Modeling and visualizing surfaces

Author: Donnelly, Robert Edward

Year: 1992

Degree: Dissertation (Ph.D.)

Advisor: Goddard, William A., III

Committee Member: Goddard, William A., III

Option: Chemistry

DOI: 10.7907/1d15-vv30

Abstract

"Modeling and Visualizing Surfaces" denotes several developments aimed at increasing our ability to model and understand molecular surfaces. The Generalized London Potential is a new method of modeling potential energy surfaces of reactions. The London Equation assumptions of zero overlap and no three-body interactions are discarded and a more general potential is derived via valence bond theory and careful substitution of two-body terms into three-body energy expressions. Three-body corrections for dispersion energy are also introduced. Using the lowest order forms of overlap and dispersion corrections, a much improved potential energy surface is found for H_3. Input is limited to H_2 potentials and information only about the H_3 saddle point region, the latter determining the two or three parameters used. The predicted surface is shown to be stable with respect to varied input. A straightforward method of extending the method to make use of additional input is discussed. The method is applied to hydrogen abstraction from terminal carbons. The development of a stable model of exchange reactions will greatly increase the complexity of systems which can be studied with the increasingly accurate force fields of molecular modeling techniques by providing the means of handling reactive dynamics at polymer and crystalline surfaces. This introduces the second major theme of modeling and visualizing molecular surfaces.

Common to most definitions of a molecule's surface and, in fact, many calculations involving local spherical symmetry is the use of spherical meshes. A method of systematically creating spherical meshes of various sizes is presented. Degrees of freedom built into the mesh design can be optimized for a variety of problems. The meshes are used in calculating molecular surfaces and determining surface area. They are separately optimized for the integration of spherical harmonics and provide lower error for integration of higher angular momentum functions than previous quadratures. Finally, methods of visualizing molecular surfaces that allow real-time manipulation of complex molecules and yield a better understanding of surface properties are presented.

Files