Charge migration induced by attosecond pulses in bio-relevant molecules

After sudden ionization of a large molecule, the positive charge can migrate throughout the system on a sub-femtosecond time scale, purely guided by electronic coherences. The possibility to actively explore the role of the electron dynamics in the photo-chemistry of bio-relevant molecules is of fundamental interest for understanding, and perhaps ultimately controlling, the processes leading to damage, mutation and, more generally, to the alteration of the biological functions of the macromolecule. Attosecond laser sources can provide the extreme time resolution required to follow this ultrafast charge flow. In this review we will present recent advances in attosecond molecular science: after a brief description of the results obtained for small molecules, recent experimental and theoretical findings on charge migration in bio-relevant molecules will be discussed

Gas Phase Oxidation of Carbon Monoxide by Sulfur Dioxide Radical Cation: Reaction Dynamics and Kinetic Trend With the Temperature

Gas phase ion chemistry has fundamental and applicative purposes since it allows the study of the chemical processes in a solvent free environment and represents models for reactions occurring in the space at low and high temperatures. In this work the ion-molecule reaction of sulfur dioxide ion SO2.+ with carbon monoxide CO is investigated in a joint experimental and theoretical study. The reaction is a fast and exothermic chemical oxidation of CO into more stable CO2 by a metal free species, as SO2.+, excited into ro-vibrational levels of the electronic ground state by synchrotron radiation. The results show that the reaction is hampered by the enhancement of internal energy of sulfur dioxide ion and the only ionic product is SO.+. The theoretical approach of variational transition state theory (VTST) based on density functional electronic structure calculations, shows an interesting and peculiar reaction dynamics of the interacting system along the reaction path. Two energy minima corresponding to [SO2–CO].+ and [OS–OCO].+ complexes are identified. These minima are separated by an intersystem crossing barrier which couples the bent 3B2 state of CO2 with C2v symmetry and the 1A1 state with linear D∞h symmetry. The spin and charge reorganization along the minimum energy path (MEP) are analyzed and eventually the charge and spin remain allocated to the SO.+ moiety and the stable CO2 molecule is easily produced. There is no bottleneck that slows down the reaction and the values of the rate coefficient k at different temperatures are calculated with capture theory. A value of 2.95 × 10−10 cm3s−1molecule−1 is obtained at 300 K in agreement with the literature experimental measurement of 3.00 × 10−10 ± 20% cm3s−1molecule−1, and a negative trend with temperature is predicted consistently with the experimental observations

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

Ultrafast Dynamics in the DNA Building Blocks Thymidine and Thymine Initiated By Ionizing Radiation

Understanding how energetic charged particles damage DNA is crucial for improving radiotherapy techniques such as hadron therapy and for the development of new radiosensitizer drugs. In the present study, the damage caused by energetic particles was simulated by measuring the action of extreme ultraviolet (XUV) attosecond pulses on the DNA building blocks thymine and thymidine. This allowed the ultrafast processes triggered by direct ionization to be probed with an optical pulse with a time resolution of a few femtoseconds. By measuring the yields of fragment ions as a function of the delay between the XUV pulse and the probe pulse, a number of transient processes typically lasting 100 femtoseconds or less were observed. These were particularly strong in thymidine which consists of the thymine base attached to a deoxyribose sugar. This dynamics was interpreted as excited states of the cation, formed by the XUV pulse, rapidly decaying via non-adiabatic coupling between electronic states. This provides the first experimental insight into the mechanisms which immediately proceed from the action of ionizing radiation on DNA and provides a basis on which further theoretical and experimental studies can be conducted

A Synchrotron Radiation Study of Nitroimidazoles and their Derivatives

Nitroimidazole derived 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. Inthis work we present the results of a bottom-up approach, which goes from the model molecule to the real drugs used in therapy. Mass spectrometry and several spectroscopic techniques (XPS, PES, NEXAFS, PEPICO) basedon the use of synchrotron radiation have been combined with computational methods to link the electronic and geometric structure of the molecule to their functions.The investigation of the fragmentation patterns of the nitroimidazole isomers [1,2] has allowed to understand their capacity to produce reactive molecular species like nitric oxide, carbon monoxide or hydrogencyanide and their potential impact on the biological system. Guided by these results, the fragmentation mechanisms of metronidazole and misonidazole, the two radiosensitisers built on the 5-nitroimidazole and 2-nitroimidazole compounds used in therapy, as well as the 1-Methyl-5-nitroimidazole have been investigated. The results on these more complex systems suggest that different mechanisms are active. The release of nitric oxideis hampered by the efficient formation of nitrous acid or nitrogen dioxide and the long and branched tails attached to the imidazole ring increase the ring stability, providing an efficient channel for excess energy dissipation

High-resolution mass spectrometry and velocity map imaging for ultrafast electron dynamics in complex biomolecules

We present a design combining a velocity map imaging electron spectrometer with a reflectron mass spectrometer. Since the two spectrometer sides have different intrinsic requirements for the electric field in the central region, a large number of electrodes and a reflectron-geometry of the mass spectrometer were employed to achieve simultaneous high resolutions. Together with femtosecond and attosecond pump-probe methods it will enable studies of ultrafast dynamics in large molecular systems

High-resolution mass spectrometry and velocity map imaging for ultrafast electron dynamics in complex biomolecules

We present a design combining a velocity map imaging electron spectrometer with a reflectron mass spectrometer. Since the two spectrometer sides have different intrinsic requirements for the electric field in the central region, a large number of electrodes and a reflectron-geometry of the mass spectrometer were employed to achieve simultaneous high resolutions. Together with femtosecond and attosecond pump-probe methods it will enable studies of ultrafast dynamics in large molecular systems

High-resolution mass spectrometry and velocity map imaging for ultrafast electron dynamics in complex biomolecules

We present a design combining a velocity map imaging electron spectrometer with a reflectron mass spectrometer. Since the two spectrometer sides have different intrinsic requirements for the electric field in the central region, a large number of electrodes and a reflectron-geometry of the mass spectrometer were employed to achieve simultaneous high resolutions. Together with femtosecond and attosecond pump-probe methods it will enable studies of ultrafast dynamics in large molecular systems

Inner shell photofragmentation of 2Cl-pyrimidine studied by mass spectrometry and electron–ion coincidence experiments

Photoelectron spectroscopy, mass spectrometry and electron–ion coincidence experiments combined with tunable synchrotron radiation have been used to study the decay and fragmentation of 2Cl-pyrimidine after Cl(2p), C(1s) and N(1s) excitations. The goal is to investigate how the state- and site-selected excitation and the chemical environment affect the fragmentation paths of the molecule and to make a comparison with fragmentation induced by direct valence ionization. It has been found that the site-selective inner shell excitation affects the branching ratio of the fragments, while the particular fragmentation channels of the cation are determined by the final state populated in the resonant decay of the core excited states. Effects of nuclear motion in the core excited states and the possible ultrafast molecular dissociation following the Cl(2p → σ*) core excitation are discussed

The role of the environment in the ion induced fragmentation of uracil

International audienceThe fragmentation of uracil molecules and pure and nano-hydrated uracil clusters by 12C4+ ion impact is investigated. This work focuses on the fragmentation behavior of complex systems and the effect of the environment. On the one hand, it is found that the environment in the form of surrounding uracil or water molecules has a significant influence on the fragmentation dynamics, providing an overall ‘protective’ effect, while on the other hand we observe the opening of specific fragmentation channels. In particular, we report on the first observation of a series of hydrated fragments. This indicates a strong interaction between uracil and water molecules, holding the water clusters bound to the observed molecular fragments