The depth of penetration of photolytically generated, gas-phase O( P) atoms into thioalkyl self-assembled monolayers (SAMs) has been investigated. Custom-synthesized, site-selectively deuterated SAMs were prepared on Au substrates and characterized by scanning tunneling microscopy (STM). Relative yields of gas-phase OD were detected by laser-induced fluorescence (LIF). Reaction was suppressed at the terminal CD by the higher abstraction barriers for primary D atoms, yielding only 16 ± 3% of the total OD. The C (first secondary) site is the individually most reactive (42 ± 5%). The remaining significant contribution (42 ± 4%) from positions as deep as C-C is a considerable surprise when compared with previous related experiments using higher-energy O ion projectiles and detecting OH products. The apparent greater penetrability of the SAM layer found here may have prior theoretical support. Furthermore, we show that NO damages the surfaces but that C SAMs are considerably more resistant than C SAMs. © 2010 American Chemical Society.