Elemetary processes of radiation damage in organic molecules of biological interest

It was observed in the ‘80s that the radiation damage on biological systems strongly depends on processes occurring at the microscopic level, involving the elementary constituents of biological cells. Since then, lot of attention has been paid to study elementary processes of photo- and ion-chemistry of isolated organic molecule of biological interest. This work fits in this framework and aims to study the radiation damage mechanisms induced by different types of radiations on simple halogenated biomolecules used as radiosensitizers in radiotherapy. The research is focused on the photofragmentation of halogenated pyrimidine molecules (5Br-pyrimidine, 2Br-pyrimidine and 2Cl-pyrimidine) in the VUV range and on the 12C4+ ion-impact fragmentation of the 5Br-uracil and its homogeneous and hydrated clusters. Although halogen substituted pyrimidines have similar structure to the pyrimidine molecule, their photodissociation dynamics is quite different. These targets have been chosen with the purpose of investigating the effect of the specific halogen atom and site of halogenation on the fragmentation dynamics. Theoretical and experimental studies have highlighted that the site of halogenation and the type of halogen atom, lead either to the preferential breaking of the pyrimidinic ring or to the release of halogen/hydrogen radicals. The two processes can subsequently trigger different mechanisms of biological damage. To understand the effect of the environment on the fragmentation dynamic of the single molecule, the ion-induced fragmentation of homogenous and hydrated clusters of 5Br-uracil have been studied and compared to similar studies on the isolated molecule. The results show that the “protective effect” of the environment on the single molecule hold in the homogeneous clusters, but not in the hydrated clusters, where several hydrated fragments have been observed. This indicates that the presence of water molecules can inhibit some fragmentation channels and promote the keto-enol tautomerization, which is very important in the mutagenesis of the DNA

Electron and ion spectroscopy of Azobenzene in the valence and core shells

Azobenzene is a prototype and building block of a class of molecules of extreme technological interest as molecularphoto-switches. We present a joint experimental and theoretical study of its response to irradiation with light across theUV to X-ray spectrum. The study of valence and inner shell photo-ionization and excitation processes, combined withmeasurement of valence photoelectron-photoion coincidence (PEPICO) and of mass spectra across the core thresholdsprovides a detailed insight onto the site- and state-selected photo-induced processes. Photo-ionization and excita-tion measurements are interpreted via the multi-configurational restricted active space self-consistent field (RASSCF)method corrected by second order perturbation theory (RASPT2). Using static modelling, we demonstrate that thecarbon and nitrogen K edges of Azobenzene are suitable candidates for exploring its photoinduced dynamics thanks tothe transient signals appearing in background-free regions of the NEXAFS and XP

Radiation Damage Mechanisms of Chemotherapeutically Active Nitroimidazole Derived Compounds

Photoionization mass spectrometry, photoelectron-photoion coincidence spectroscopic technique, and computational methods have been combined to investigate the fragmentation of two nitroimidazole derived compounds: the metronidazole and misonidazole. These molecules are used in radiotherapy thanks to their capability to sensitize hypoxic tumor cells to radiation by “mimicking” the effects of the presence of oxygen as a damaging agent. Previous investigations of the fragmentation patterns of the nitroimidazole isomers (Bolognesi et al., 2016; Cartoni et al., 2018) have shown their capacity to produce reactive molecular species such as nitric oxide, carbon monoxide or hydrogen cyanide, and their potential impact on the biological system. The results of the present work suggest that different mechanisms are active for the more complex metronidazole and misonidazole molecules. The release of nitric oxide is hampered by the efficient formation of nitrous acid or nitrogen dioxide. Although both metronidazole and misonidazole contain imidazole ring in the backbone, the side branches of these molecules lead to very different bonding mechanisms and properties

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

Formation of H3O+ and OH by CO2 and N2O trace gases in the atmospheric environment

The impact of cosmic rays’ energetic subatomic particles on climate and global warming is still controversial and under debate. Cosmic rays produce ions that can trigger fast reactions affecting chemical networks in the troposphere and stratosphere especially when a large amount of relevant trace gases such as carbon dioxide, methane, sulfur dioxide and water are injected by volcanic eruptions. This work focuses on synchrotron experiments and an ab initio theoretical study of the ion chemistry of carbon dioxide and nitrous oxide radical cations reacting with water. These molecules catalyze a fast exothermic formation of hydronium ions H3O+ and the hydroxyl radical OH, the main oxidant in the atmosphere. Moreover, theoretical calculations demonstrate that at the end of the catalytic cycle, CO2 and N2O are produced vibrationally excited and subsequently they quench in the microsecond time scale by collision with the surrounding atmospheric molecules at the pressure and temperature of upper-troposphere/stratosphere. The chemistry involved in these reactions has a strong impact on the oxidant capacity of the atmosphere, on the sulfate aerosol production, on the cloud formation and eventually on the chemical networks controlling climate and global warming models

