Effect of substrate thickness on ejection of phenylalanine molecules adsorbed on free-standing graphene bombarded by 10 keV C₆₀

Highlights: • Substrate thickness has a prominent effect on the molecular ejection mechanism. • Collisions with projectile atoms leads to molecular ejection at thin substrates. • Interactions with deforming graphene sheet ejects molecules from thicker substrates. • Probability of fragmentation process decreases with the graphene substrate thickness. - Abstract: Molecular dynamics computer simulations have been employed to investigate the effect of substrate thickness on the ejection mechanism of phenylalanine molecules deposited on free-standing graphene. The system is bombarded from the graphene side by 10 keV C₆₀ projectiles at normal incidence and the ejected particles are collected both in transmission and reflection directions. It has been found that the ejection mechanism depends on the substrate thickness. At thin substrates mostly organic fragments are ejected by direct collisions between projectile atoms and adsorbed molecules. At thicker substrates interaction between deforming topmost graphene sheet and adsorbed molecules becomes more important. As this process is gentle and directionally correlated, it leads predominantly to ejection of intact molecules. The implications of the results to a novel analytical approach in Secondary Ion Mass Spectrometry based on ultrathin free-standing graphene substrates and a transmission geometry are discussed.