The self-assembled and highly ordered first layer of terephthalic acid on Cu(100) as well as its bilayer on the same surface are studied here using high-resolution electron energy loss spectroscopy (HREELS), Auger electron spectroscopy, and low energy electron diffraction. These experiments show completion of the first layer before growth of the second layer. HREELS measurements show that the first layer of the acid deprotonates, which is seen in the absence of the OH stretching mode for the acid groups. However, this mode is present in the bilayer structure, confirming that the deprotonation is due to a reaction with the Cu surface and suggesting that there is little mixing of the layers. It has been suggested previously that the TPA monolayer structure is stabilized by an intermolecular hydrogen bonding interaction, but we are not able to resolve any distortion of the CH stretching mode for such an interaction, but instead see evidence for direct bonding to the Cu surface.