Reliability of AM1 in determining the equilibrium structures of unionized amino acids

Abstract

The object of this report is to estimate the reliability of the newest semiempirical molecular orbital method, AM1, in determining the equilibrium structures of unionized amino acids. For this purpose, the optimized structures for the three conformations of unionized glycine, the two conformations of unionized alanine, and the two conformations of unionized serine obtained by AM1 are compared with those obtained by the ab initio 4-21G method. The optimized structural parameters of these conformations by AM1 are generally acceptable and, in most cases, superior to those generated by MNDO. The mean absolute difference between the optimized bond lengths by AM1 and 4-21G is 0.020 Å, the difference in bond angles is 2.1°, and the difference in torsional angles is 6.1°. The correlation coefficient between the optimized bond lengths by AM1 and 4-21G is more than 0.99, the coefficient for the bond angles is greater than 0.83, and the coefficient for the torsional angles is greater than 0.99. These results suggest that AM1 is reliable in determining the equilibrium structures of unionized amino acids.