Valence Photoionization of Thymine: Ionization Energies, Vibrational Structure, and Fragmentation Pathways from the Slow to the Ultrafast

Selective Tautomer Production and Cryogenic Ion Spectroscopy of Radical Cations: The Uracil and Thymine Cases

The vibrational and electronic spectroscopy of the radical cations of two nucleobases (NB) (uracil and thymine) was studied by cryogenic ion photodissociation spectroscopy. The radical cations have been generated from the photodissociation of NB-Ag+ complexes. A charge transfer process from the NB to Ag+ governs the deactivation mechanism, leading to the formation of the radical cation without further tautomerization. Single- and double-resonance spectroscopy allows for structural assignments of both the silver complexes and the radical cations by comparison with DFT-based calculations. Interestingly, a tautomer-dependent fragmentation is observed in the thymine enol form that involves the loss of NCO, a fragment which was never reported before for this NB. This selective photodissociation of silver complexes containing aromatic chromophore greatly expands the current technique to produce isomer-selected radical cations in the gas phase providing benchmark experimental data to assess calculations of open-shell species.

The Unimolecular Chemistry of Methyl Chloroformate Ions and Neutrals: A Story of Near-Threshold Decomposition

The near-threshold dissociation of ionized and neutral methyl chloroformate (CH3COOCl, MCF) was explored with imaging photoelectron photoion coincidence spectroscopy. The threshold photoelectron spectrum (TPES) for MCF was acquired for the first time; the large geometry changes upon ionization of MCF result in a broad, poorly defined TPES. Franck-Condon simulations are consistent with an adiabatic ionization energy (IE) of 10.90 ± 0.05 eV. Ionized MCF dissociates by chlorine atom loss at a measured 0 K appearance energy (AE) of 11.30 ± 0.01 eV. Together with the above IE, this AE suggests a reaction barrier of 0.40 ± 0.05 eV, consistent with the SVECV-f12 computational result of 0.41 eV. At higher internal energies, the loss of CH3O• becomes competitive due to its lower entropy of activation. Pyrolysis of neutral MCF formed the anticipated major products CH3Cl + CO2 (R1) and the minor products HCl + CO + CH2O (R2). The thermal decomposition products were identified by their photoion mass-selected threshold photoelectron spectrum (ms-TPES). Possible reaction pathways were explored computationally to confirm the dominant ones: R1 proceeds by a concerted Cl atom migration via a four-membered transition state in agreement with the mechanism proposed in the literature. R2 is a two-step reaction first yielding 2-oxiranone by HCl loss, which then decomposes to CH2O and CO. Kinetic modeling of the neutral decomposition could simulate the observed reactions only if the vibrational temperature of the MCF was assumed not to cool in the expansion.

Secondary ionization of pyrimidine nucleobases and their microhydrated derivatives in helium nanodroplets

Radiation damage in biological systems by ionizing radiation is predominantly caused by secondary processes such as charge and energy transfer leading to the breaking of bonds in DNA. Here, we study the fragmentation of cytosine (Cyt) and thymine (Thy) molecules, clusters and microhydrated derivatives induced by direct and indirect ionization initiated by extreme-ultraviolet (XUV) irradiation. Photofragmentation mass spectra and photoelectron spectra of free Cyt and Thy molecules are compared with mass and electron spectra of Cyt/Thy clusters and microhydrated Cyt/Thy molecules formed by aggregation in superfluid helium (He) nanodroplets. Penning ionization after resonant excitation of the He droplets is generally found to cause less fragmentation compared to direct photoionization and charge-transfer ionization after photoionization of the He droplets. When Cyt/Thy molecules and oligomers are complexed with water molecules, their fragmentation is efficiently suppressed. However, a similar suppression of fragmentation is observed when homogeneous Cyt/Thy clusters are formed in He nanodroplets, indicating a general trend. Penning ionization electron spectra (PIES) of Cyt/Thy are broad and nearly featureless but PIES of their microhydrated derivatives point at a sequential ionization process ending in unfragmented microsolvated Cyt/Thy cations.

