Density functional theory (DFT) was used to study different possible bonding geometries of 1,3-cyclohexadiene (1,3-CHD) on the Si(100)-2x1 surface and for comparison with recent STM experiments. Full geometry-optimized structures were obtained for all adducts, including intra- and interdimer reaction products. These results were analyzed both in terms of the total energy values and the detailed optimized geometries. Comparison with the product distribution observed by STM demonstrates that the reaction is kinetically controlled. However, the inability to explain the observed product distribution within the framework of the present total energy calculations and earlier cluster calculations of the transition state indicates that there are serious gaps in our understanding of the reaction dynamics of 1,3-CHD oil Si(100).