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.

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

Azobenzene is a prototype and a building block of a class of molecules of extreme technological interest as molecular photo-switches. We present a joint experimental and theoretical study of its response to irradiation with light across the UV to x-ray spectrum. The study of valence and inner shell photo-ionization and excitation processes combined with measurement of valence photoelectron-photoion coincidence and mass spectra across the core thresholds provides a detailed insight into the site- and state-selected photo-induced processes. Photo-ionization and excitation measurements are interpreted via the multi-configurational restricted active space self-consistent field method corrected by second order perturbation theory. Using static modeling, we demonstrate that the carbon and nitrogen K edges of azobenzene are suitable candidates for exploring its photoinduced dynamics thanks to the transient signals appearing in background-free regions of the NEXAFS and XPS.

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.

Real-time observation of a correlation-driven sub 3 fs charge migration in ionised adenine

Sudden ionisation of a relatively large molecule can initiate a correlation-driven process dubbed charge migration, where the electron density distribution is expected to rapidly move along the molecular backbone. Capturing this few-femtosecond or attosecond charge redistribution would represent the real-time observation of electron correlation in a molecule with the enticing prospect of following the energy flow from a single excited electron to the other coupled electrons in the system. Here, we report a time-resolved study of the correlation-driven charge migration process occurring in the nucleic-acid base adenine after ionisation with a 15-35 eV attosecond pulse. We find that the production of intact doubly charged adenine - via a shortly-delayed laser-induced second ionisation event - represents the signature of a charge inflation mechanism resulting from many-body excitation. This conclusion is supported by first-principles time-dependent simulations. These findings may contribute to the control of molecular reactivity at the electronic, few-femtosecond time scale.

Core Shell Investigation of 2-nitroimidazole

Tunability and selectivity of synchrotron radiation have been used to study the excitation and ionization of 2-nitroimidazole at the C, N, and O K-edges. The combination of a set of different measurements (X-ray photoelectron spectroscopy, near-edge photoabsorption spectroscopy, Resonant Auger electron spectroscopy, and mass spectrometry) and computational modeling have successfully disclosed local effects due to the chemical environment on both excitation/ionization and fragmentation of the molecule.

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 SO 2 . + 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 SO 2 . + , 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 C_2v 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.

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.

Ultrafast Hydrogen Migration in Photoionized Glycine

Hydrogen migration in the glycine cation has been investigated using a combination of a short train of attosecond extreme ultraviolet pulses with few-optical-cycle near-infrared pulses. The yield of the photofragments produced has been measured as a function of pump-probe delay. These time-dependent measurements reveal the presence of a hydrogen migration process occurring in 48 fs. Previous mass spectrometric experiments and theoretical calculations have allowed us to identify the conformations and cation states involved in the process induced by the broad band extreme ultraviolet radiation.

An experimental and theoretical investigation of XPS and NEXAFS of 5-halouracils

The C, N and O 1s excitation and ionization processes of 5X-uracil (X = F, Cl, Br, and I) were investigated using near edge X-ray absorption fine structure (NEXAFS) and X-ray photoemission (XPS) spectroscopies. This study aims at the fine assessment of the effects of the functionalization of uracil molecules by halogen atoms having different electronegativity and bound to the same molecular site. Two DFT-based approaches, which rely on different paradigms, have been used to simulate the experimental spectra and to assign the corresponding features. The analysis of the screening of the core holes of the different atoms via electronic charge density plots has turned out to be a useful tool to illustrate the competition between the partially aromatic and partially conjugate properties of this class of molecules.

Time-Resolved Measurement of Interatomic Coulombic Decay Induced by Two-Photon Double Excitation of Ne_{2}

The hitherto unexplored two-photon doubly excited states [Ne^{*}(2p^{-1}3s)]_{2} were experimentally identified using the seeded, fully coherent, intense extreme ultraviolet free-electron laser FERMI. These states undergo ultrafast interatomic Coulombic decay (ICD), which predominantly produces singly ionized dimers. In order to obtain the rate of ICD, the resulting yield of Ne_{2}^{+} ions was recorded as a function of delay between the extreme ultraviolet pump and UV probe laser pulses. The extracted lifetimes of the long-lived doubly excited states, 390(-130/+450)  fs, and of the short-lived ones, less than 150 fs, are in good agreement with ab initio quantum mechanical calculations.

Slow Interatomic Coulombic Decay of Multiply Excited Neon Clusters

Ne clusters (∼5000  atoms) were resonantly excited (2p→3s) by intense free electron laser (FEL) radiation at FERMI. Such multiply excited clusters can decay nonradiatively via energy exchange between at least two neighboring excited atoms. Benefiting from the precise tunability and narrow bandwidth of seeded FEL radiation, specific sites of the Ne clusters were probed. We found that the relaxation of cluster surface atoms proceeds via a sequence of interatomic or intermolecular Coulombic decay (ICD) processes while ICD of bulk atoms is additionally affected by the surrounding excited medium via inelastic electron scattering. For both cases, cluster excitations relax to atomic states prior to ICD, showing that this kind of ICD is rather slow (picosecond range). Controlling the average number of excitations per cluster via the FEL intensity allows a coarse tuning of the ICD rate.

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

The fragmentation of uracil molecules and pure and nano-hydrated uracil clusters by ¹²C⁴⁺ ion impact is investigated.