compared to optical and UV spectroscopy for the investigation of ultrafast relaxation processes.

The importance of molecular axis alignment and symmetry-breaking in photoelectron elliptical dichroism

Photoelectron angular distributions (PADs) produced from the photoionization of chiral molecules using elliptically polarized light exhibit a forward/backward asymmetry with respect to the optical propagation direction. By recording these distributions using the velocity-map imaging (VMI) technique, the resulting photoelectron elliptical dichroism (PEELD) has previously been demonstrated as a promising spectroscopic tool for studying chiral molecules in the gas phase. The use of elliptically polarized laser pulses, however, produces PADs (and consequently, PEELD distributions) that do not exhibit cylindrical symmetry about the propagation axis. This leads to significant limitations and challenges when employing conventional VMI acquisition and data processing strategies. Using novel photoelectron image analysis methods based around Hankel transform reconstruction tomography and machine learning, however, we have quantified-for the first time-significant symmetry-breaking contributions to PEELD signals that are of a comparable magnitude to the symmetric terms in the multiphoton ionization of (1R,4R)-(+)- and (1S,4S)-(-)-camphor. This contradicts any assumptions that symmetry-breaking can be ignored when reconstructing VMI data. Furthermore, these same symmetry-breaking terms are expected to appear in any experiment where circular and linear laser fields are used together. This ionization scheme is particularly relevant for investigating dynamics in chiral molecules, but it is not limited to them. Developing a full understanding of these terms and the role they play in the photoionization of chiral molecules is of clear importance if the potential of PEELD and related effects for future practical applications is to be fully realized.

Design and characterization of an optical-fiber-coupled laser-induced desorption source for gas-phase dynamics experiments

Preparation of neutral non-volatile molecules intact in the gas phase for mass spectrometry or chemical dynamics experiments remains a challenge for many classes of molecules. Here, we report the design and characterization of a fiber-coupled laser-based thermal desorption source capable of preparing intact neutral molecules at high molecular densities in the gas phase for use in velocity-map imaging experiments. Within this source, the sample is deposited onto a thin tantalum foil. Irradiation of the foil from the reverse side by a focused laser beam leads to highly localized heating of the sample, resulting in desorption of a plume of molecules into the gas phase. The fiber-coupled design simplifies the alignment of the desorption laser beam, and the ability to rotate the foil relative to the fixed laser beam allows the sample to be continually refreshed under vacuum. We use 118 nm photoionization of three test molecules-uracil, adenine, and phenylalanine-to characterize the source and to demonstrate various aspects of its performance. These include the dependence of the velocity-map imaging performance on the size of the interaction region and the dependence of the laser-induced desorption source emission on desorption laser power and heating time. Signal levels recorded in these measurements are comparable to those we typically obtain in similar experiments using a pulsed supersonic molecular beam, and we, therefore, believe that the source has considerable potential for use in a wide range of chemical dynamics and other experiments.

High-Throughput UV Photoionization and Fragmentation of Neutral Biomolecules as a Structural Fingerprint

We present UV photofragmentation studies of the structural isomers paracetamol, 3-Pyridinepropionic acid (3-PPIA) and (R)-(-)-2-Phenylglycine. In particular, we utilized a new laser-based thermal desorption source in combination with femtosecond multiphoton ionization at 343 nm and 257 nm. The continuous nature of our molecule source, combined with the 50 kHz repetition rate of the laser, allowed us to perform these experiments at high throughput. In particular, we present detailed laser intensity dependence studies at both wavelengths, producing 2D mass spectra with highly differential information about the underlying fragmentation processes. We show that UV photofragmentation produces highly isomer-specific mass spectra, and assign all major fragmentation pathways observed. The intensity-dependence measurements, furthermore, allowed us to evaluate the appearance intensities for each fragmentation channel, which helped to distinguish competing from consecutive fragmentation pathways.

Vaporization of Intact Neutral Biomolecules Using Laser-Based Thermal Desorption

The production of a clean neutral molecular sample is a crucial step in many gas-phase spectroscopy and reaction dynamics experiments investigating neutral species. Unfortunately, conventional methods based on heating cannot be used with most nonvolatile biomolecules due to their thermal instability. In this paper, we demonstrate the application of laser-based thermal desorption (LBTD) to produce neutral molecular plumes of biomolecules such as dipeptides and lipids. Specifically, we report mass spectra of glycylglycine, glycyl-l-alanine, and cholesterol obtained using LBTD vaporization, followed by soft femtosecond multiphoton ionization (fs-MPI) at 400 nm. For all molecules, the signal from the intact precursor ion was observed, highlighting the softness and applicability of the LBTD and fs-MPI approach. In more detail, cholesterol underwent hardly any fragmentation. Both dipeptides fragmented significantly, although mostly through only a single channel, which we attribute to the fs-MPI process.

