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Identification of isomers using traditional mass spectroscopy methods has proven an interesting challenge due to their identical mass to charge ratios. This proves particularly consequential for gold clusters, as subtle variations in the ligand and cluster structure can have drastic effects on the cluster functionalization, solubility, and chemical properties. Biological nanopores have proven an effective tool in identifying subtle variations at the single molecule limit. This paper reports on the ability of an α-hemolysin (αHL) pore to differentiate between para -, meta -, and ortho - ( p -, m -, and o -, respectively) mercaptobenzoic acid ligands attached to gold clusters at the single cluster limit. Detecting differences between p -MBA and m -MBA requires pH-dependent studies that illustrate the role inter-ligand binding plays in stabilizing m -MBA-capped clusters. Additionally, this paper investigates the difference in behavior for these clusters when isolated, and when surrounded by small ligand–Au complexes (Au n L m , n = 0, 1, 2… and m = 1, 2,…) that are present following cluster synthesis. It is found that continuous exposure of clusters to freely diffusing ligand complexes stabilizes the clusters, while isolated clusters either disintegrate or exit the nanopore in seconds. This has implications for long term cluster stability.