Low-energy ion-surface collisions were used to probe the reactivity, electron barrier properties, and relative degree of order of self-assembled monolayer films after transfer of the films from solution to vacuum (10(-7) Torr). Mass-selected polyatomic projectiles (ionized benzene, benzene-d6, and fluorobenzene) collided with self-assembled monolayer films at collision energies in the range of 20-70 eV, and the resulting ions were mass-analyzed and detected. The surfaces were prepared by the spontaneous assembly of n-alkanethiols (CH3(CH2)(n)SH, n = 3, 11, 17), perdeuterioeicosanethiol (CD3(CD2)19SH), and 2-(perfluorooctyl)ethanethiol (CF3(CF2)7CH2CH2SH) on both gold foil and vapor-deposited gold. Chemical reactions between the benzene molecular ion and the monolayer films (e.g., H, CH3, D, CD3, F, and CF3 additions) are evident from deuterium labeling results. Ion-surface collision spectra for ionized benzene are sensitive to (i) the chemical composition of the monolayer, (ii) the chain length of the alkanethiol used to prepare the film, (iii) the preparation of the gold surface prior to reaction (mechanically polished gold foil vs vapor-deposited gold vs plasma-cleaned vapor-deposited gold), and (iv) the exposure time between the alkanethiol solution and the gold. For comparison with our experimental results, ab initio calculations have also been carried out to predict the energetics of the loss of H and H-2 from selected ion-surface reaction adducts (H, F, and CH3 addition products). Experimental data not directly available from the tandem mass spectra (i.e., total ion signals and surface currents) are used to characterize the relative degree of neutralization of the projectiles at the films. The data suggest that the relative electron barrier properties of the films in vacuum mimic those reported for electrochemistry experiments in solution. The mass spectra and the current measurements indicate that the relative degree of order of the monolayers is retained upon transfer of the films from solution to vacuum.