Norbornadiene (NBE) chemisorbs to a Si(001) surface in a flagpolelike structure that has potential as an anchor point for nanoscale molecular devices to the surface. Its bindings to the reconstructed Si(001)-(2×1) surface and a partially depassivated Si(001)-(2×1)-H surfaces are modeled by slab-based density functional theory using the PW91 density functional. This method is shown to quantitatively and qualitatively reproduce many known properties of bulk silicon, the silicon surface reconstruction, and the gas-phase NBE molecule. Four strongly bound adsorbate configurations are found, with the C–C bonds located either above a Si–Si dimer row or trough, oriented either parallel or perpendicular to each other. The calculated binding energies are 96, 85, 81, and 72 kcal mol−1 for the perpendicular row, perpendicular trough, parallel row, and parallel trough configurations, respectively, evaluated at quarter-monolayer coverage on the bare surface, with hydrogen passivation of the surrounding sites having little influence. These results indicate that the observed structural disorder for NBE adsorption on the bare surface at very high coverage results from kinetic rather than thermodynamic control of the reaction products. Such kinetic control is shown to be associated with large barriers in excess of 40 kcal mol−1 for possible adsorbate annealing processes, with desorption into a (partially or fully) physisorbed precursor state being required. Enhanced disorder is also predicted arising from the strong partial binding of NBE through one alkene linkage only, with the analogous four structural motifs being calculated to be very similar in energy. The lowest-energy single-alkene-bonded structure is predicted to be of the parallel–above-row type, consistent with the observed structures for most monoalkene adducts. Preference for the uncommon perpendicular binding of NBE is predicted to arise from unfavorable interactions within the silicon lattice when parallel binding occurs on adjacent rows, a binding motif that is observed for only the simplest monoalkene, ethylene, and only at high coverage. The primary reaction products of NBE are not those predicted by a [2+2] cycloaddition reaction between C☒C and Si☒Si double bonds, suggesting that, in general, this is not the mechanism for chemisorption of alkenes on Si(001). Rather, the reaction products are those expected on the basis that the silicon dimer bond is biradical in nature. Careful structural, polarization, and band-structure analyses of the reconstructed surface are also shown to provide no evidence for the existence for a doubly bonded silicon dimer. © 2003 American Institute of Physics.