The molecule-metal interface formed by pyridine-2,5-dicarboxylic acid chemically bonded to the Cu (110) surface is investigated by scanning tunneling microscopy and first-principles calculations. Our current-voltage spectroscopy studies reveal an electronic mapping of molecular orbitals as a function of tip position. By combining experimental and theoretical investigations, individual molecular orbitals are characterized by their energy and spatial distribution. The importance of adsorption geometries and conformational changes on the electron transport properties is highlighted. DOI: 10.1103/PhysRevLett.105.066801 PACS numbers: 73.63.Àb, 31.15.AÀ, 68.37.Ef, 82.37.Gk In the past decade, we have witnessed significant progress in integrating organic molecules in functional molecular devices like single molecule diodes [1,2] or in organic field-effect transistors [3,4]. To improve the functionality of such molecular electronic devices, an essential prerequisite is to gain a substantial understanding of the electronic structure of molecule-surface interfaces near the Fermi level that ultimately controls the performance of such a device [5][6][7].In this context, the precise energetic alignment of the molecular orbitals with respect to the Fermi level of the substrate, in particular, that of the highest occupied molecular orbitals and the lowest unoccupied molecular orbitals, is a key component of the electronic structure of the molecule-surface system under consideration. Therefore, in this Letter we present a detailed electronic mapping of molecular orbitals (MOs) by distance-dependent currentvoltage (I-V) spectroscopy. Combining the spatially resolved scanning tunneling spectroscopy (STS) results with density functional theory (DFT) investigations, we show how to identify the electronic structure of a molecule chemically bonded to a metallic surface. As a model system we investigate the adsorption of the pyridine-2,5-dicarboxylic acid (PyDCAH 2 ) on Cu(110).Our ab initio total-energy calculations have been performed in the framework of DFT [8] by using the PerdewBurke-Ernzerhof [9] exchange-correlation energy functional as implemented in the VASP code [10,11]. A detailed description is available in the supplementary material [12]. We first note that, in the case of the PyDCAH 2 molecule, which adsorbs on the Cu(110) surface under deprotonation of one carboxyl group, forming PyDCAH, several different adsorption geometries must be taken into account due to the presence of a nitrogen atom in the aromatic ring. Therefore, we differentiate in the following between C 7 H 4 N ð2Þ O 4 , describing a PyDCAH molecule with the nitrogen on position two in the ring (counting the ring atoms from the carbon atom located at the bonded carboxylate unit), and C 7 H 4 N ð3Þ O 4 , denoted as configuration f1g and f2g, respectively. Experimentally, there is no possibility to influence the orientation of the molecule during the adsorption process or to monitor topographically which configuration is preferentially adsorbed. If the ...