High-throughput UV-photofragmentation studies of thymine and guanine

High-throughput photofragmentation studies of thymine and guanine were performed at 257 and 343 nm and for a wide range of ionisation laser intensities. Combining a continuous laser-based thermal desorption source with femtosecond multiphoton ionisation using a 50 kHz repetition rate laser allowed us to produce detailed 2D maps of fragmentation as a function of incident laser intensity. The fragmentation was distinctly soft, the parent ions being at least an order of magnitude more abundant than fragment ions. For thymine there was a single dominant fragmentation channel, which involves consecutive HNCO and CO losses. In contrast, for guanine there were several competing ones, the most probable channel corresponding to CH₂N₂ loss through opening of the pyrimidine ring. The dependence of parent ion abundance on the ionisation laser intensity showed that at 257 nm the ionisation of thymine is a 1 + 1 resonance enhanced process through its open-shell singlet state.

Photoionization Dynamics and Proton Transfer within the Adenine-Thymine Nucleobase Pair

Studying the stability of hydrogen-bonded nucleobase pairs, at the heart of the genetic code, is of utmost importance for an in-depth understanding of basic mechanisms of life and biomolecular evolution. We present here a VUV single photon ionization dynamic study of the nucleobase pair adenine-thymine (AT), revealing its ionization and dissociative ionization thresholds via double imaging electron/ion coincidence spectroscopy. The experimental data, consisting of cluster mass-resolved threshold photoelectron spectra and photon energy-dependent ion kinetic energy release distributions, allow the unambiguous distinction of the dissociation of AT into protonated adenine AH⁺ and a dehydrogenated thymine radical T(-H) from dissociative ionization processes of other nucleobase clusters. Comparison to high-level ab initio calculations indicates that our experimental observations can be explained by a single hydrogen-bonded conformer present in our molecular beam and allows the estimation of an upper limit of the barrier of the proton transfer in the ionized AT pair.

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.

Formation of Long-Lived Dark States during Electronic Relaxation of Pyrimidine Nucleobases Studied Using Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy

Ultrafast electronic relaxation of nucleobases from ¹ππ* states to the ground state (S₀) is considered essential for the photostability of DNA. However, transient absorption spectroscopy (TAS) has indicated that some nucleobases in aqueous solutions create long-lived ¹nπ*/³ππ* dark states from the ¹ππ* states with a high quantum yield of 0.4-0.5. We investigated electronic relaxation in pyrimidine nucleobases in both aqueous solutions and the gas phase using extreme ultraviolet (EUV) time-resolved photoelectron spectroscopy. Femtosecond EUV probe pulses cause ionization from all electronic states involved in the relaxation process, providing a clear overview of the electronic dynamics. The ¹nπ* quantum yields for aqueous cytidine and uracil (Ura) derivatives were found to be considerably lower (<0.07) than previous estimates reported by TAS. On the other hand, aqueous thymine (Thy) and thymidine exhibited a longer ¹ππ* lifetime and a higher quantum yield (0.12-0.22) for the ¹nπ* state. A similar trend was found for isolated Thy and Ura in the gas phase: the ¹ππ* lifetimes are 39 and 17 fs and the quantum yield for ¹nπ* are 1.0 and 0.45 for Thy and Ura, respectively. The result indicates that single methylation to the C₅ position hinders the out-of-plane deformation that drives the system to the conical intersection region between ¹ππ* and S₀, providing a large impact on the photophysics/photochemistry of a pyrimidine nucleobase. The significant reduction of ¹nπ* yield in aqueous solution is ascribed to the destabilization of the ¹nπ* state induced by hydrogen bonding.

