On the use of isovalued surfaces to determine molecule shape and reaction pathways

• Published in: Journal of computer-aided molecular design Vol. 5; no. 1; p. 55
• Main Author: Purvis, 3rd, G D
• Format: Journal Article
• Language: English
• Published: Netherlands 01.02.1991
• Subjects: Chemical Phenomena; Chemistry, Physical; Computer Graphics; Models, Molecular; Molecular Conformation; Molecular Structure; Structure-Activity Relationship
• DOI: 10.1007/bf00173470
• ISSN: 0920-654X

Novel insights into local molecule structure and reactivity can be gained from viewing isovalued surfaces of the molecular electron density, electrostatic potential and molecular orbitals rendered as colored, 3-D objects. For example, drawing positive and negative electrostatic isopotential surfaces partitions the molecule into regions subject to nucleophilic or electrophilic attack. Similarly, coloring isodensity surfaces to indicate the magnitude of the gradient of the electron density maps the molecule surface into regions of high and low electronegativity. A basic understanding of reaction mechanisms can also come from viewing and manipulating isovalued surfaces. A theory of molecular interactions, based upon second-order perturbation theory, provides for the decomposition of the intermolecular interaction energy into steric, electrostatic and orbital interactions. Color figures illustrate the docking of reactant molecular densities, electrostatic potentials and orbitals on low-energy pathways. The figures are used to visualize the steric, electrostatic and orbital contributions to molecular interaction energy. The visualization not only identifies low-energy reaction pathways, but it frequently reveals local interactions which determine the magnitude of the total interaction energy. Similar insight is not easily obtained by simple evaluation of the total interaction energy. Approximate transition states, built from structures along low-energy approach pathways, are excellent starting points for transition state searches.