SymApps: A 3-D point group calculation and visualization tool

COMP 98

Victoria Rafalovsky, Karl Nedwed, Marie Scandone, Gregory M. Banik, and Deborah Kernan. Bio-Rad Laboratories, Informatics Division, 3316 Spring Garden Street, Philadelphia, PA 19104
The 3D visualization of point groups and, in general, symmetry of chemical structures is a difficult and important concept in lectures on molecular symmetry. Bio-Rad’s SymApps™ application, offered free to academia, calculates the point group of any structure automatically, displays symmetry elements, and allows the student to create movies of symmetry operations with atoms and bonds being rotated, mirrored, etc. Since the real-world coordinates of an entered 3D molecule will not always exactly define a specific symmetry, or the symmetry is distorted, SymApps uses an uncertainty parameter to establish point group at various degrees of distortion. Thus it is possible to find different point groups and measure the degree of distortion of the structure. For example, in a Jahn-Teller-distorted structure (e.g. CuF6), SymApps reports both point groups D4h and Oh. Symmetry elements are displayed graphically, and by turning and resizing the structure the user can more clearly visualize the molecule.