Dynamics of energy-selected fragments from nucleobase–protein interaction molecular models revealed by combined photoelectron–photoion coincidence spectroscopy and theoretical simulation

Abstract

A combined experimental and computational approach aimed at systematically exploring unimolecular reaction channels of ionized gas-phase systems—including rearrangements, intramolecular bonds formation, and fragmentation—has been applied to 5- and 6-benzyluracil (5BU and 6BU) molecules, which are used as molecular models of photo-induced interactions between nucleobases and aromatic aminoacids. Photoelectron–photoion coincidence experiments offer a unique view of energy-selected fragmentation channels, while ab initio molecular dynamics of the ionic system, performed with semi-empirical potentials and for long simulation times, can extensively explore possible unimolecular reactive pathways, revealing the detailed molecular identity of the products. Results show that, at lower binding energies, ionized 5- and 6-benzyluracil molecules do not fragment but may nevertheless rearrange to give, mainly in 6BU, cross-linked products. This suggests that ionization can efficiently promote covalent cross-links between interacting proteins and nucleic acids, which can be exploited to isolate and characterize such transient complexes occurring in cellular environments. At higher binding energies, however, fragmentation channels are predominant, mainly involving the decomposition and photo-damage of the uracil moiety. Several fragmentation products have been characterized, and the differences in fragment abundances and fragmentation mechanisms between the two benzyluracil isomers have been outlined.