Identification of complex molecules at surfaces: G-SIMS and SMILES fragmentation pathways

In this study, we develop a simple method using the SMILES molecular structure format to simulate fragmentation pathways in secondary ion mass spectrometry (SIMS). These pathways are found to have good agreement with fragmentation pathways identified using G-SIMS-FPM (Fragmentation Pathway Mapping) using the two examples of folic acid and Irganox 1010. G-SIMS is an easy-to-use method that considerably simplifies complex static SIMS spectra. G-SIMS-FPM allows the molecular structure to be re-assembled by following fragmentation pathways as the G-SIMS surface plasma temperature is varied. The simulated pathways help reduce the wide choice of possible structures faced by analysts as the molecular structure is reassembled, leading to more reliable molecular identification. A rapid method to establish a foundation database of simulated pathways using the community and a web-based system is proposed.