PARAMETRIC AND MOLECULAR STRUCTURAL RELATIONSHIPS OF DIPEPTIDES

A principal component analysis is applied to the study of dipeptides c orresponding to the 20 naturally-occurring amino acids and Avian polyp eptide, APP, to quantitatively assess (1) force field parametric and ( 2) structural relations. The parametric principal component analysis h as provided insight into the relationship between the molecular struct ure and the potential energy function. The molecular structures are mo st sensitive to the bond and angle reference parameters. The nonbond p arameters also significantly influence molecular structure. The struct ural space of the dipeptides and APP is very closely linked to the par ameter space of the potential. The bond length and bond angle internal s are tightly controlled by the bond and angle reference value paramet ers. Torsional motion is the most sensitive degree of structural freed om and is generally controlled by nonbonded influences. In the second part of the research, principal component analysis of the molecular st ructure Green's function matrix provides a means to elucidate how the molecular structure will respond to internal forces introduced in the molecule. The eigenvectors of the Green's function matrix correspondin g to the maximum eigenvalues determine the internal coordinates respon sible for the largest molecular responses. It is found that the torsio nal degrees of freedom are responsible for the greatest molecular resp onse. To complement the analysis of APP, the sensitivities of centroid s associated with each residue to changes in the backbone internals we re determined. The coefficients indicate the local molecular response and were found to be in agreement with previous characterization of re gional flexibility.