The adsorption and reaction of acetonitrile (CH3CN) on the Si(001) surface are investigated by first-principles density-functional calculations within the generalized gradient approximation. We find that two di-sigma configurations in which CH3CN bonds on top of a Si dimer and across the ends of two adjacent Si dimers in the same dimer row have adsorption energies of 1.43 and 1.35 eV, respectively. On the other hand, our calculated adsorption energy for the cross-row bridging structure (in which CH3CN adsorbs between two dimer rows) is 0.52 eV, much smaller than that (0.91 eV) of a precursor state where the N atom bonds to the down-buckled atom of the Si dimer. This result does not support the conclusion drawn from a combination of temperature programmed desorption spectroscopy and density functional cluster calculations, where one of the two observed desorption states was assigned to the cross-row bridging structure. Based on our results for the energetics of various adsorption configurations and the energy profile of the reaction pathways, we provide a reinterpretation for the observed desorption states. (C) 2003 American Institute of Physics.