In this work, was studied the adsorption and orientation of three dipyridinic derivatives 9,10-bis-((E)-2-(pyridin-4-yl)vinyl)anthracene (DPAC), 1,4-bis-((E)-2-(pyridin-4-yl)vinyl)naphthalene (DPNA-T) and 2,6-bis-((E)-2-(pyridin-4-yl)vinyl)naphthalene (DPNA-L) on gold nanoparticles, using Surface Enhanced Raman Scattering (SERS). Systematic modification in the shapes of the bifunctional systems (Cross-shape, T-shape and Linear-shape) shows changes significant in the preferential orientation of these analytes on the nanostructured gold surface. Additional data from UV-vis measurements and TEM images are in agreement with the Reaction Limited Colloid Aggregation (RLCA) mechanisms for DPAC and DPNA-T and Diffusion Limited Colloid Aggregation (DLCA) mechanisms for DPNA-L, showing that for the same analyte concentration, the aggregation mechanism depends on the molecular shape. These results allow us to rationalize the fundamental aspects involved in the development of devices based on plasmonic resonance with potential applications in the field of molecular electronics.