Theoretical and Experimental Photoelectron Spectroscopy Characterization of the Ground State of Thymine Cation

Accurate Prediction of Adiabatic Ionization Energies for PAHs and Substituted Analogues

The accurate calculation of adiabatic ionization energies (AIEs) for polycyclic aromatic hydrocarbons (PAHs) and their substituted analogues is essential for understanding their electronic properties, reactivity, stability, and environmental/health implications. This study demonstrates that the M06-2X density functional theory method excels in predicting the AIEs of polycyclic aromatic hydrocarbons and related molecules, rivaling the (R)CCSD(T)-F12 method in terms of accuracy. These findings suggest that M06-2X, coupled with an appropriate basis set, represents a reliable and efficient method for studying polycyclic aromatic hydrocarbons and related molecules, aligning well with the experimental techniques. The set of molecules examined in this work encompasses numerous polycyclic aromatic hydrocarbons from m/z 67 up to m/z 1,176, containing heteroatoms that may be found in biofuels or nucleic acid bases, making the results highly relevant for photoionization experiments and mass spectrometry. For coronene-derivative molecular species with the C6n2H6n chemical formula, we give an expression to predict their AIEs (AIE (n) = 4.359 + 4.8743n-0.72057, in eV) upon extending the π-aromatic cloud until reaching graphene. In the long term, the application of this method is anticipated to contribute to a deeper understanding of the relationships between PAHs and graphene, guiding research in materials science and electronic applications and serving as a valuable tool for validating theoretical calculation methods.

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.

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.

Flying DNA Cation Radicals in the Gas Phase: Generation and Action Spectroscopy of Canonical and Noncanonical Nucleobase Forms

Gas-phase chemistry of cation radicals related to ionized nucleic acids has enjoyed significant recent progress thanks to the development of new methods for cation radical generation, ion spectroscopy, and reactivity studies. Oxidative methods based on intramolecular electron transfer in transition-metal complexes have been used to generate nucleobase and nucleoside cation radicals. Reductive methods relying on intermolecular electron transfer in gas-phase ion-ion reactions have been utilized to generate a number of di- and tetranucleotide cation radicals, as well as charge-tagged nucleoside radicals. The generated cation radicals have been studied by infrared and UV-visible action spectroscopy and ab initio and density functional theory calculations, providing optimized structures, harmonic frequencies, and excited-state analysis. This has led to the discovery of stable noncanonical nucleobase cation radicals of unusual electronic properties and extremely low ion-electron recombination energies. Intramolecular proton-transfer reactions in cation radical oligonucleotides and Watson-Crick nucleoside pairs have been studied experimentally, and their mechanisms have been elucidated by theory. Whereas the range of applications of the oxidative methods is currently limited to nucleobases and readily oxidizable guanosine, the reductive methods can be scaled up to generate large oligonucleotide cation radicals including double-strand DNA. Challenges in the experimental and computational approach to DNA cation radicals are discussed.

Unimolecular decomposition of methyl ketene and its dimer in the gas phase: theory and experiment

We present a combined theoretical and experimental investigation on the single photoionization and dissociative photoionization of gas-phase methyl ketene (MKE) and its neutral dimer (MKE2). The performed experiments entail the recording of photoelectron photoion coincidence (PEPICO) spectra and slow photoelectron spectra (SPES) in the energy regime 8.7-15.5 eV using linearly polarized synchrotron radiation. We observe both dimerization and trimerization of the monomer which brings about significantly complex and abstruse dissociative ionization patterns. These require the implementation of theoretical calculations to explore the potential energy surfaces of the monomer and dimer's neutral and ionized geometries. To this end, explicitly correlated quantum chemical methodologies involving the coupled cluster with single, double and perturbative triple excitations (R)CCSD(T)-F12 method, are utilized. An improvement in the adiabatic ionization energy of MKE is presented (AIE = 8.937 ± 0.020 eV) as well as appearance energies for multiple fragments formed through dissociative ionization of either the MKE monomer or dimer. In this regard, the synergy of experiment and theory is crucial to interpreting the obtained results. We discuss the potential astrochemical implications of this work in the context of recent advances in the field of astrochemistry and speculate on the potential presence and eventual fate of interstellar MKE molecules.

Isomer-sensitive characterization of low temperature oxidation reaction products by coupling a jet-stirred reactor to an electron/ion coincidence spectrometer: case of n-pentane

Using a tunable vacuum ultraviolet synchrotron beam line and first principle computations, a jet-stirred reactor was coupled for the first time to a photoionization mass spectrometer using electron/ion coincidence imaging.

