Dynamics of charged biomoleculesFragmentation, molecular growth and solvation

Résumé

Close range ion/atom collisions may deposit a large amount of energy on the target (molecule or cluster). The interaction projectile/target is dependent on the nature of the projectile, its charge state and its initial energy. Tuning the experimental conditions, thus the kinetic energy of the projectile, one may be in dominant nuclear stopping regime or dominant electronic stopping regime. The former implies that non-statistical processes, where the energy deposited is not evenly distributed among all the vibrational degrees of freedom of the target, are likely to play an important role in the target decay. The latter sees a largely dominant ’slow’ statistical decay for the target. Understanding the relative weight of these two processes and unveiling the fine chemistry of the fragmentation pathways involved may found applications in understanding e.g., the origin and evolution of complex molecules in space, the radiosensitivity of biomolecules and the role of the water environment in the process. In this work we have used classical and ab initio molecular dynamics simulations combined with electronic structure calculations to reproduce entire sequences of collisions and to get insights on the fragmentation pathways induced by the energy deposition consequent to the collision. Chapter 3 summarizes the basics of the electronic structure methods used; while chapters 4 and 5 describe the classical and the ab-initio methods employed, respectively. In this thesis we have investigated four four di erent systems: butadiene clusters, porphyrin, protonated and deprotonated, and 5-halo-substituted uracils. Polycyclic Aromatic Hydrocarbons (PAHs) are ubiquitous in space. Previous studies have already observed molecular growth, induced by nonstatistical decay. In Chapter 6, we have explored the possibilities of forming ring structures, which may be PAHs precursors, from butadiene clusters. We have used a combination of a reactive force-field potential (AIREBO) and a Coulombian screened potential (ZBL) to reproduce the nuclear scattering dominated processes visible in the experiments. The analysis of the results indicates the prompt atom knockout as the main responsible for the molecular growth observed in the experimental mass spectrum. DFT electronic structure calculations, at B3LYP/cc-pVDZ level of theory, suggest the formation of benzene-like ring structure products. In the biological world, porphyrins are among the most common molecules, for this reason they have been proposed as a biomarker for assessing the origin of extra-terrestrial planets, meteorites, comets and so on. Chapter 7 explores the influence of knockout on the mass spectrum of 5,10,15,20-tetraphenylporphin (TPP) and its metallate derivatives, FeTPP+ and ZnTPP+, with a computational approach similar to the one adopted in Chapter 6. To the best of our knowledge, fingerprints of heavy atom knockout have not been identified so far in porphyrins mass spectra. The comparison between simulated and experimental mass spectra evidences the presence of heavy atom knockout. The calculations of the heavy atom knockout cross sections made us conclude they constitute the ≥ 40%(≥ 70%) of the total experimental cross sections of TPP in collision with He (and Ne). Adenine is the nucleobasis which could best survive in an harsh environment like the Insterstellar Medium. In addition, the study of its protonated and deprotonated forms may give insights on the protonation and deprotonation e ects in DNA. In Chapter 8, the stability of protonated and deprotonated adenine has been subject of a combined experimental and theoretical study. The computational approach consisted of a mixed statical and dynamical approach. We have performed ab initio molecular dynamics (ADMP type, at B3LYP/6-31++G(d,p) level of theory) in order to quantitatively reproduce the experimental mass spectrum features, such that fragments structures and fragmentation pathways could be identified. 5-bromo-uracil (5BrU) is a known mutagen and may be used as a model system for the radiosensitizer 5-bromo-2-deoxy-uridine. In Chapter 9, we have explored the influence of the water environment in the decay of 5BrU. This work uses a statical-dynamical approach similar to the one already described in Chapter 8 to study the nano-hydrated 5-bromo-uracil cluster. The ab initio molecular dynamics (BOMD type, at M06-2X/SVP level of theory) suggested an unexpected channel: the water insertion on the [5BrU-H]+ residue. The electronic structure PES exploration (at M06-2X/6-311++G(d,p) level of theory) of the neutral, ionized, protonated and [5BrU-H]+ species has provided pathways and structures, which could explain some of the interesting features of the experimental mass spectrum of hydrated 5BrU, provided from our collaborators from Caen University and CNR Rome. Following the results of Chapter 9, we have investigated the nucleophilic water attack on other halo-substituted uracil (5ClU and 5FU) and uracil (U) itself. As all these molecules are mutagens and/or model systems of radiosensitizers, we aimed, through the observation of similarities and differences in the chemistry of all of them, to shed some light on the chemical mechanisms of mutagenesis and radiosensitivity. The PES sampling involved all the neutral, ionized, protonated and [5XU-H]+ species for each molecule. The results not only suggest an influence of the substituted moiety in position 5 on the reaction mechanism, but also an influence of additional water molecules when bound to the nucleophile.