PAPQMD/AM1 PARAMETRIZATION OF THE BONDED TERM OF AROMATIC BIOMOLECULES

The suitability of the PAPQMD/AM1 (Program for Approximate Parametrization from Quantum Mechanical Data/based on AM1 calculations) strategy to provide force-field parameters for large heteroaromatic compounds was studied. For this purpose, PAPQMD/AM1 stretching and bending parameters for adenine, cytosine, thymine, guanine, and uracil were computed and compared with experimentally derived force-field parameters. Furthermore, equilibrium geometries and vibrational spectra for the five nucleic acid bases obtained from molecular mechanical calculations using both PAPQMD/AM1 and AMBER (Assisted Model Building with Energy Refinement) All Atoms force fields were compared with the available experimental data. (C) 1994 John Wiley and Sons, Inc.