Organic modification of semiconductor surfaces enables the incorporation of organic functionalities onto semiconductor substrates to possibly combine the advantages of organic and semiconductor systems. The diversity of organic functional groups provides access to a wide variety of adjustable functions and properties while semiconductor processing provides a technology for reliably and efficiently fabricating complex systems of nanoscale electronic devices. Reactions of amino acids at the Si(100)-2x1 surface have been investigated using density functional theory. Amino acids provide a diverse set of organic functional groups, several of which have not been studied previously for their reactivity on semiconductor surfaces. The amino acid common group is found to react through several low energy pathways, with OH dissociation of the carboxyl group being the most kinetically favorable. Consequently, reaction of amino acids through the amine and carboxyl functionalities is not expected to be selective. The reactivity of many of the amino acids are similar to those of their simpler organic analogues, although we have found several cases which display unique, and possibly useful properties not exhibited by organic functionalities previously considered. These include pericyclic ene reactions of the imine functional group of arginine and the cyclic imine of the imidazole side chain of histidine. Both of these reactions involve formation of Si-N dipolar (dative) bonds which are significantly stronger than any previously observed on Si(100)-2x1.