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

The photoionization of thymine has been studied by using vacuum ultraviolet radiation and imaging photoelectron photoion coincidence spectroscopy after aerosol flash vaporization and bulk evaporation. The two evaporation techniques have been evaluated by comparison of the photoelectron spectra and breakdown diagrams. The adiabatic ionization energies for the first four electronic states were determined to be 8.922±0.008, 9.851±0.008, 10.30±0.02, and 10.82±0.01 eV. Vibrational features have been assigned for the first three electronic states with the help of Franck-Condon factor calculations based on density functional theory and wave function theory vibrational analysis within the harmonic approximation. The breakdown diagram of thymine, as supported by composite method ab initio calculations, suggests that the main fragment ions are formed in sequential HNCO-, CO-, and H-loss dissociation steps from the thymine parent ion, with the first step corresponding to a retro-Diels-Alder reaction. The dissociation rate constants were extracted from the photoion time-of-flight distributions and used together with the breakdown curves to construct a statistical model to determine 0 K appearance energies of 11.15±0.16 and 11.95±0.09 eV for the m/z 83 and 55 fragment ions, respectively. These results have allowed us to revise previously proposed fragmentation mechanisms and to propose a model for the final, nonstatistical H-loss step in the breakdown diagram, yielding the m/z 54 fragment ion at an appearance energy of 13.24 eV.

Energetics and ionization dynamics of two diarylketone molecules: benzophenone and fluorenone

Single photon ionization and subsequent unimolecular ion decomposition were studied on jet-cooled benzophenone and fluorenone separately, using VUV synchrotron radiation in a photoion/photoelectron coincidence setup. Slow PhotoElectron Spectra (SPES) were recorded in coincidence with either the parent or the fragment ions for hν < 12.5 eV. Dissociative ionization is observed for benzophenone only. The full interpretation of the measurements, including the identification of the neutral and ionic species when dissociative ionization is at play, benefits from high level ab initio computations for determining the equilibrium structures and the energetics of the neutral and ionized molecules and of their fragments. Electronically excited states of the parent molecular ions were calculated also. From this analysis, an accurate experimental determination of the energetics of the benzophenone and fluorenone ions and of their fragmentation channels is available: adiabatic ionization energies of benzophenone at 8.923 ± 0.005 eV and of fluorenone at 8.356 ± 0.007 eV; and appearance energies of benzophenone fragment ions at 11.04 ± 0.02 eV (loss of C₆H₅), 11.28 ± 0.02 eV (loss of H) and 11.45 ± 0.02 eV (loss of CO). The corresponding fragmentation mechanisms are explored, showing likely concerted bonds rearrangement. Possible pre-ionizing fragmentation is discussed in light of the spectra presented. The structural rigidity of fluorenone diarylketone seems to be the origin of the inhibition of the fragmentation of its cation.

Photoionization and dissociative photoionization of propynal in the gas phase: theory and experiment

Propynal (HCCCHO) is a complex organic compound (COM) of astrochemical and astrobiological interest. We present a combined theoretical and experimental investigation on the single photon ionization of gas-phase propynal, in the 10 to 15.75 eV energy range. Fragmentation pathways of the resulting cation were investigated both theoretically and experimentally. The adiabatic ionization energy (AIE) has been measured to be AIEexp = 10.715 ± 0.005 eV using tunable VUV synchrotron radiation coupled with a double imaging photoelectron photoion coincidence (i2PEPICO) spectrometer. In the energy range under study, three fragments formed by dissociative photoionization were identified experimentally: HC3O+, HCO+ and C2H2+, and their respective appearance energies (AE) were found to be AE = 11.26 ± 0.03, 13.4 ± 0.3 and 11.15 ± 0.03 eV, respectively. Using explicitly correlated coupled cluster calculations and after inclusion of the zero point vibrational energy, core-valence and scalar relativistic effects, the AIE is calculated to be AIEcalc = 10.717 eV, in excellent agreement with the experimental finding. The appearance energies of the fragments were calculated using a similar methodological approach. To further interpret the observed vibrational structure, anharmonic frequencies were calculated for the fundamental electronic state of the propynal cation. Moreover, MRCI calculations were carried out to understand the population of excited states of the cationic species. This combined experimental and theoretical study will help to understand the presence and chemical evolution of propynal in the external parts of interstellar clouds where it has been observed.

Single photon ionization of methyl isocyanide and the subsequent unimolecular decomposition of its cation: experiment and theory

Methyl isocyanide, CH₃NC, is a key compound in astrochemistry and astrobiology.

