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The chemical modification caused by prolonged exposure to X-rays on a series of para-substituted phenyl moieties (-NO2, -CN, -CHO, -COOH, -CO2Me, and -CO2(1)Bu) at the surface of thiolate-Au self-assembled monolayers (SAMs) has been investigated by X-ray photoelectron spectroscopy (XPS). Furthermore, the influence that the phenyl group has on the chemical modification induced by the X-ray irradiation on the SAMs was investigated by comparing the XPS results obtained from irradiation on a NO2-aromatic-terminated SAM (6-(4-nitro-phenoxy)-hexane-1-thiolate (NPHT)) and NO2-aliphatic-terminated SAM (thioacetic acid S-(12-nitrododecyl) ester (TNDDE)). The NPHT and TNDDE SAMs have been shown to behave differently to X-ray exposure. The irradiation of the NPHT SAM led to the reduction of the nitro (-NO2) moiety to the amine (-NH2) moiety, as shown by the decrease in the intensity of the N 1s photoelectron peak for -NO2 (406 eV) in the XPS spectra with the concomitant increase in the N 1s photoelectron peak for -NH2 (399 eV). On the TNDDE SAM, XPS showed the -NO2 photoelectron peak again decreasing with prolonged X-ray irradiation whereas no peak was observed at 399 eV; therefore, the -NO2 moieties are selectively cleaved. No change was observed on the other functionalized monolayers apart from the -CO2(t)Bu-functionalized monolayer, where after 100 min of X-ray irradiation approximately 11% of the carbon content was lost. The S 2p and O 1s spectra remained unchanged during the irradiation suggesting the conversion of the -CO2(t)Bu to the -COOH moiety, although the conversion was not complete because the tertiary butyl moiety contributes 25% to the total carbon content of the SAM. Also, there was no evidence of the molecules desorbing from the substrate for any of the SAMs studied during the X-ray irradiation as shown by no change in the S 2p and C 1s XPS spectra taken during the X-ray irradiation.