A possibility to influence the response of self-assembled monolayers (SAM) of alkanethiolates (AT) to low-energy electron irradiation through the incorporation of specific molecular groups into the alkyl chains has been studied by using 11-(hexylmercapto)undecane-1-thiol (HMUT, CH3(CH2)(5)S(CH2)(11) SH) SAM on gold substrate as a model system. In situ near-edge X-ray absorption fine structure spectroscopy and X-ray photoelectron spectroscopy (XPS) were applied as experimental tools. HMUT was found to form a dense, well-ordered self-assembled monolayer on Au with a coverage close to that of AT SAMs, a thickness of 19.8 +/- 0.5 Angstrom, and an average molecular tilt angle of 40 degrees +/- 2 degrees. Features related to the thiolate and sulfide species could be easily distinguished in the S 2p XP spectra. Electron irradiation of the HMUT film gives rise to the same effects previously observed for AT SAMs such as disordering, partial dehydrogenation with C=C double bonds formation, desorption of the film fragments, reduction of the thiolate moieties, and the appearance of a new sulfur species. At the same time the extent of irradiation-induced desorption from the HMUT film is found to be noticeably larger (by approximate to 35%) than in AT SAMs, which is attributed to a higher sensitivity of the C-S bond to electron irradiation as compared to a C-C one. Some other differences with respect to AT SAMs such as sulfide-derived formation of C=S double bonds and a slightly reduced extent of irradiation-induced damage at the Au-alkanethiolate interface were also observed. The close resemblance of the binding energies of alkyl sulfide and the irradiation-induced sulfur species in AT SAMs implies an alternative assignment for the latter entities along with the commonly approved disulfide formation model, namely an incorporation of sulfur into the alkyl matrix via bonding to irradiation-induced carbon radicals in the adjacent aliphatic chains.