Unveiling the complex vibronic structure of the canonical adenine cation

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

The surprisingly high ligation energy of CO to ruthenium porphyrins

A combined theoretical and experimental approach has been used to investigate the binding energy of a ruthenium metalloporphyrin ligated with CO, ruthenium tetraphenylporphyrin [RuII TPP], in the RuII oxidation degree. Measurements performed with VUV ionization using the DESIRS beamline at Synchrotron SOLEIL led to adiabatic ionization energies of [RuII TPP] and its complex with CO, [RuII TPP-CO], of 6.48 ± 0.03 eV and 6.60 ± 0.03 eV, respectively, while the ion dissociation threshold of [RuII TPP-CO]+ is measured to be 8.36 ± 0.03 eV using the ground-state neutral complex. These experimental data are used to derive the binding energies of the CO ligand in neutral and cationic complexes (1.88 ± 0.06 eV and 1.76 ± 0.06 eV, respectively) using a Born-Haber cycle. Density functional theory calculations, in very satisfactory agreement with the experimental results, help to get insights into the metal-ligand bond. Notably, the high ligation energies can be rationalized in terms of the ruthenium orbital structure, which is singular compared to that of the iron atom. Thus, beyond indications of a strengthening of the Ru-CO bond due to the decrease in the CO vibrational frequency in the complex as compared to the Fe-CO bond, high-level calculations are essential to accurately describe the metal ligand (CO) bond and show that the Ru-CO bond energy is strongly affected by the splitting of triplet and singlet spin states in uncomplexed [Ru TPP].

Advances in spectroscopy and dynamics of small and medium sized molecules and clusters

Investigations of the spectroscopy and dynamics of small- and medium-sized molecules and clusters represent a hot topic in atmospheric chemistry, biology, physics, atto- and femto-chemistry and astrophysics.

Electronic, structural and vibrational induced effects upon ionization of 2-quinolinone

Using first principle methodologies, we characterize the lowest electronic states of 2-quinolinone(+) cation. The ground state of this ion is of X˜(2)A(″) nature. We deduce the adiabatic ionization energy of 2-quinolinone to be equal 8.249eV using the explicitly correlated coupled cluster level and where zero point vibrational energy, core-valence and scalar relativistic effects are taken into account. We examine also the ionization induced structural changes and vibrational shifts and analyze the electron density differences between the neutral and ionic species. These data show that the formation of 2-quinolinone(+)X˜(2)A(″) from 2-quinolinone affects strongly the HNCO group, whereas the carbon skeletal is perturbed when the upper electronic cationic states are populated. The comparison to 2-pyridone allows the elucidation of the effect of benzene ring fused with this heterocyclic ring. Since quinolones and pyridones are both model systems of DNA bases, these findings might help in understanding the charge redistribution in these biological entities upon ionization.

Photoionization of Benzophenone in the Gas Phase: Theory and Experiment

We report on the single photoionization of jet-cooled benzophenone using a tunable source of VUV synchrotron radiation coupled with a photoion/photoelectron coincidence acquisition device. The assignment and the interpretation of the spectra are based on a characterization by ab initio and density functional theory calculations of the geometry and of the electronic states of the cation. The absence of structures in the slow photoelectron spectrum is explained by a congestion of the spectrum due to the dense vibrational progressions of the very low frequency torsional mode in the cation either in pure form or in combination bands. Also a high density of electronic states has been found in the cation. Presently, we estimate the experimental adiabatic and vertical ionization energy of benzophenone at 8.80 ± 0.01 and 8.878 ± 0.005 eV, respectively. The ionization energy as well as the energies of the excited states are compared to the calculated ones.

Vibrationally resolved photoelectron spectroscopy of electronic excited states of DNA bases: application to the ã state of thymine cation

For fully understanding the light-molecule interaction dynamics at short time scales, recent theoretical and experimental studies proved the importance of accurate characterizations not only of the ground (D0) but also of the electronic excited states (e.g., D1) of molecules. While ground state investigations are currently straightforward, those of electronic excited states are not. Here, we characterized the à electronic state of ionic thymine (T(+)) DNA base using explicitly correlated coupled cluster ab initio methods and state-of-the-art synchrotron-based electron/ion coincidence techniques. The experimental spectrum is composed of rich and long vibrational progressions corresponding to the population of the low frequency modes of T(+)(Ã). This work challenges previous numerous works carried out on DNA bases using common synchrotron and VUV-based photoelectron spectroscopies. We provide hence a powerful theoretical and experimental framework to study the electronic structure of ionized DNA bases that could be generalized to other medium-sized biologically relevant systems.