VUV photoprocessing of oxygen-containing polycyclic aromatic hydrocarbons: iPEPICO study of the unimolecular dissociation of ionized benzofuran

Oxygen-containing polycyclic aromatic hydrocarbons (OPAHs) are potential contributors to the 11.3 m band in interstellar observations. To further explore their role in the interstellar medium, we have investigated their fate after photoprocessing by VUV radiation; in particular, we studied the dissociative photoionization of the simplest OPAH, benzofuran, with imaging photoelectron photoion coincidence spectroscopy, iPEPICO. Ionized benzofuran dissociates by loss of CO, followed by a sequential H atom loss. The parallel HCO-loss channel, leading to the same bicyclic C7H5+ fragment ion, is not competitive at low excess energies above the ionization threshold. However, the collision-induced dissociation tandem mass spectrometry results suggest that CO and HCO may be formed in parallel at higher energies. An RRKM fragmentation model reproduced the iPEPICO data well assuming the initial 1,2-H shift transition state to be rate determining to CO loss. The breakdown diagram and the measured dissociation rates agreed well at the CBS-QB3-calculated activation energy of 2.99 eV, which could be relaxed to 3.25 eV, and only a slight adjustment of the ab initio activation entropy. The model barrier to sequential H-loss is larger than the computed H-loss threshold and the breakdown diagram rises less steeply than predicted, which indicates suprastatistical kinetic energy release after the tight H-transfer transition state of the first step. HCO cleavage is possible after a ring-opening transition state, which is looser than and isoenergetic with the CO-loss transition state. However, a subsequent ring formation transition state at 3.85 eV is moderately tight, which suppresses HCO loss at low excess energies.

Photoionization of Two Potential Biofuel Additives: γ-Valerolactone and Methyl Butyrate

The photoionization of two potential biofuel additives, γ-valerolactone (GVL, C₅H₈O₂) and methyl butyrate (MB, C₅H₁₀O₂) has been studied by imaging photoelectron photoion coincidence spectroscopy (iPEPICO) at the VUV beamline of the Swiss Light Source (SLS). The vibrational fine structure in the photoelectron spectrum is compared with a Franck-Condon simulation for the electronic ground-state band of the GVL cation. In the lowest energy dissociative photoionization channel of GVL, CO₂ is lost, resulting in a 1-butene fragment ion with a 0 K appearance energy of E₀ = 10.35 ± 0.01 eV. A newly calculated 1-butene ionization energy of 9.595 ± 0.015 eV establishes the reverse barrier height to CO₂ loss as 66.6 ± 4.3 kJ mol^-1. Methyl butyrate cations undergo McLafferty rearrangement, which explains the missing ion signal at the computed adiabatic ionization energy of 9.25 eV. After H transfer, ethylene is lost in the lowest energy dissociation channel to yield the methyl acetate enol ion at E₀ = 10.24 ± 0.04 eV. This value connects the energetics of methyl butyrate with that of methyl acetate enol ion, which is established at Δ_fH^o_0K[CH₂C(OH)OCH₃⁺] = 502 ± 6 kJ mol^-1. Parallel to ethylene loss, methyl loss is also observed from the enol tautomer of the parent ion. Both samples exhibit low-energy nonstatistical dissociative ionization channels. In GVL, the methyl-loss abundance rises quickly but levels off suddenly in the energy range of the first electronically excited states, indicating nonstatistical competition between CH₃ and CO₂ loss. In MB, the major parallel dissociation channel is the loss of a methoxy radical. Calculations indicate that McLafferty rearrangement is inhibited on the excited-state surface. Indeed, breakdown curve modeling of this and a sequential CO-loss channel confirms a second statistical regime in dissociative photoionization, decoupled from ethylene loss.

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.

