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.

On the theory of the spin I = 1/2 double quantum NMR: Effects of spins spatial displacements between RF pulses.

Spatial displacements of spins between radio frequency pulses in a Double-Quantum (DQ) nuclear magnetic resonance pulse sequence generate additional terms in the effective DQ Hamiltonian. We derive a simple expression that allows the estimation and control of these contributions to the initial rise of the DQ build up function by variation of experimental parameters in systems performing anomalous diffusion. The application of polymers is discussed.

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.

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.

On the theory of deuteron NMR free induction decay of reptating polymer chains: Effect of end segment dynamics.

A self-consistent approximation beyond the Redfield limit and without using the Anderson-Weiss approximation for the Free Induction Decay (FID) of deuteron spins belonging to polymer chains undergoing reptation is formulated. The dynamical heterogeneity of the polymer segments created by the end segments is taken into account. Within an accuracy of slow-changing logarithmic factors, FID can be qualitatively described by a transition from an initial pseudo-Gaussian to a stretched-exponential decay at long times. With an increase in observation time, the contribution from end effects to the FID increases. In the regime of incoherent reptation, contributions to the FID from central segments yield an exponent of 1/4 for the stretched decay and contributions from end segments yield an exponent of 3/16. In the regime of coherent reptation, the central segments generate a stretching exponent of 1/2, whereas the end segments contribute with an exponent of 1/4. These predictions are shown to be in qualitative agreement with the experimental FIDs of perdeuterated poly(ethylene oxide) with molecular masses of 132 kg/mol and 862 kg/mol.

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 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.

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.

Segmental dynamics of polyethylene-alt-propylene studied by NMR spin echo techniques.

Segmental dynamics of a highly entangled melt of linear polyethylene-alt-propylene with a molecular weight of 200 kDa was studied with a novel proton nuclear magnetic resonance (NMR) approach based upon 1H → 2H isotope dilution as applied to a solid-echo build-up function ISE(t), which is constructed from the NMR spin echo signals arising from the Hahn echo (HE) and two variations of the solid-echo pulse sequence. The isotope dilution enables the separation of inter- and intramolecular contributions to this function and allows one to extract the segmental mean-squared displacements in the millisecond time range, which is hardly accessible by other experimental methods. The proposed technique in combination with time-temperature superposition yields information about segmental translation in polyethylene-alt-propylene over 6 decades in time from 10-6 s up to 1 s. The time dependence of the mean-squared displacement obtained in this time range clearly shows three regimes of power law with exponents, which are in good agreement with the tube-reptation model predictions for the Rouse model, incoherent reptation and coherent reptation regimes. The results at short times coincide with the fast-field cycling relaxometry and neutron spin echo data, yet, significantly extending the probed time range. Furthermore, the obtained data are verified as well by the use of the dipolar-correlation effect on the Hahn echo, which was developed before by the co-authors. At the same time, the amplitude ratio of the intermolecular part of the proton dynamic dipole-dipole correlation function over the intramolecular part obtained from the experimental data is not in agreement with the predictions of the tube-reptation model for the regimes of incoherent and coherent reptation.

On the theory of the proton dipolar-correlation effect as a method for investigation of segmental displacement in polymer melts.

A thorough theoretical description of the recently suggested method [A. Lozovoi et al. J. Chem. Phys. 144, 241101 (2016)] based on the proton NMR dipolar-correlation effect allowing for the investigation of segmental diffusion in polymer melts is presented. It is shown that the initial rise of the proton dipolar-correlation build-up function, constructed from Hahn Echo signals measured at times t and t/2, contains additive contributions from both inter- and intramolecular magnetic dipole-dipole interactions. The intermolecular contribution depends on the relative mean-squared displacement of polymer segments from different macromolecules, which provides an opportunity for an experimental study of segmental translational motions at the millisecond range that falls outside the typical range accessible by other methods, i.e., neutron scattering or NMR spin echo with the magnetic field gradients. A comparison with the other two proton NMR methods based on transverse spin relaxation phenomena, i.e., solid echo and double quantum resonance, shows that the initial rise of the build-up functions in all the discussed methods is essentially identical and differs only in numerical coefficients. In addition, it is argued that correlation functions constructed in the same manner as the dipolar-correlation build-up function can be applied for an experimental determination of a mean relaxation rate in the case of systems possessing multi-exponential magnetization decay.

Communication: Proton NMR dipolar-correlation effect as a method for investigating segmental diffusion in polymer melts.

A simple and fast method for the investigation of segmental diffusion in high molar mass polymer melts is presented. The method is based on a special function, called proton dipolar-correlation build-up function, which is constructed from Hahn Echo signals measured at times t and t/2. The initial rise of this function contains additive contributions from both inter- and intramolecular magnetic dipole-dipole interactions. The intermolecular contribution depends on the relative mean squared displacements (MSDs) of polymer segments from different macromolecules, while the intramolecular part reflects segmental reorientations. Separation of both contributions via isotope dilution provides access to segmental displacements in polymer melts at millisecond range, which is hardly accessible by other methods. The feasibility of the method is illustrated by investigating protonated and deuterated polybutadiene melts with molecular mass 196 000 g/mol at different temperatures. The observed exponent of the power law of the segmental MSD is close to 0.32 ± 0.03 at times when the root MSD is in between 45 Å and 75 Å, and the intermolecular proton dipole-dipole contribution to the total proton Hahn Echo NMR signal is larger than 50% and increases with time.

