Scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) were used to examine the surface structure and adsorption conditions of hexanethiol (HT) and cyclohexanethiol (CHT) self-assembled monolayers (SAMs) on Au(111) as a function of storage period in ultrahigh vacuum (UHV) conditions of 3 x 10(-7) Pa at room temperature (RT). STM imaging revealed that after storage for 7 days, HT SAMs underwent phase transitions from c(4 x 2) phase to low coverage 4 x root 3 phase. This transition is due to a structural rearrangement of hexanethiolates that results from the spontaneous desorption of chemisorbed HT molecules on Au(111) surface. XPS measurements showed approximately 28% reduction in sulfur coverage, which indicates desorption of hexanethiolates from the surfaces. Contrary to HT SAMs, the structural order of CHT SAMs with (5 x 2 root 3)R35 degrees phase completely disappeared after storage for 3 or 7 days. XPS results show desorption of more than 80% of the cyclohexanethiolates, even after storage for 3 days. We found that spontaneous desorption of CHT molecules on Au(1 1 1) in UHV at RT occurred quickly, whereas spontaneous desorption of HT molecules was much slower. Thermal desorption spectroscopy (TDS) results suggest CHT SAMs in UHV at RT can desorb more efficiently than HT SAMs due to formation of thiol desorption fragments that result from chemical reactions between surface hydrogen atoms and thiolates on Au(1 1 1) surfaces. This study clearly demonstrated that organic thiols chemisorbed on gold surfaces are desorbed spontaneously in UHV at RT and van der Waals interactions play an important role in determining the structural stability of thiolate SAMs in UHV. (C) 2012 Elsevier Inc. All rights reserved.