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

Valence Photoionization and Energetics of Vanillin, a Sustainable Feedstock Candidate

We studied the valence photoionization of vanillin by photoelectron photoion coincidence spectroscopy in the 8.20-19.80 eV photon energy range. Vertical ionization energies by EOM-IP-CCSD calculations reproduce the photoelectron spectral features. Composite method calculations and Franck-Condon simulation of the weak, ground-state band yield the adiabatic ionization energy of the most stable vanillin conformer as 8.306(20) eV. The lowest energy dissociative photoionization channels correspond to hydrogen atom, carbon monoxide, and methyl losses, which form the dominant C₈H₇O₃⁺ (m/z 151) and the less intense C₇H₈O₂⁺ (m/z 124) and C₇H₅O₃⁺ (m/z 137) fragment ions in parallel dissociation channels at modeled 0 K appearance energies of 10.13(1), 10.40(3), and 10.58(10) eV, respectively. On the basis of the breakdown diagram, we explore the energetics of sequential methyl and carbon monoxide loss channels, which dominate the fragmentation mechanism at higher photon energies. The 0 K appearance energy for sequential CO loss from the m/z 151 fragment to C₇H₇O₂⁺ (m/z 123) is 12.99(10) eV, and for sequential CH₃ loss from the m/z 123 fragment to C₆H₄O₂⁺ (m/z 108), it is 15.40(20) eV based on the model. Finally, we review the thermochemistry of the bi- and trifunctionalized benzene derivatives guaiacol, hydroxybenzaldehyde, anisaldehyde, and vanillin. On the basis of isodesmic functional group exchange reactions, we propose new enthalpies of formations, among them Δ_fH°_298K(vanillin, g) = -383.5 ± 2.9 kJ mol^-1. These mechanistic insights and ab initio thermochemistry results will support analytical works to study lignin conversion involving vanillin.

A guinea pig for conformer selectivity and mechanistic insights into dissociative ionization by photoelectron photoion coincidence: fluorocyclohexane

We studied fluorocyclohexane (C₆H₁₁F, FC6) by double imaging photoelectron photoion coincidence spectroscopy in the 9.90-13.90 eV photon energy range. The photoelectron spectrum can identify species isomer and, in this case, even conformer selectively. Ab initio results indicated that the axial conformer has two, close-lying cation electronic states. With the help of Franck-Condon simulations of the vibrational fine structure, we determined the origin of three transitions, (i) axial FC6 → axial FC6⁺ of C₁ symmetry (X[combining tilde]⁺, A'' in C_S), (ii) equatorial FC6 → equatorial FC6⁺ of C₁ symmetry (X[combining tilde]⁺, A'' in C_S), and (iii) axial FC6 → A' axial FC6⁺ of C_S symmetry (Ã⁺) as 10.12 ± 0.01, 10.15 ± 0.01 and 10.15 ± 0.02 eV, respectively. At slightly higher energies, the FC6 cation starts fragmenting by HF loss (E₀ = 10.60 eV), followed by sequential CH₃ (E₀ = 10.71 eV) or C₂H₄ (E₀ = 11.06 eV) loss. Surprisingly, the methyl-loss step has an effective barrier of only 0.11 eV, and yet it is a slow process at threshold. Based on the statistical model, this is explained by isomerization and stabilization of the C₆H₁₀⁺ intermediate. The highest energy channel observed, vinyl fluoride (C₂H₃F) loss yielding C₄H₈⁺ appears in the breakdown diagram at 12 eV, which agrees with the computed threshold to cyclobutane cation formation. However, the model predicted a ca. 1 eV competitive shift for this parallel channel, i.e., an E₀ = 11.23 eV. This led us to explore the potential energy surface to find a lower-lying fragmentation channel including H-transfer steps. Rate constant measurements and statistical modeling thus yield fundamental insights into the reaction mechanism beyond what is immediately seen in the mass spectra.

New analytical tools for advanced mechanistic studies in catalysis: photoionization and photoelectron photoion coincidence spectroscopy

How can we detect reactive and elusive intermediates in catalysis to unveil reaction mechanisms? In this mini review, we discuss novel photoionization tools to support this quest.