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[a] During recent years self-assembled monolayers (SAMs) have been recognized as model structures for different areas in nanotechnology, ranging from nanolithography and molecular electronics to sensors and biocompatible materials.[1] A growing range of possible new SAM applications demands better understanding of their detailed molecular structure, which is a result of balancing molecule-molecule and molecule-substrate interactions in the monolayer. Despite the numerous structural studies of SAMs available nowadays, the structure and stability of the SAM-substrate interface is still poorly understood. Even for a most simple SAM system of methanethiol on Au(111), identification of the adsorption geometry (the AuÀS interface) remains controversial. [2,3] As a consequence, the experimental and theoretical analysis of the bonding geometry and the stability of the molecule-substrate interface for technologically relevant, and therefore more complicated SAMs, is extremely difficult. Importantly, this missing information remains fundamental for most of SAMs potential applications with molecular electronics in particular.[4]Herein we propose using ion-induced desorption in combination with neutral fragment mass spectrometry as a method to analyze the chemical stability of the molecule-substrate interface in complicated and technologically relevant SAMs. This work builds on previous studies analyzing the behavior of SAMs on a Au(111) substrate upon bombardment with beams of Ar + ions in the keV range. [5][6][7][8] It was shown that the bombardment of aromatic thiol SAMs on a Au(111) substrate results in the ejection of neutral molecular fragments via two distinct desorption mechanisms. A minor percentage of the SAM fragments leave the surface with high kinetic energy (~eV) as a result of the direct momentum transfer from the collision cascade developed in the substrate upon primary ion impact. The overwhelming majority of desorbing particles leaves the surface with low kinetic energies (~10 À2 eV) as a result of "gentle"cleavage of chemical bonds (with no significant momentum transfer) within the organic layer by chemical reactions initiated by reactive fragments (e.g. radicals) created in the organic film as a result of the primary ion impact. Following these findings, ion-induced desorption experiments were performed for aromatic SAMs that form different structural phases on the Au(111) surface. [9] These experiments unambiguously demonstrated that the ion-induced cleavage of chemical bonds in SAMs is extremely sensitive to details of their geometric and electronic configuration, due to the chemical reaction mechanisms involved. To further investigate this effect, a homologue series of 4,4'-biphenyl-substituted alkanethiols [CH 3 ÀC 6 H 4 ÀC 6 H 4 À(CH 2 ) n ÀSH; BPnS; n = 1-6] deposited on a Au(111) substrate was analyzed.[10] Former microscopic [11] and spectroscopic [12,13] experiments demonstrated that, depending on the parity of the number of CH 2 units (the parameter n is odd or even), two different structure...

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