Coincidence measurements of photodouble ionization of benzene and thiophene.

Photodouble ionization (PDI) triple-differential cross sections (TDCSs) of benzene and thiophene have been measured in electron-electron coincidence experiments under 10-10 eV and 20-20 eV equal energy sharing conditions. A multi-Gaussian fit method has been employed to characterize the TDCSs. The trends and features observed for benzene and thiophene do highlight differences with helium most likely from molecular PDI contributions to the TDCS. A comparison with the well-known helium PDI TDCS for equal energy sharing conditions [Avaldi and Huetz J. Phys. B: At. Mol. Opt. Phys., 2005, 38, S861-S891] supported the validity of the multi-Gaussian fitting method and contextualized the benzene and thiophene fits. The molecular targets and energy sharing conditions were chosen to provide insight into the unexpected resonances observed in aromatic hydrocarbons but not aromatic heterocyclic molecules [Wehlitz et al., Phys. Rev. Lett., 2012, 109, 193001]. Contrary to the work of [Wehlitz et al., Phys. Rev. Lett., 2012, 109, 193001], no significant differences between benzene and thiophene were found.

Probing the conformational dynamics of an Ago-RNA complex in water/methanol solution.

Argonaute (Ago) proteins mediate target recognition guiding miRNA to bind complementary mRNA primarily in the seed region. However, additional pairing can occur beyond the seed, forming a supplementary duplex that can contribute to the guide-target affinity. In order to shed light on the connection, between protein-RNA interactions and miRNA-mRNA seed and supplementary duplex mobility, we carried out molecular dynamics simulations at the microsecond time-scale using a different approach compared to the ones normally used. Until now, theoretical investigations with classical MD on Ago-RNA complexes have been focused primarily on pure water solvent, which mimics the natural environment of biological molecules. Here, we explored the conformational space of a human Ago2 (hAgo2) bound to the seed + supplementary miRNA-mRNA duplex, using the solvent environment as a molecular probe. MD simulations have been performed in a mixture of water/MeOH at a molar ratio of 70 : 30 as well as in pure water for comparison. Our findings revealed that the mixed solvent promotes protein RNA association, principally enhancing salt-linkages between basic amino acid side-chains and acidic phosphates of the sugar-phosphate backbone. The primary effect registered was the restriction of supplementary duplex flexibility and the stabilization of the miRNA 3' terminus. Interestingly, we observed that the influence of the solvent appears to have almost no impact on the conformation of the seed duplex.

In search of universalities in the dissociative photoionization of PANHs via isomerizations.

In search of the cause behind the similarities often seen in the fragmentation of PANHs, vacuum ultraviolet (VUV) photodissociation of two pairs of isomers quinoline-isoquinoline and 2-naphthylamine-3-methyl-quinoline are studied using the velocity map imaging technique. The internal energy dependence of all primary fragmentation channels is obtained for all four target molecules. The decay dynamics of the four molecules is studied by comparing their various experimental signatures. The dominant channel for the first pair of isomers is found to be hydrogen cyanide (HCN) neutral loss, while the second pair of isomers lose HCNH neutral as its dominant channel. Despite this difference in their primary decay products and the differences in the structures of the four targets, various similarities in their experimental signatures are found, which could be explained by isomerization mechanisms to common structures. The fundamental role of these isomerization in controlling different dissociative channels is explored via a detailed analysis of the experimental photoelectron-photoion coincidences and the investigation of the theoretical potential energy surface. These results add to the notion of a universal PANH fragmentation mechanism and suggests the seven member isomerization as a key candidate for this universal mechanism. The balance between isomerization, dissociation, and other key mechanistic processes in the reaction pathways, such as hydrogen migrations, is also highlighted for the four molecules.

H2O˙+ and OH+ reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage.

Radiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This work reports the first experimental study of the ion-molecule reactions of the H2O˙+ and OH+ ions, produced by photoionization with synchrotron radiation, with a furan (c-C4H4O) molecule, a template for deoxyribose sugar in DNA. The present experiments, performed as a function of the collision energy of the ions and the tunable photoionization energy, provide key parameters for the theoretical modelling of the effect of radiation dose, like the absolute cross sections for producing protonated furan (furanH+) and a radical cation (furan˙+), the most abundant products, which can amount up to 200 Å2 at very low collision energies (<1.0 eV). The experimental results show that furanH+ is more fragile, indicating how the protonation of the sugar component of the DNA may favor its dissociation with possible major radiosensitizing effects. Moreover, the ring opening of furanH+ isomers and the potential energy surface of the most important fragmentation channels have been explored by molecular dynamics simulations and quantum chemistry calculations. The results show that, in the most stable isomer of furanH+, the ring opening occurs via a low energy pathway with carbon-oxygen bond cleavage, followed by the loss of neutral carbon monoxide and the formation of the allyl cation CH2CHCH2+, which instead is not observed in the fragmentation of furan˙+. At higher energies the ring opening through the carbon-carbon bond is accompanied by the loss of formaldehyde, producing HCCCH2+, the most intense fragment ion detected in the experiments. This work highlights the importance of the secondary processes, like the ion-molecule reactions at low energies in the radiation damage due to their very large cross sections, and it aims to provide benchmark data for the development of suitable models to approach this low collision energy range.

Autoionization from the plasmon resonance in isolated 1-cyanonaphthalene.

Polycyclic aromatic hydrocarbons have widely been conjectured to be ubiquitous in space, as supported by the recent discovery of two isomers of cyanonaphthalene, indene, and 2-cyanoindene in the Taurus molecular cloud-1 using radioastronomy. Here, the photoionization dynamics of 1-cyanonaphthalene (1-CNN) are investigated using synchrotron radiation over the hν = 9.0-19.5 eV range, revealing that prompt autoionization from the plasmon resonance dominates the photophysics for hν = 11.5-16.0 eV. Minimal photo-induced dissociation, whether originating from an excited state impulsive bond rupture or through internal conversion followed by a statistical bond cleavage process, occurs over the microsecond timescale (as limited by the experimental setup). The direct photoionization cross section and photoelectron angular distributions are simulated using an ezDyson model combining Dyson orbitals with Coulomb wave photoejection. When considering these data in conjunction with recent radiative cooling measurements on 1-CNN+, which showed that cations formed with up to 5 eV of internal energy efficiently stabilize through recurrent fluorescence, we conclude that the organic backbone of 1-CNN is resilient to photodestruction by VUV and soft XUV radiation. These dynamics may prove to be a common feature for the survival of small polycyclic aromatic hydrocarbons in space, provided that the cations have a suitable electronic structure to support recurrent fluorescence.

Photofragmentation specificity of photoionized cyclic amino acids (diketopiperazines) as precursors of peptide building blocks.

The photoionisation and photofragmentation of the two cyclic dipetides cyclo(alanyl-glycine) cGA and cyclo(glycyl-glycine) cGG, have been studied combining experiments and simulations. State selected fragments from the ionized molecules are detected using photo-electron photo-ion coincidence (PEPICO) measurements and specific fragmentation paths are identified and characterized via the use of ion-neutral coincidence maps. The simulations, performed using Quantum Chemistry methods, allow us to infer the fragmentation mechanisms of the ionized and excited molecules. We show that ring opening is followed by emission of the neutral fragments CO and HNCO. In the case of cGG the emission of neutral CO leads to a metastable structure that breaks producing small cationic fragments. The studied cyclic dipeptides evolve under ionizing radiation generating different small aziridin moieties and oxazolidinones. These two species are key reactants to elongate producing peptide chains. The corresponding mechanisms have been computed and show that the reaction requires very low energy and may occur in the presence of ionizing radiation.

A study of the valence photoelectron spectrum of uracil and mixed water-uracil clusters.

The valence ionization of uracil and mixed water-uracil clusters has been studied experimentally and by ab initio calculations. In both measurements, the spectrum onset shows a red shift with respect to the uracil molecule, with the mixed cluster characterized by peculiar features unexplained by the sum of independent contributions of the water or uracil aggregation. To interpret and assign all the contributions, we performed a series of multi-level calculations, starting from an exploration of several cluster structures using automated conformer-search algorithms based on a tight-binding approach. Ionization energies have been assessed on smaller clusters via a comparison between accurate wavefunction-based approaches and cost-effective DFT-based simulations, the latter of which were applied to clusters up to 12 uracil and 36 water molecules. The results confirm that (i) the bottom-up approach based on a multilevel method [Mattioli et al. Phys. Chem. Chem. Phys. 23, 1859 (2021)] to the structure of neutral clusters of unknown experimental composition converges to precise structure-property relationships and (ii) the coexistence of pure and mixed clusters in the water-uracil samples. A natural bond orbital (NBO) analysis performed on a subset of clusters highlighted the special role of H-bonds in the formation of the aggregates. The NBO analysis yields second-order perturbative energy between the H-bond donor and acceptor orbitals correlated with the calculated ionization energies. This sheds light on the role of the oxygen lone-pairs of the uracil CO group in the formation of strong H-bonds, with a stronger directionality in mixed clusters, giving a quantitative explanation for the formation of core-shell structures.