Photophysics of uracil: an explicit time-dependent generating function-based method combining both nonadiabatic and spin-orbit coupling effects

We present a composite framework for calculating the rates of non-radiative deactivation processes, namely internal conversion (IC) and intersystem crossing (ISC), on an equal footing by explicitly computing the non-adiabatic coupling (NAC) and spin-orbit coupling (SOC) constants, respectively. The stationary-state approach uses a time-dependent generating function based on Fermi's golden rule. We validate the applicability of the framework by computing the rate of IC for azulene, obtaining comparable rates to experimental and previous theoretical results. Next, we investigate the photophysics associated with the complex photodynamics of the uracil molecule. Interestingly, our simulated rates corroborate experimental observations. Detailed analyses using Duschinsky rotation matrices, displacement vectors and NAC matrix elements are presented to interpret the findings alongside testing the suitability of the approach for such molecular systems. The suitability of the Fermi's golden rule based method is explained qualitatively in terms of single-mode potential energy surfaces.

Ultrafast Photo-Ion Probing of the Relaxation Dynamics in 2-Thiouracil

In this work, we investigate the relaxation processes of 2-thiouracil after UV photoexcitation to the S₂ state through the use of ultrafast, single-colour, pump-probe UV/UV spectroscopy. We place focus on investigating the appearance and subsequent decay signals of ionized fragments. We complement this with VUV-induced dissociative photoionisation studies collected at a synchrotron, allowing us to better understand and assign the ionisation channels involved in the appearance of the fragments. We find that all fragments appear when single photons with energy > 11 eV are used in the VUV experiments and hence appear through 3+ photon-order processes when 266 nm light is used. We also observe three major decays for the fragment ions: a sub-autocorrelation decay (i.e., sub-370 fs), a secondary ultrafast decay on the order of 300-400 fs, and a long decay on the order of 220 to 400 ps (all fragment dependent). These decays agree well with the previously established S₂ → S₁ → Triplet → Ground decay process. Results from the VUV study also suggest that some of the fragments may be created by dynamics occurring in the excited cationic state.

Velocity-map imaging of photoelectron circular dichroism in non-volatile molecules using a laser-based desorption source

We present an initial demonstration of a velocity-map imaging (VMI) experiment using a back-irradiation laser-based desorption source directly integrated into the electrode assembly. This has the potential to greatly expand the utility of the popular VMI approach by permitting its use with high density plumes of non-volatile molecular samples. Photoelectron circular dichroism measurements on the phenylalanine molecule using 400 nm multiphoton ionization are used to illustrate this novel method, revealing forward-backward emission asymmetries on the order of 7%.

A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate

It is well-known that photolysis of pyrimidine nucleobases, such as uracil, in an aqueous environment results in the formation of hydrate as one of the main products. Although several hypotheses regarding photohydration have been proposed in the past, e.g., the zwitterionic and "hot" ground-state mechanisms, its detailed mechanism remains elusive. Here, theoretical nonadiabatic simulations of the uracil photodynamics reveal the formation of a highly energetic but kinetically stable intermediate that features a half-chair puckered pyrimidine ring and a strongly twisted intracyclic double bond. The existence and the kinetic stability of the intermediate are confirmed by a variety of computational chemistry methods. According to the simulations, the unusual intermediate is mainly formed almost immediately (∼50-200 fs) upon photoabsorption and survives long enough to engage in a hydration reaction with a neighboring water. A plausible mechanism of uracil photohydration is proposed on the basis of the modeling of nucleophilic insertion of water into the twisted double bond of the intermediate.

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.

Time Resolved Photoelectron Spectroscopy as a Test of Electronic Structure and Nonadiabatic Dynamics

We compare different levels of theory for simulating excited state molecular dynamics and use time-resolved photoelectron spectroscopy measurements to benchmark the theory. We perform trajectory surface hopping simulations for uracil excited to the first bright state (ππ*) using three different levels of theory (CASSCF, MRCIS, and XMS-CASPT2) in order to understand the role of dynamical correlation in determining the excited state dynamics, with a focus on the coupling between different electronic states and internal conversion back to the ground state. These dynamics calculations are used to simulate the time-resolved photoelectron spectra. The comparison of the calculated and measured spectra allows us to draw conclusions regarding the relative insights and quantitative accuracy of the calculations at the three different levels of theory, demonstrating that detailed quantitative comparisons of time-resolved photoelectron spectra can be used to benchmark methodology.

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.

Effect of dynamic correlation on the ultrafast relaxation of uracil in the gas phase

High level multi-reference non-adiabatic dynamics simulations reveal that uracil’s photoexcited S₂ state decays very quickly without any significant trapping.

