The interfaces formed between pentacene (PEN) and perfluoropentacene (PFP) molecules and Cu(111) were studied using photoelectron spectroscopy, X-ray standing wave (XSW), and scanning tunneling microscopy measurements, in conjunction with theoretical modeling. The average carbon bonding distances for PEN and PFP differ strongly, that is, 2.34 A for PEN versus 2.98 A for PFP. An adsorption-induced nonplanar conformation of PFP is suggested by XSW (F atoms 0.1 A above the carbon plane), which causes an intramolecular dipole of approximately 0.5 D. These observations explain why the hole injection barriers at both molecule/metal interfaces are comparable (1.10 eV for PEN and 1.35 eV for PFP) whereas the molecular ionization energies differ significantly (5.00 eV for PEN and 5.85 eV for PFP). Our results show that the hypothesis of charge injection barrier tuning at organic/metal interfaces by adjusting the ionization energy of molecules is not always readily applicable.