We demonstrate that weak chemical interactions between untethered moieties in molecular nanolayers on metal surfaces can strongly influence the effective work function Φeff. Electron spectroscopy shows that nanolayers of mercaptan-anchored organophosphonates on Au and Pt decrease Φeff. The measured Φeff shifts correlate with the chemical state of phosphonic acid moieties, and scale with molecular length. These results are contrary to predictions of ab initio calculations of monolayer-capped surfaces, but are consistent with calculations of bilayer-capped surfaces with face-to-face hydrogen-bonded phosphonic acid moieties. Our findings indicate that intra-layer bonding and layering in molecular nanolayers can be key to tailoring heterointerfacial electronic properties for applications.

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