Photodissociation of quinoline cation: Mapping the potential energy surface.

A detailed exploration of the potential energy surface of quinoline cation (C9H7N·+) is carried out to extend the present understanding of its fragmentation mechanisms. Density functional theory calculations have been performed to explore new fragmentation schemes, giving special attention to previously unexplored pathways, such as isomerization and elimination of HNC. The isomerization mechanisms producing five- to seven-membered ring intermediates are described and are found to be a dominant channel both energetically and kinetically. Energetically competing pathways are established for the astrochemically important HNC-loss channel, which has hitherto never been considered in the context of the loss of a 27 amu fragment from the parent ions. Elimination of acetylene was also studied in great detail. Overall, the computational results are found to complement the experimental observations from the concurrently conducted PEPICO investigation. These could potentially open the doors for rich and interesting vacuum ultraviolet radiation-driven chemistry on planetary atmospheres, meteorites, and comets.

Comprehensive survey of dissociative photoionization of quinoline by PEPICO experiments.

Dissociative photoionization of quinoline induced by vacuum ultraviolet radiation is investigated using photoelectron-photoion coincidence spectroscopy. Branching ratios of all the detectable fragment ions are measured as a function of internal energy ranging from 2 to 30 eV. A specific generation hierarchy is observed in the breakdown curves of a set of dissociation channels. Moreover, a careful comparison of the breakdown curves of fragments among the successive generations allowed to establish a decay sequence in the fragmentation of quinoline cation. This enabled us to revisit and refine the understanding of the first generation decay and reassign the origin of a few of the higher generation decay products of quinoline cation. With the help of the accompanying computational work (reported concurrently), we have demonstrated the dominance of two different HCN elimination pathways over previously interpreted mechanisms. For the first time, a specific pathway for acetylene elimination is identified in quinoline+ and the role of isomerization in both acetylene as well as hydrogen cyanide loss is also demonstrated. The experiment also established that the acetylene elimination exclusively occurs from the non-nitrogen containing rings of quinoline cation. The formation of a few astronomically important species is also discussed.

Ion Chemistry of Carbon Dioxide in Nonthermal Reaction with Molecular Hydrogen.

The exothermic hydrogen transfer from H2 to CO2·+ leading to H and HCO2+ is investigated in a combined experimental and theoretical work. The experimental mass/charge ratios of the ionic product (HCO2+) and the ionic reactant (CO2·+) are recorded as a function of the photoionization energy of the synchrotron radiation. Theoretical density functional calculations and variational transition state theory are employed and adapted to analyze the energetic and the kinetics of the reaction, which turns out to be barrierless and with nonthermal rate coefficients controlled by nonstatistical processes. This study aims to understand the mechanisms and energetics that drive the reactivity of the elementary reaction of CO2·+ with H2 in different processes.

Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide.

Dipeptides, the prototype peptides, exist in both linear (l-) and cyclo (c-) structures. Since the first mass spectrometry experiments, it has been observed that some l-structures may turn into the cyclo ones, likely via a temperature-induced process. In this work, combining several different experimental techniques (mass spectrometry, infrared and Raman spectroscopy, and thermogravimetric analysis) with tight-binding and ab initio simulations, we provide evidence that, in the case of l-phenylalanyl-l-alanine, an irreversible cyclization mechanism, catalyzed by water and driven by temperature, occurs in the condensed phase. This process can be considered as a very efficient strategy to improve dipeptide stability by turning the comparatively fragile linear structure into the robust and more stable cyclic one. This mechanism may have played a role in prebiotic chemistry and can be further exploited in the preparation of nanomaterials and drugs.

