The interactions between pentacene and the Si(001)-(2 x 1) surface have been investigated using Fourier transform infrared spectroscopy (FTIR), ultraviolet photoelectron spectroscopy (UPS), and X-ray photoelectron spectroscopy (XPS). The pentacene molecules in the first layer react with the Si surface atoms through the C=C double bonds and via cleavage of C-H bonds. This chemisorption is accompanied by disruption of the conjugated pi electron system. The disrupted interfacial layer is stable throughout deposition and evaporation of thicker pentacene films. Pentacene molecules in layers beyond the first layer adsorb molecularly and yield well-defined valence band features that are characteristic of a conjugated pi electron system. Functionalization of the Si surface with a monolayer of cyclopentene inhibits dissociation of subsequently deposited pentacene molecules.