As an example, a significant fraction of articles in the Journal of Chemical Education include one or more molecular structures—naturally in a two-dimensional representation. We would like to build a collection of interactive Chime-based structures¹ for some of these molecules. While many such structures exist in other Web-based collections, having them in one location and linked to a specific article in JCE will greatly benefit both teachers and students. Follow this link to see an example of such a collection, derived from a paper in C & E News (1).

Many students have difficulty "seeing" molecules in three dimensions and linking two-dimensional with three-dimensional representations of molecular structures. The more they practice doing so, the more skilled they will become. Additionally, as we try to teach students to draw "form/function" conclusions about molecular behavior, "seeing" the three-dimensional structure is crucial.

Structure 1 might appear in a paper on bicyclic systems and the corresponding structure 2 at the JCE WebWare site, which can be rotated, translated, resized, and in which bond lengths, bond angles, and torsion angles may be easily measured.

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Figure 1. Structure 1 is a 2-D representation from a structure-drawing program and structure 2 is an interactive Chime-based structure that has been energy-minimized.
See supplement for non-interactive version of the structure and for a larger sized version of the Chime structure (access limited to JCE subscribers only).

To initiate this program, we invite authors of manuscripts accepted by JCE for publication in print to consider including the appropriate molecular files (.pdb or .mol preferred) with their manuscripts. This is in no way a requirement for publication. If the files are not available, members of the JCE WebWare staff may prepare them, with the author's permission.

Another example of a graphical image from print that might have significant value added on the Web is a diagram of a reaction mechanism that can be represented as an animation on the Web. If an animation would enhance your article, why not submit one?

Authors who are interested in participating in this endeavor should contact JCE WebWare.

Note

1. The Chime plug-in is available online.

Literature Cited

1. Rouhi, A. M. C & E News, 1999, 77 (43), 38-44.

The collection of Chime-based structure files referenced is availalble.

• Example Monthly Molecules
• Download Chime (free registration required)

Structure 2 from Figure 1. A larger interactive Chime-based structure and a non-interactive2-D representation from a structure-drawing program.