Electron and ion spectroscopy of the cyclo-alanine-alanine dipeptide.

The VUV photoionisation and photofragmentation of cyclo-alanine-alanine (cAA) has been studied in a joint experimental and theoretical work. The photoelectron spectrum and the photoelectron-photoion coincidence (PEPICO) measurements, which enable control of the energy being deposited, combined with quantum chemistry calculations, provide direct insight into the cAA molecular stability after photoionisation. The analysis of the ion-neutral coincidence experiments with the molecular dynamics simulations and the exploration of the potential energy surface allows a complete identification of the fragmentation pathways. It has been found that the fragmentation always starts with the ring opening through the C-C bond cleavage, followed by release of neutral CO or HNCO moieties.

Fabrication of a New, Low-Cost, and Environment-Friendly Laccase-Based Biosensor by Electrospray Immobilization with Unprecedented Reuse and Storage Performances.

The fabrication of enzyme-based biosensors has received much attention for their selectivity and sensitivity. In particular, laccase-based biosensors have attracted a lot of interest for their capacity to detect highly toxic molecules in the environment, becoming essential tools in the fields of white biotechnology and green chemistry. The manufacturing of a new, metal-free, laccase-based biosensor with unprecedented reuse and storage capabilities has been achieved in this work through the application of the electrospray deposition (ESD) methodology as the enzyme immobilization technique. Electrospray ionization (ESI) has been used for ambient soft-landing of laccase enzymes on a carbon substrate, employing sustainable chemistry. This study shows how the ESD technique can be successfully exploited for the fabrication of a new promising environment-friendly electrochemical amperometric laccase-based biosensor, with storage capability up to two months without any particular care and reuse performance up to 63 measurements on the same electrode just prepared and 20 measurements on the one-year-old electrode subjected to redeposition. The laccase-based biosensor has been tested for catechol detection in the linear range 2-100 µM, with a limit of detection of 1.7 µM, without interference from chrome, cadmium, arsenic, and zinc and without any memory effects.

A systematic study of the valence electronic structure of cyclo(Gly-Phe), cyclo(Trp-Tyr) and cyclo(Trp-Trp) dipeptides in the gas phase.

The electronic energy levels of cyclo(glycine-phenylalanine), cyclo(tryptophan-tyrosine) and cyclo(tryptophan-tryptophan) dipeptides are investigated with a joint experimental and theoretical approach. Experimentally, valence photoelectron spectra in the gas phase are measured using VUV radiation. Theoretically, we first obtain low-energy conformers through an automated conformer-rotamer ensemble sampling scheme based on tight-binding simulations. Then, different first principles computational schemes are considered to simulate the spectra: Hartree-Fock (HF), density functional theory (DFT) within the B3LYP approximation, the quasi-particle GW correction, and the quantum-chemistry CCSD method. Theory allows assignment of the main features of the spectra. A discussion on the role of electronic correlation is provided, by comparing computationally cheaper DFT scheme (and GW) results with the accurate CCSD method.

Ionization of 2- and 4(5)-Nitroimidazoles Radiosensitizers: A "Kinetic Competition" Between NO2 and NO Losses.

Nitroimidazoles are a class of chemicals with a remarkable broad spectrum of applications from the production of explosives to the use as radiosensitizers in radiotherapy. The understanding of thedynamics of their fragmentation induced by ionizing sources is of fundamental interest. The goal of this work is to theoretically investigate the kinetic competition between the two most important decomposition channels of 2, 4 and 5-Nitroimidazole cations: the NO and NO2 losses. The calculated rate constants of the two processes are in very good agreement with the experimental Photoelectron-Photoion Coincidence (PEPICO) branching ratio. This study solves the intriguing and theoretically unexplained experimental observation that 2-Nitroimidazole, at variance with the other two regio-isomers is a source for only NO at low energies (<12.76 eV). This is a key point for biomedical application of the nitroimidazoles, because NO is the vasodilator that favors the reoxigenation of hypoxic tumor tissues.

Water-biomolecule clusters studied by photoemission spectroscopy and multilevel atomistic simulations: hydration or solvation?