Internal conversion and intersystem crossing dynamics of uracil upon double thionation: a time-resolved photoelectron spectroscopy study in the gas phase

The photophysical properties of 2,4-dithiouracil (2,4-DTU) in the gas phase are studied by time-resolved photoelectron spectroscopy (TRPES) with three different excitation wavelengths in direct extension of previous work on uracil (U), 2-thiouracil (2-TU) and 4-thiouracil (4-TU). Non-radiative deactivation in the canonical nucleobases like uracil mainly occurs via internal conversion (IC) along singlet excited states, although intersystem crossing (ISC) to a long-lived triplet state was confirmed to play a minor role. In thionated uracils, ISC to the triplet state becomes ultrafast and highly efficient with a quantum yield near unity; however, the lifetime of the triplet state is strongly dependent on the position of the sulfur atom. In 2-TU, ISC back to the ground state occurs within a few hundred picoseconds, whereas the population remains trapped in the lowest triplet state in the case of 4-TU. Upon doubling the degree of thionation, ISC remains highly efficient and dominates the photophysics of 2,4-DTU. However, several low-lying excited states contribute to competing IC and ISC pathways and a complex deactivation mechanism, which is evaluated here based on TRPES measurements and discussed in the context of the singly thionated uracils.

Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain

Gas-phase, double resonance IR spectroscopy has proven to be an excellent approach to obtain structural information on peptides ranging from single amino acids to large peptides and peptide clusters. In this review, we discuss the state-of-the-art of infrared action spectroscopy of peptides in the far-IR and THz regime. An introduction to the field of far-IR spectroscopy is given, thereby highlighting the opportunities that are provided for gas-phase research on neutral peptides. Current experimental methods, including spectroscopic schemes, have been reviewed. Structural information from the experimental far-IR spectra can be obtained with the help of suitable theoretical approaches such as dynamical DFT techniques and the recently developed Graph Theory. The aim of this review is to underline how the synergy between far-IR spectroscopy and theory can provide an unprecedented picture of the structure of neutral biomolecules in the gas phase. The far-IR signatures of the discussed studies are summarized in a far-IR map, in order to gain insight into the origin of the far-IR localized and delocalized motions present in peptides and where they can be found in the electromagnetic spectrum.

State-Dependent Fragmentation of Protonated Uracil and Uridine

Action spectroscopy using photon excitation in the VUV range (photon energy 4.5-9 eV) was performed on protonated uracil (UraH⁺) and uridine (UrdH⁺). The precursor ions with m/ z 113 and m/ z 245, respectively, were produced by an electrospray ionization source and accumulated inside a quadrupole ion trap mass spectrometer. After irradiation with tunable synchrotron radiation, product ion mass spectra were obtained. Fragment yields as a function of excitation energy show several maxima that can be attributed to the photoexcitation into different electronic states. For uracil, vertically excited states were calculated using the equation-of-motion coupled cluster approach and compared to the observed maxima. This allows to establish correlations between electronic states and the resulting fragment masses and can thus help to disentangle the complex de-excitation and fragmentation pathways of nucleic acid building blocks. Photofragmentation of the nucleoside uridine shows a significantly lower variety of fragments, indicating stabilization of the nucleobase by the attached sugar.

Dynamics of electronically excited states in the eumelanin building block 5,6-dihydroxyindole

We report the first excited state dynamics study of gas-phase 5,6-dihydroxyindole (5,6-DHI), a key building block of eumelanin pigments that are found throughout nature and serve as important photo-protective compounds. Time-resolved ion-yield measurements over the 241-296 nm ultraviolet photoexcitation region revealed non-adiabatic processes occurring on up to three distinct timescales. These reflect ultrafast (i.e. sub-picosecond) internal conversion within the excited state singlet manifold, and much longer-lived processes ranging from 10 ps to in excess of 1 ns. Our investigation paves the way for precisely targeted future studies of 5,6-DHI that exploit more differential measurement techniques. The work was facilitated by the use of soft laser-based thermal desorption to introduce 5,6-DHI samples into the gas phase. This approach, based on low-cost, readily available diode lasers, is straightforward, easily controllable and potentially applicable to a wide range of non-volatile molecular species.

Simulated and Experimental Time-Resolved Photoelectron Spectra of the Intersystem Crossing Dynamics in 2-Thiouracil

We report time-dependent photoelectron spectra recorded with a single-photon ionization setup and extensive simulations of the same spectra for the excited-state dynamics of 2-thiouracil (2TU) in the gas phase. We find that single-photon ionization produces very similar results as two-photon ionization, showing that the probe process does not have a strong influence on the measured dynamics. The good agreement between the single-photon ionization experiments and the simulations shows that the norms of Dyson orbitals allow for qualitatively describing the ionization probabilities of 2TU. This reasonable performance of Dyson norms is attributed to the particular electronic structure of 2TU, where all important neutral and ionic states involve similar orbital transitions and thus the shape of the Dyson orbitals do not strongly depend on the initial neutral and final ionic state. We argue that similar situations should also occur in other biologically relevant thio-nucleobases, and that the time-resolved photoelectron spectra of these bases could therefore be adequately modeled with the techniques employed here.