AVS 56th International Symposium & Exhibition
    Applied Surface Science Thursday Sessions
       Session AS1-ThM

Paper AS1-ThM2
A New Web-Based System for Identifying Molecules and Molecular Structure using G-SIMS and SMILES

Thursday, November 12, 2009, 8:20 am, Room C2

Session: Advances in Surface Analysis
Presenter: I.S. Gilmore, National Physical Laboratory, UK
Authors: I.S. Gilmore, National Physical Laboratory, UK
M.A. Phillips, National Physical Laboratory, UK
F.M. Green, National Physical Laboratory, UK
T.S. Salter, National Physical Laboratory, UK
M.P. Seah, National Physical Laboratory, UK
Correspondent: Click to Email

G-SIMS[1] 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[2,3] 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 Tp, is varied, known as G-SIMS-FPM. Recently, we have developed a novel approach[4], based on SMILES[5] (Simplified Molecular Input Line Entry Specification), to assist the reassembly process in an automated way through evaluation of the fragmentation pathways for given molecular structures. A computer program takes a parent structure and goes through every possible fragmentation to provide a tree structure of fragmentation products and simulated fragmentation pathways. For any fragment it is then possible to identify the molecular structure, its mass and a pathway to the parent. We find that there is a good correlation with peak evolution in G-SIMS-FPM data and simulated pathways for two amino acids and a simple peptide. This significantly enhances the application of G-SIMS-FPM to unknown materials. Once fragmentation pathways have been calculated for a molecule they are added to a library.

We have now developed an informatics database system with a web-based front-end that allows analysts to generate fragmentation pathways for any molecule in SMILES format. For new molecules, the pathways are added to the library. Analysts may then explore the fragment pathways for comparison with the G-SIMS spectra. The free web-based facility allows the library to grow rapidly as use by the community grows. Recent developments in G-SIMS including G-tip technology and the use of cluster ions will be discussed. Examples of the use of G-SIMS and SMILES to identify the structure for different molecules are provided as well as examples of how to use the web-based system.

[1] I. S. Gilmore and M. P. Seah, Appl. Surf. Sci., 161 (2000), 465.

[2] I. S. Gilmore and M. P. Seah, Appl. Surf. Sci., 231-232 (2004) 224.

[3] I. S. Gilmore, F. M. Green and M. P. Seah, Appl. Surf. Sci., 252 (2006) 6601.

[4] F.M. Green, E.A. Dell, I. S. Gilmore, M.P. Seah, Int J Mass Spectrom 272 (2008) 38

[5] SMILES, Daylight Chemical Information Systems, http://www.daylight.com/smiles/ .