Selective adherence on bioactive glass surfaces of various biological molecules associated with osteogenesis appears to be responsible for the correlation of in vitro reaction kinetics with the rate of bone bonding. Chemical interaction of organic molecules with hydrated silica is also important in osteogenesis and bone mineralization and affects, in as yet an unknown manner, extracellular bond and cartilage matrix formation. The AM-1 molecular orbital method is used to calculate the reaction pathways for bond formation between alanine and trisiloxane rings to simulate organic interactions with hydrated silica. The results show that there are low energy reaction pathways for the organic-inorganic bonding. Different types of interfacial bonds can be formed depending upon the structure and orientations of the organic or inorganic molecules. The differences in reaction pathways and binding energies for formation of -Si-O-C- linkages with the amino acids versus formation of -Si-N- bonds may account for the variety of biochemical effects observed for silicon in nature and for bioactive glass.