A NEW METHOD TO CALCULATE REACTION PATHS FOR CONFORMATIONAL TRANSITIONS OF LARGE MOLECULES

Path energy minimization (PEM), a novel method for the generation of a reaction path linking two known conformers of a molecule, is presented. The technique is based on optimizing a function which closely approximates the peak potential energy of a quasi-continuous path between the fixed end points. A transition involving the change in the pucker angle of alpha-D-xylulofuranose is used as a test case. The method is shown to be capable of identifying transition state structures and energy barriers. The utility of the method is demonstrated by an application to substantial conformational transition of the ion-channel forming polypeptide gramicidin A.