Molecular mechanics is an empirical calculational method that allows one to determine structural and energy relationships in molecules for which the method has been parameterized. The parameterization is accomplished by comparing calculated results with available experimental data. Present molecular mechanics programs reproduce structures accurately for hydrocarbons and simple monofunctionalized molecules. We would like to improve the ability of the molecular mechanics program, MM2, to calculate the structural and energy properties of biological molecules. We would do this in three ways. First we would improve the capability of the program for calculating hydrogen bonding interactions. These interactions are important in determining the conformations of biological molecules. Second, we will do calculations on dipeptides to determine which parameters necessary for this task are missing and to include these parameters in the program so that studies on polypeptides can continue. Finally, we will enlarge the MM2 program to do more than 255 atoms. Studies on large biological systems can then be undertaken. The results of this work will be incorporated into the MM2 program of Dr. N.L. Allinger (University of Georgia) and made available to the public through the Quantum Chemistry Program Exchange.
