The biomimic reactions of N-phosphoryl amino acids are very important in the study of many biochemical processes, such as origin of proteins and phosphorylation of amino acid residues in the proteins. The differences in reactivities between (alpha-COOH and gamma-COOH in phosphoryl amino acids were studied by ab initio and density functional methods. The pentacoordinate phosphoric intermediates 2 containing five-membered rings were predicted to be more stable than 3 with seven-membered rings. For intermediates 3, the isomers with apical-equatorial ring spanning arrangement were predicted to be more stable than those with diequatorial ring spanning arrangment. At the B3LYP/6-31G** level, intermediates 2 were 66.56 kJ/mol lower in energy than 3. It was shown that the transition states 4 and 5 involving an alpha-COOH or gamma-COOH group had energy barriers of DeltaE = 57.59 kJ mol(-1) and 120.93 kJ mol(-1), respectively. The theoretical calculations suggested that the (alpha-COOH group could be differentiated from the gamma-COOH intramolecularly in amino acids by N-phosphorylation. These might be helpful to understand why only alpha-COOH, not gamma-COOH, was involved in the biomimic reactions.