Scanning tunneling microscopy (STM) experiments and density-functional theory (DFT) calculations are combined to unravel the complex shifts and splittings of molecular orbitals (MOs) for the prototype system of a single $\pi$-conjugated molecule bonded to a semiconductor surface. Intramolecular resolution in STM images of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) on $\text{Si}\left(111\right)\text{−}\left(7\times 7\right)$ cannot be understood as resulting from a simple rigid shift of the MOs of the free molecule. DFT calculations and simulations of STM images with realistic tips show large splittings of the original MOs that contribute in a complex way to the tunnel current and are understood under symmetry and charge-transfer arguments. The system is characterized by a strong, partially ionic covalent bonding involving the carboxyl groups of the PTCDA and the Si dangling bonds.

• Received 19 July 2010

DOI:https://doi.org/10.1103/PhysRevB.82.075402