Supramolecular Secondary Ion Mass Spectrometry - Revealing Molecular Surroundings and Inter-Molecular Interactions in Organic Matter

19 October 2020, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


While supramolecular chemistry is a firmly established research field in laboratory conditions, the experimental study of non-covalent interactions, such as hydrogen bonding and piinteractions, between different molecules in chemically rich, non-crystalline matter remains highly challenging. We demonstrate that soft ion bombardment can trigger the joint desorption of weakly interacting adjacent molecules, and that this in turn allows molecular interaction probabilities, surroundings, and arrangement in organic matter to be probed. Assemblies of organic molecules linked by hydrogen bonds or dipole- interactions are extracted here with preservation of chemistry and structure as single-charged supramolecular secondary ions. Among the examples shown is the desorption of stable 12-molecular clusters of the amino acid L-proline, which suggest an icosahedral on-surface self-assembly, and the desorption of supramolecular linear oligomers of 2,5-piperazinedione. The second half of the study lays down the statistical framework for the reconstruction of a molecular interactome based on the relative abundances of supramolecular dimers of different compositions within a mass spectrum acquired on organic matter containing more than one type of molecule.


Supramolecular chemistry
Supramolecular secondary ions
Molecular Clusters
Mass spectrometry


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