A theoretical analysis of the orientation of biofunctionalized thiolate has been made by changing the surface configuration. The results show that it is possible to match the experimental data by changing the molecular density and also that it is possible to match the experimental data using only hollow sites in the gold surface as placements for the molecules. Some configurations that match available data using only hollow sites positions have been suggested. Moving away from the (sqrt(3) x sqrt(3)) R30° configuration result in a large energy gain for Bor Capped.