The properties of mixed water-uracil nanoaggregates have been probed by core electron-photoemission measurements to investigate supramolecular assembly in the gas phase driven by weak interactions. The interpretation of the measurements has been assisted by multilevel atomistic simulations, based on semi-empirical tight-binding and DFT-based methods. Our protocol established a positive-feedback loop between experimental and computational techniques, which has enabled a sound and detailed atomistic description of such complex heterogeneous molecular aggregates. Among biomolecules, uracil offers interesting and generalized skeletal features; its structure encompasses an alternation of hydrophilic H-bond donor and acceptor sites and hydrophobic moieties, typical in biomolecular systems, that induces a supramolecular core-shell-like organization of the mixed clusters with a water core and an uracil shell. This structure is far from typical models of both solid-state hydration, with water molecules in defined positions, or liquid solvation, where disconnected uracil molecules are completely surrounded by water.

"Smart Decomposition" of Cyclic Alanine-Alanine Dipeptide by VUV Radiation: A Seed for the Synthesis of Biologically Relevant Species.

A combined experimental and theoretical study shows how the interaction of VUV radiation with cyclo-(alanine-alanine), one of the 2,5-diketopiperazines (DKPs), produces reactive oxazolidinone intermediates. The theoretical simulations reveal that the interaction of these intermediates with other neutral and charged fragments, released in the molecular decomposition, leads either to the reconstruction of the cyclic dipeptide or to the formation of longer linear peptide chains. These results may explain how DKPs could have, on one hand, survived hostile chemical environments and, on the other, provided the seed for amino acid polymerization. Shedding light on the mechanisms of production of such prebiotic building blocks is of paramount importance to understanding the abiotic synthesis of relevant biologically active compounds.

Carbon and Nitrogen K-Edge NEXAFS Spectra of Indole, 2,3-Dihydro-7-azaindole, and 3-Formylindole.

The near-edge X-ray absorption fine structure (NEXAFS) spectra of indole, 2,3-dihydro-7-azaindole, and 3-formylindole in the gas phase have been measured at the carbon and nitrogen K-edges. The spectral features have been interpreted based on density functional theory (DFT) calculations within the transition potential (TP) scheme, which is accurate enough for a general description of the measured C 1s NEXAFS spectra as well as for the assignment of the most relevant features. For the nitrogen K-edge, the agreement between experimental data and theoretical spectra calculated with TP-DFT was not quite satisfactory. This discrepancy was mainly attributed to the many-body effects associated with the excitation of the core electron, which are better described using the time-dependent density functional theory (TDDFT) with the range-separated hybrid functional CAM-B3LYP. An assignment of the measured N 1s NEXAFS spectral features has been proposed together with a complete description of the observed resonances. Intense transitions from core levels to unoccupied antibonding π* states as well as several transitions with mixed-valence/Rydberg or pure Rydberg character have been observed in the C and N K-edge spectra of all investigated indoles.

A general approach to study molecular fragmentation and energy redistribution after an ionizing event.

We propose to combine quantum chemical calculations, statistical mechanical methods, and photoionization and particle collision experiments to unravel the redistribution of internal energy of the furan cation and its dissociation pathways. This approach successfully reproduces the relative intensity of the different fragments as a function of the internal energy of the system in photoelectron-photoion coincidence experiments and the different mass spectra obtained when ions ranging from Ar+ to Xe25+ or electrons are used in collision experiments. It provides deep insights into the redistribution of the internal energy in the ionized molecule and its influence on the dissociation pathways and resulting charged fragments. The present pilot study demonstrates the efficiency of a statistical exchange of excitation energy among various degrees of freedom of the molecule and proves that the proposed approach is mature to be extended to more complex systems.

Unravelling molecular interactions in uracil clusters by XPS measurements assisted by ab initio and tight-binding simulations.

The C, N and O 1s XPS spectra of uracil clusters in the gas phase have been measured. A new bottom-up approach, which relies on computational simulations starting from the crystallographic structure of uracil, has been adopted to interpret the measured spectra. This approach sheds light on the different molecular interactions (H-bond, π-stacking, dispersion interactions) at work in the cluster and provides a good understanding of the observed XPS chemical shifts with respect to the isolated molecule in terms of intramolecular and intermolecular screening occurring after the core-hole ionization. The proposed bottom-up approach, reasonably expensive in terms of computational resources, has been validated by finite-temperature molecular dynamics simulations of clusters composed of up to fifty molecules.