Studying transformation in a chemical system by considering its energy as a function
of coordinates of the system's components provides insight and changes our
understanding of this process. Currently, a lack of effective visualization
techniques for high-dimensional energy functions limits chemists to plot energy with
respect to one or two coordinates at a time. In some complex systems, developing a
comprehensive understanding requires new visualization techniques that show
relationships between all coordinates at the same time. We propose a
new visualization technique that combines concepts from topological analysis,
multi-dimensional scaling, and graph layout to enable the analysis of energy
functions for a wide range of molecular structures. We demonstrate our technique by
studying the energy function of a dimer of formic and acetic acids and a LTA zeolite
structure, in which we consider diffusion of methane
