Understanding the chemical reaction mechanisms governing how small organic molecules attach to semiconductor surfaces can lead to new strategies for creating specific surface patterns such as single adduct monolayers. In this study, room-temperature ab initio molecular dynamics simulations of one and two 1,3-cyclohexadiene (CHD) molecule(s) reacting with the Si(100)-2x 1 surface reveal that adducts form via a carbocation-mediated two-step mechanism. Dimer flipping can either promote or prevent bond formation depending on how the CHD approaches. CHDs often travel past several Si dimers before finding the proper local environment. The resulting intermediate can persist for more than 4 ps, allowing the second bond to form with any adjacent Si dimer. The additional reactive site accounts for a large portion of the discrepancy between the predicted thermodynamic and observed experimental product distribution. Surface adducts protect a 5.6 angstrom region, direct unbound CHID exploration, and can cause adjacent dimers to flip.