Photoionization of methanol: a molecular source for the prebiotic chemistry

Methanol is one of the most abundant and ubiquitous molecules in the space. Its chemistry is fundamental to understand the molecular growing from prebiotic molecules, ions and radicals. In this work the reaction of labelled methanol CD3OH•+ radical cation, produced with different internal energies by monochromatic synchrotron radiation, with neutral CD3OH was studied. The dynamics of the main reaction channels were investigated by theoretical calculations. The results show how these processes can be considered suitable pathways for the formation of fundamental species as CH3O(H)H+, CH3O•, •CH2OH, CH2O which are potential precursors to prebiotic molecules

Insights into 2-Chloropyrimidine fragmentation through a thermochemical analysis of the ionic fragments

In the present work we have studied the photoinduced ion chemistry of the 2Cl-pyrimidine molecule in the energy region 9−14 eV. The theoretical gas phase enthalpies of formation of the main fragments calculated using the G3B3 and G2 ab initio methods are compared to the experimental values, derived by the measured appearance energy of the fragments. This approach provides new insights into both the geometric structure of the ionic fragments and the basic mechanisms governing the molecular fragmentation

Perspectives of Gas Phase Ion Chemistry: Spectroscopy and Modeling

The study of ions in the gas phase has a long history and has involved both chemists and physicists. The interplay of their competences with the use of very sophisticated commercial and/or homemade instrumentations and theoretical models has improved the knowledge of thermodynamics and kinetics of many chemical reactions, even if still many stages of these processes need to be fully understood. The new technologies and the novel free-electron laser facilities based on plasma acceleration open new opportunities to investigate the chemical reactions in some unrevealed fundamental aspects. The synchrotron light source can be put beside the FELs, and by mass spectrometric techniques and spectroscopies coupled with versatile ion sources it is possible to really change the state of the art of the ion chemistry in different areas such as atmospheric and astro chemistry, plasma chemistry, biophysics, and interstellar medium (ISM). In this manuscript we review the works performed by a joint combination of the experimental studies of ion–molecule reactions with synchrotron radiation and theoretical models adapted and developed to the experimental evidence. The review concludes with the perspectives of ion–molecule reactions by using FEL instrumentations as well as pump probe measurements and the initial attempt in the development of more realistic theoretical models for the prospective improvement of our predictive capability

Insights into 2-Chloropyrimidine fragmentation through a thermochemical analysis of the ionic fragments

In the present work we have studied the photoinduced ion chemistry of the 2Cl-pyrimidine molecule in the energy region 9−14 eV. The theoretical gas phase enthalpies of formation of the main fragments calculated using the G3B3 and G2 ab initio methods are compared to the experimental values, derived by the measured appearance energy of the fragments. This approach provides new insights into both the geometric structure of the ionic fragments and the basic mechanisms governing the molecular fragmentation

VUV Photofragmentation of Chloroiodomethane: The Iso-CH2I–Cl and Iso-CH2Cl–I Radical Cation Formation

Dihalomethanes XCH2Y (X and Y= F, Cl, Br and I) are a class of compounds involved in several processes leading to the release of halogen atoms, ozone consumption and aerosol particle formation. Neutral dihalomethanes have been largely studied, but chemical physics properties and processes involving their radical ions, like the pathways of their decomposition, have not been completely investigated. In this work the photodissociation dynamics of the ClCH2I molecule has been explored in the photon energy range 9-21 eV using both VUV rare gas discharge lamps and synchrotron radiation. The experiments show that among the different fragment ions, CH2I+ and CH2Cl+, which correspond to the Cl- and I-losses, respectively, play a dominant role. The experimental ionization energy of ClCH2I and the appearance energies of the CH2I+ and CH2Cl+ ions are in agreement with the theoretical results obtained at the MP2/CCSD(T) level of theory. Computational investigations have been also performed to study the isomerization of geminal [ClCH2I].+ into the iso-chloroiodomethane isomers: [CH2I-Cl].+ and [CH2Cl-I].+