AVS 53rd International Symposium
    Applied Surface Science Monday Sessions
       Session AS-MoA

Paper AS-MoA1
Molecular Structure - G-SIMS with SMILES

Monday, November 13, 2006, 2:00 pm, Room 2005

Session: Developing Methods for Data Analysis
Presenter: I.S. Gilmore, National Physical Laboratory, UK
Authors: I.S. Gilmore, National Physical Laboratory, UK
F.M. Green, National Physical Laboratory, UK
M.P. Seah, National Physical Laboratory, UK
Correspondent: Click to Email
G-SIMS is a powerful method for the identification of organics and complex molecules at surfaces. For complex molecules, evaluating the molecular structure can be key to correct identification. We have shown@footnote 1,2@ that the molecular structure may be reassembled from fragment ions by studying the evolution of G-SIMS intensities as the surface plasma, with effective temperature T@sub p@, is varied, known as G-SIMS-FPM. Here, we develop a novel approach based on SMILES (Simplified Molecular Input Line Entry Specification), to assist the reassembly process through evaluation of the fragmentation pathways of given molecular structures. The SMILES molecular model format allows the molecular structure to be expressed in a logical computer readable way. A computer program has been developed that takes a parent structure and goes through every possible fragmentation providing a tree-structure of fragmentation products. This fragmentation map thus comprises all the possible products without considering relative intensities. For any fragment it is then possible to identify the molecular structure, the mass and the pathway to the parent. By applying this process to many types of parent molecule a foundation library of fragments and pathways is developed. Using G-SIMS-FPM some of these pathways for the unknown molecule can be mapped out. Not all pathways are mapped because some of the fragmentation cascades may be weak and some may only occur for the neutral molecules that are not observed by SIMS. We find that there is a good correlation with peaks in G-SIMS-FPM and the fragmentation maps generated using this approach. The SMILES-based fragmentation maps provide significant help in identifying the molecular structure and this will be illustrated with different complex molecules. @FootnoteText@ @footnote 1@ I. S. Gilmore and M. P. Seah, Appl. Surf. Sci., 231-232 (2004) 224.@footnote 2@ I. S. Gilmore, F. M. Green and M. P. Seah, Appl. Surf. Sci., In the press.