Conquer without dividing: Volume rendering of intact molecular charge densities effectively illustrates key concepts in bonding and reactivity


Preston J. MacDougall, Department of Chemistry, Middle Tennessee State University, 1301 E. Main St., Murfreesboro, TN 37132 and Christopher E. Henze, Data Analysis Group, NASA Ames Research Center, MS T27A, Moffett Field, CA 94035.
Our volume rendering software enables the user to interactively explore a molecule’s electronic charge density for topological features that make manifest key concepts in bonding and reactivity, such as lone pairs and sites of nucleophilic attack. Using novel volume rendering techniques, the entire molecule can be probed without obstruction by opaque surfaces or preselection of specific orbitals or contours. Thus even core/valence division is not done artificially. Rather such sub-atomic partitioning is evident in the rendering of the Laplacian of computed or measured electron density distributions. The concept of the “charge cloud” is introduced early in the chemistry curriculum, and is one that is readily grasped. Visualizations with direct recourse to this entity, avoiding molecular orbital models, make concepts of chemical reactivity more accessible. The same methodology that is applied to small inorganic or organic molecules, is also applied to large biomolecules. Thus instead of a variety of visual textures for molecular models in the different sub-disciplines, which can disorient students, there is consistency.