JCE Online Journal of Chemical Education
 | Subscriptions  | Software Orders  | Support  | Contributors  | Advertisers  | 

JCE Print

JCE Digital Library

JCE Software

Only@JCE Online

About JCE


  Home > JCE Print > Journal of Chemical Education > Issues > 2005  > November  >
Information • Textbooks • Media • Resources
JCE WebWare: Web-Based Learning Aids
3D Molecular Symmetry Shockwave: A Web Application for Interactive Visualization and Three-Dimensional Perception of Molecular Symmetry
Nickolas D. Charistos, Constantinos A. Tsipis, and Michail P. Sigalas
Department of Chemistry, Laboratory of Applied Quantum Chemistry, , Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece

Cover
November 2005
Vol. 82 No. 11
p. 1741

Full Text
One of the ongoing challenges in teaching chemistry is helping students explore various structural features of molecules. It can be difficult for students to visualize the three-dimensional shape of a molecule from a two-dimensional printed image. Using a molecular modelling kit in the classroom helps, but such models can be difficult for students to see when demonstrated by an instructor. These difficulties are more pronounced in teaching symmetry, especially recognition of various symmetry elements within a molecule and conceptualization of the symmetry operations.

3D Molecular Symmetry Shockwave is a Web-based application for interactive visualization and three-dimensional perception of molecular symmetry. The user interface is simple, and students learn how to use the program from the built-in help screens. The animation uses the Macromedia Shockwave browser plug-in, and requires a download of only 256 KB, allowing it to be used even with low bandwidth Internet connections. Its performance is comparable to a desktop application.

With 3D Molecular Symmetry Shockwave students and instructors can:

  • Display molecules in ball-and-stick or wireframe representation
  • Display each symmetry element of a molecule in a 3D environment and animate the corresponding symmetry operation
  • Rotate, translate, or zoom a molecule to any viewpoint
  • Store and recall preferred viewpoints of the molecule for later use
  • View information about the selected molecule, its symmetry elements and its point group

3D Molecular Symmetry Shockwave also serves as a searchable database of structural and symmetry data for 47 organic and inorganic molecules, including all symmetry point groups of chemical interest. This database can be accessed in two modes. In the Symmetry Elements mode the user can search the database to find all molecules having symmetry elements of a certain type (for example Cn) or a particular symmetry element (σv). In the Point Groups mode the user can search the database to find all molecules having a point group of a certain type (Cnh) or a particular point group (D2d).

Figure 1. The main screen from Symmetry Elements mode of 3D Molecular Symmetry Shockwave.

The main screen from Symmetry Elements mode is shown in Figure 1. A user has searched the database to find all molecules having C3 rotation axes. She has selected cubane from the results, and one of its six C3 rotation axes, and is ready to start the animation of this symmetry operation.

Figure 2. The main screen from Point Groups mode of 3D Molecular Symmetry Shockwave.

The main screen from Point Groups mode is shown in Figure 2. A user has searched the database to find all molecules having point groups of Dnd type. He has selected ferrocene from the list of molecules, and one of its two C5 rotation axes, and is ready to start the animation.

3D Molecular Symmetry Shockwave is suitable for undergraduate students in chemistry, and can be used with typical textbooks (1, 2) as a self-paced learning tool, as well as a presentation tool.

Symmetry Elements and Operations and Symmetry and Point Groups are similar programs for Mac OS and Windows respectively, previously published by JCE Software (3, 4). However, they have limited capabilities of manipulating a molecule and its symmetry elements in a 3D environment. Also, they do not have a database of molecules that can be searched according to specific symmetry criteria. On the other hand, Symmetry and Point Groups does lead students through a flow chart of questions to help them identify the point group of a molecule, a feature that is not available in 3D Molecular Symmetry Shockwave.

Literature Cited

  1. Douglas, B. E.; Holingsworth, C. A. Symmetry in Bonding and Spectra, An Introduction; Academic Press: New York, 1985.
  2. Cotton, F. A. Chemical Applications of Group Theory, 2nd ed.; John Wiley & Sons: New York, 1971.
  3. Vining, William J.; Grosso, Robert P., Jr. J. Chem. Educ. 2003, 80, 110.
  4. Lee, A. W. M.; Leung, K. M.; Kwong, D. W. J.; Chan, C. L. J. Chem. Educ. Software 8C2.
Supplement
You can find 3D Molecular Symmetry Shockwave in the peer-reviewed collection of JCE WebWare.
More Information
*  Citation
Charistos, Nickolas D.; Tsipis, Constantinos A.; Sigalas, Michail P. J. Chem. Educ. 2005 82 1741.
*  Keywords
Chemoinformatics; Computer-Based Learning; First-Year Undergraduate / General; Group Theory / Symmetry; Internet / Web-Based Learning; Molecular Modeling; Molecular Properties / Structure; Physical Chemistry; Second-Year Undergraduate; Upper-Division Undergraduate
*  History
Created:
Last Updated:
9/22/2005
9/29/2005
  Home > JCE Print > Journal of Chemical Education > Issues > 2005  > November  > Page 1741


Subscriptions

JCE HS CLIC

Our Secondary School editors work hard to distill all the JCE materials to produce a fraction of particular interest to high school teachers. We call it CLIC.


Contributions Welcome
JCE welcomes your submission

Advertisers
In recent years we have worked hard to better match our advertisers with our readers. When shopping for chemistry education materials, visit our advertisers' WWW sites first.

Be An Ambassador
Take JCE along on your outreach missions. Copies of the Journal, guest access to JCE Online, our publications catalog, and more are available for your participants.