Visualization of the Intrinsic Reaction Coordinate and Global Reaction Route Map by Classical Multidimensional Scaling

Abstract

A classical multidimensional scaling (CMDS) method is employed to visualize an intrinsic reaction coordinate (IRC) and a global reaction route map consisting of the equilibrium minima and transition state structures connected by the IRC network. As demonstrations, the method was applied to the IRCs of the intramolecular proton transfer in malonaldehyde and the S_N2 reaction of OH^- + CH₃F → CH₃OH + F^-, which are both well described by two principal coordinates. Next, the method was applied to the global reaction route map of the Au₅ cluster; the resulting map shows appropriate positions of five minima and 14 transition states in a reduced 2- or 3-dimensional coordinate space successfully.