Reactions of the Si(100) surface with a class of organic molecules known as 1,3-dipoles are studied by density functional theory calculations. A prototype reaction with diazomethane is found to occur with no activation barrier. The adsorbed species are strongly bound, but in some cases they are unstable with respect to further reaction. Several examples are given to show how the possibility of further reaction is related to the identity of the molecule. Comparisons to relevant experimental data are drawn and strategies fur using this class of reactions to systematically modify Si(100) surfaces are discussed.