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 (12)C(4+) 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.

NMR relaxation induced by iron oxide particles: testing theoretical models.

Superparamagnetic iron oxide particles find their main application as contrast agents for cellular and molecular magnetic resonance imaging. The contrast they bring is due to the shortening of the transverse relaxation time T 2 of water protons. In order to understand their influence on proton relaxation, different theoretical relaxation models have been developed, each of them presenting a certain validity domain, which depends on the particle characteristics and proton dynamics. The validation of these models is crucial since they allow for predicting the ideal particle characteristics for obtaining the best contrast but also because the fitting of T 1 experimental data by the theory constitutes an interesting tool for the characterization of the nanoparticles. In this work, T 2 of suspensions of iron oxide particles in different solvents and at different temperatures, corresponding to different proton diffusion properties, were measured and were compared to the three main theoretical models (the motional averaging regime, the static dephasing regime, and the partial refocusing model) with good qualitative agreement. However, a real quantitative agreement was not observed, probably because of the complexity of these nanoparticulate systems. The Roch theory, developed in the motional averaging regime (MAR), was also successfully used to fit T 1 nuclear magnetic relaxation dispersion (NMRD) profiles, even outside the MAR validity range, and provided a good estimate of the particle size. On the other hand, the simultaneous fitting of T 1 and T 2 NMRD profiles by the theory was impossible, and this occurrence constitutes a clear limitation of the Roch model. Finally, the theory was shown to satisfactorily fit the deuterium T 1 NMRD profile of superparamagnetic particle suspensions in heavy water.

On the theory of double quantum NMR in polymer systems: the second cumulant approximation for many spin I = 1/2 systems.

General analytical expressions for Double Quantum Nuclear Magnetic Resonance (DQ NMR) kinetic curves of many-spin I = 1∕2 systems are derived with an accuracy of the second cumulant approximation. The expressions obtained exactly describe the initial part of the kinetic curves and provide a reasonable approximation up to times of about the effective spin-relaxation time. For the case when the system contains two isolated spins, this result exactly reproduces known expressions. In the case of polymer melts, the intermolecular magnetic dipole-dipole interactions significantly influence the time dependence of the DQ NMR kinetic curves.

On the theory of the proton free induction decay and Hahn echo in polymer systems: the role of intermolecular magnetic dipole-dipole interactions and the modified Anderson-Weiss approximation.

The influence of the intermolecular magnetic dipole-dipole interaction on the free induction decay (FID) as well as on the Hahn-echo of proton spins in polymer melts is investigated. It is shown that for isotropic models of polymer dynamics, when polymer segment displacements do not correlate with an initial chain conformation, the influence of the intermolecular magnetic dipole-dipole interactions to the FID and Hahn echo is increasing more rapidly with evolution time than the corresponding influence of the intramolecular magnetic dipole-dipole interactions. On the other hand, the situation is inverted for the tube-reptation model: here the influence of the intramolecular magnetic dipole-dipole interactions to the FID and Hahn echo is increasing faster with time than the contribution from intermolecular interactions. A simple expression for the relative mean squared displacements of polymer segments from different chains is obtained from the intermolecular contribution to the FID. A modified Anderson-Weiss approximation, taking into account flip-flop transitions between different spins, is proposed and on that basis, the conditions for extracting the relative intermolecular mean squared displacements of polymer segments from the intermolecular contribution to the proton FID is established. Systematic investigations of intermolecular contributions, which were considered as an unimportant factor for FID and Hahn echo in polymer systems by most previous works, actually cannot be considered as negligible and opens a new dimension for obtaining information about polymer dynamics in the millisecond regime.

Molecular exchange dynamics in partially filled microscale and nanoscale pores of silica glasses studied by field-cycling nuclear magnetic resonance relaxometry.

Nuclear magnetic spin-lattice relaxation experiments have been performed in partially filled porous glasses with wetting and nonwetting fluids. The frequency dependence of the spin-lattice relaxation rate in Vycor (4 nm pores) and VitraPOR #5 (1 microm pores) silica glasses was studied as a function of the filling degree with the aid of field-cycling NMR relaxometry. The species of primary interest were water ("polar") and cyclohexane ("nonpolar"). Spin-lattice relaxation was examined in the frequency range from 1 kHz to 400 MHz with the aid of a field-cycling NMR relaxometer and an ordinary 400 MHz NMR spectrometer. Three different mobility states of the fluid molecules are distinguished: The adsorbed state at the pore walls, the bulklike liquid phase, and the vapor phase. The adsorbate spin-lattice relaxation rate is dominated by the "reorientation mediated by translational displacements" (RMTD) mechanism taking place at the adsorbate/matrix interface at frequencies low enough to neglect rotational diffusion of the molecules. The experimental data are analyzed in terms of molecular exchange between the different mobility states. Judged from the dependence of the spin-lattice relaxation rates on the filling degree, limits for slow and fast exchange (relative to the RMTD time scale) can be distinguished and identified. It is concluded that water always shows the features of slow exchange irrespective of the investigated pore sizes and filling degrees. This is in contrast to cyclohexane which is subject to slow exchange in micrometer pores, whereas fast exchange occurs in nanoscopic pores. The latter case implies that the vapor phase contributes to molecular dynamics in this case at low filling degrees while it is negligible otherwise.