Unravelling molecular interactions in uracil clusters by XPS measurements assisted by ab initio and tight-binding simulations

Abstract

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 corehole 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.

Ultraefficiently Calming Cytokine Storm Using Ti3C2Tx MXene

“…[ 26 ] According to previous reports, this obvious shift toward lower binding energy is because of the formation of hydrogen bonds, which are formed between O groups and peptides of IL‐6 such as TiO⋅⋅⋅HNC or CO⋅⋅⋅HNC. [ 27 ] Figure 4d elucidates the shifts corresponding to CF (−0.28 eV) and TiF (−0.93 eV) bonds after IL‐6 adsorption, which also verifies the formation of hydrogen bonds between MXene nanosheets and IL‐6. The hydrogen bonds usually endow stronger binding energy than that of other intermolecular forces such as van der Waals forces.…”

Roadmap on dynamics of molecules and clusters in the gas phase

“…Also, in this case the main challenge is the production of a controlled cluster beam with enough density. First attempts in this direction combining a gas aggregation source to produce neutral uracil clusters and XPS, where the weak, non-covalent interactions modulate the chemical shift, have been reported [37].…”

Water–biomolecule clusters studied by photoemission spectroscopy and multilevel atomistic simulations: hydration or solvation?

“…In a previous work 10 we have studied homogeneous uracil clusters in the gas phase and highlighted the key role of H-bonds in the organization of supramolecular aggregates. It was found that the formation of large clusters (up to 50 uracil molecules) is driven by the anisotropic distribution of H-bond donor and acceptor sites, which can be also modulated by weaker dispersion forces, particularly involving p-conjugate charge distributions.…”

“…The simulations, once properly benchmarked, can be indeed used to describe structures and properties of large aggregates at a precision unattainable by experiments, which use beams with a distribution of cluster sizes, as already shown in the case of homogeneous uracil clusters. 10 In the present work, the inclusion of water in the formation of mixed water-uracil clusters produced by a gas aggregation cluster source 11,12 has been first probed by C, N and O 1s XPS spectra, measured at the PLEIADES beamline of the SOLEIL synchrotron. Beside the comparison with the XPS spectra of uracil clusters and isolated uracil molecules, 13 the structure of mixed uracil-water clusters is interpreted via thorough computational simulations.…”