The surface structure of self-assembled monolayers of hexanethiolate (HT) on the Au(100)-(1 x 1) surface has been studied by density functional theory (DFT) calculations and their results compared to scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) data. We have found two novel surface structure models consisting of adsorbed thiolates on the Au(100)-(1 x 1) surface that fairly account for experimental STM and XPS observations. Surprisingly, these models exhibit better thermodynamic stability than those consisting of thiolate-Auad-thiolate moieties on a reconstructed Au(100)-(1 x 1) surface. Also these proposed models are more stable than the thiolate-Auad-thiolate containing c(4 x 2) lattice on the reconstructed Au(111) suggesting a surface dependent chemistry for thiolates on Au. However, the possible existence of other models with similar or better stability than those proposed in this work and also the possible coexistence of different surface structures and chemistry on the substrate surface cannot be excluded.