A combined study of scanning tunneling microscopy ͑STM͒ and density functional theory ͑DFT͒ reveals that 3,4,9,10-perylene-tetracarboxylic-dianhydride ͑PTCDA͒ adsorbs on Ag͑111͒ at bridge sites in two nonequivalent orientations, one nearly aligned with the ͓101͔ substrate axis and the other 18°misaligned. Site-specific spectroscopy reveals that molecules in the two configurations exhibit subtle differences in their electronic structure. DFT-based STM simulations trace these back to the influence of distinct local adsorption geometries on the chemical molecule-substrate and molecule-molecule interactions.

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