Spectroscopically-tested, improved, semi-empirical potentials for biological molecules: Calculations for glycine, alanine and proline

Abstract

A modification of the semi-empirical PM3 electronic structure method is proposed. It employs a coordinate scaling procedure, such that the harmonic frequencies from the modified PM3 potentials for lower-energy conformers of glycine (conformer I), alanine (conformers I and II) and proline (conformer II), fit more closely with ab initio (MP2/DZP) harmonic frequencies. The anharmonic frequencies are then calculated using the modified PM3 surfaces with the Vibrational Self-Consistent Field (VSCF) and Correlation-Corrected VSCF (CC-VSCF) methods. The computed anharmonic frequencies are in very good accord with spectroscopic experiments for the three amino acids. The results are much superior to those obtained from standard (unscaled) PM3 potentials, indicating that the modified PM3 potentials may be used as high quality potentials for biological molecules, at least in the configuration ranges pertinent to vibrational spectroscopy. The scaling parameters computed for the lowest energy conformers listed above were tested for transferability: they were used in computing the anharmonic spectra of two other conformers (glycine II and proline I). The good agreement of the resulting frequencies with observed frequencies, indicates the transferability of the scaling parameters. It is concluded from this study that the improved PM3 potentials offer accurate and computationally efficient force fields for vibrational spectroscopy calculations of biological molecules. Possible additional applications of the new potentials are discussed.