The use of small organic molecules to control structure as well as electronic and chemical functionality of a surface is a critical field of surface chemistry. Interest in problems related to bonding, charge transfer and self-assembly of organic species at metal surfaces has grown, in correlation with stronger needs for inexpensive and highly functional organic technologies in energy conversion, sensors, electronics, and other applications. We have studied a prototypical system, terephthalic acid on Cu(100), using a set of complementary analysis tools to develop a complete picture of the chemisorption and structural transitions in this dynamic system, which is of key importance for structural control and organic-to-metal interface design. Scanning tunneling microscopy has been used to achieve molecular resolution structural characterization of the first layer structural transitions and of the second layer structures. High-resolution electron energy loss spectroscopy reveals orientation of the molecule in each layer and lends insight into the bonding interaction with the surface. X-ray standing wave spectroscopy and density functional theory calculations show a strong chemical bond to the surface and indicate that the apparent attractive interaction between molecules is likely due to a substrate mediated interaction, sufficient to overcome any electrostatic repulsion between the negatively charged carboxylate groups on the molecules. This system has also laid the ground work for related advances in using terephthalic acid layers and related molecules for coordination bonded structures, some of which show high levels of chemical selectivity, and for ionically bonded structures. These results provide general insight in the development of self-assembled organic thin films at surfaces, especially with regard to the nature of the metal/organic interface and growth transitions to obtain a second layer that bridges substrate commensurability and a more bulk-like structure, key issues in organic thin film design.