Density functional methods on cluster models are used to examine the nature of the geometry, bonding, and energetics involved in the formation of molecular thiol junctions at gold electrode interfaces. The two gold electrodes are modeled as four atom clusters, without geometric constraint. We observe that the geometry nearly always favors twofold coordination of the thiol to a nearly planar array of four gold atoms. There are four essential structural motifs, that seem to characterize these interactions for alkyne, alkane, xylyl, and benzene dithiols. Bonding interactions are relatively strong, and correspond to a polarized covalent interaction. Results are given for different charge and spin components on the molecular bridge. (C) 2003 American Institute of Physics.