The adsorption structure and hydrogen-bonded complexes of alkane and alkene derivatives self-assembled on HOPG were studied by scanning tunneling microscopy (STM) and Molecular Mechanics (MM) simulations. The effect of different interior -CH=CH- conformations and functional groups in molecules on the structure and stability of self-assembled monolayers was considered. It was found that octadecanol and trans-oleic acid could form stable structure on HOPG and their high-resolution images could be obtained by STM. Octadecanol exhibited two kinds of packing by alkyl-alkyl and adsorbate-substrate interactions. The interior trans-CH=CH- group in trans-oleic acid had a slight influence on the self-assembly configuration. However, owing to the cis-double bond in the interior of cis-oleyamine molecule, the ordered monolayer could not be easily imaged by STM at ambient conditions. The adsorption conformations of three kinds of molecules on HOPG surface were optimized by MM simulation, respectively. The analysis of hydrogen-bond interactions by computation stimulation also revealed that the stability of cis-oleyamine on HOPG was the worst. These results demonstrated that molecular self-assembly and its stability could be significantly tailored by changing the molecular structure. (C) 2010 Elsevier B. V. All rights reserved.