Introduction

As chemists, we often deal with applying macroscopic observations to a microscopic world. Unfortunately, this leaves us with the difficult task of trying to somehow explain what we cannot actually see. Over the course of recent history, theory has evolved such that we now know a great deal about what happens to compounds at the molecular level even though we still cannot physically see them.

This leaves a staggering problem. When research has shown that students learn best when they feel a connection to the material, and science educators in particular stress “hands-on” activities, how are we as teachers supposed to bridge that gap? The traditional method uses model kits, but even these useful tools have their drawbacks.

Chem3D Pro

Chem3D Pro is a sister program of the incredibly powerful ChemBioDraw tool created by CambridgeSoft. This software package is the industry standard for creating graphics of chemical and biological molecules, and scientists worldwide use it on a daily basis. The user can create and manipulate virtually any compound known or imaginary with just a few clicks of the mouse.

Even though the amount of operations that can be performed on any single molecule numbers in the hundreds, the bare bones operation of the program is very simple. The following drawing of a common molecule was created simply by clicking the single bond button that is circled in red, drawing four bonds that radiated outwards from a common point, hovering the mouse over the end of one of the lines and typing “o-.”

Figure 1

Virtually all of the drawing commands are very intuitive, and when students have completed the drawing of their molecule, they can begin to interact with it. For instance, let us say the student drew a simple hydrocarbon molecule like this:

Figure 2

Now we can clearly see that this is chloromethane (one carbon bonded to three hydrogen and one chlorine atom), but it is also clear that the shape is incorrect. If we click on the button circled in red (the minimize energy button) the software will give us this picture:

Figure 3

ChemDraw has calculated the correct bond angles and lengths by using preprogrammed energy calculations. From here there are many different things you can do. For instance, if you wanted to see the bond lengths, click “Structure>>Measurements>>Generate All Bond Lengths.” Now the bond lengths are shown in a new panel on the left and can be inserted into the 3-D model by clicking the checkbox. Students could be asked to explain differing bond lengths using principles they have learned, such as why the carbon-chlorine bond is so much longer than the carbon-hydrogen bonds.

Figure 4

A key point here is that model kits will not differentiate between bonds of different lengths. Every bond is exactly the same size. This is a common misconception that Chem3D Pro can easily help to avoid.

You can do many other physical manipulations to the model as well just by using the buttons on the toolbar. Some examples are translation, rotation, size increase/decreasing, movement of individual molecules, and computer controlled rotation around any arbitrary axis. The versatility of ChemDraw and Chem3D Pro really shows through when students are allowed for independent exploration and project designs.

A more in-depth “webinar” for novice chemists provided by the company to subscribing individuals and organizations can be found here.

A short, independent “how to” for the classroom based on a previous version can be found here.

Use in the Classroom

Mark Langella talks about using the software in both introductory and AP courses and its versatility: http://chembionews.cambridgesoft.com/Articles/Default.aspx?articleID=402

Chad Ronish talks about using ChemDraw to introduce simple organic chemistry concepts: http://www.adeptscience.co.uk/pressroom/article/104

A key concept talked about in both articles is using Chem3D to calculate bond angles and lengths as described earlier. The major difference between using Chem3D and traditional models in regards to structures is that tetrahedral model angles are always 109° and bond lengths are always identical, whereas the program clearly shows that is not realistically the case. Again, while this may make things a little more complicated for the students to remember, it also helps lessen the number of misconceptions they will obtain due to oversimplification.

The following two paragraphs are an excerpt from the article "Computational Chemistry in the Classroom."

"Computational chemistry can be integrated into chemical education at all levels. For example, Professor Foresman has designed lecture examples and laboratory exercises for introductory chemistry, organic chemistry and physical chemistry courses.

"In an organic chemistry course, the isomeric orientation on electrophilic substitution can be illustrated by examining the electron densities of the various transition structures that result during the nitration of nitrobenzene and chlorobenzene. Viewing slices through the electron density or the electrostatic potential mapped onto an isodensity surface clearly illustrates that the meta isomer is favored in the former while the para isomer is favored in the latter. Similarly, in his physical chemistry course, Foresman uses graphical results such as optimized structures, illustrations of atomic orbitals and molecular orbitals, and plots of the potential energy surface for a reaction can be used to enhance both lecture and laboratory explorations of the central concepts. For example, the effects of dielectric media can be illustrated by studying the rotational barrier between the E and Z forms of n-methyl-2-nitrovinylamine (illustrated in the figure) in different solutions." [source]

While the inner workings of electrophilic aromatic substitution are a little hard for high school students to deal with, there are a couple of relevant items Dr. Foresman used that can be introduced into high school classrooms. One is an electrostatic potential map. This kind of drawing uses color shading and a contour map to show where the highest electron densities are in molecules. This technique can be used to illustrate how atoms with different electronegativities do "pull" more electron density towards them. This is another example of a concept that students may have a difficult time coming to terms with because they normally do not have a way to see electron densities.

Finally, three chemistry professors at Fairfield discuss their ingenius use in an organic classroom here. They used the idea of creating individual molecular models to create animated movies that illustrate important concepts. Even though this is at the college level, this is a technique that can easily be replicated for simple reactions, hydrogen bonding, or virtually any other topic. What makes this application even more powerful is the ability to deliver the animation itself rather than the students needing to recreate it if there is something they do not understand. If a teacher were to use this idea, he could either create the animation for a lecture or he could have the students create the animations themselves in an activity and supply the animation afterwards so that the students have an artifact to take with them.

Unfortunately, this tool is not currently used in high school classrooms very often, probably due to the high price. Many examples, however, are available of labs and activities done at the college level using Chem3D Pro, and the concepts can easily be adapted to fit high school classes. Hopefully, as schools become more and more technologically savvy, this program will continue to gain proponents.

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This work is licensed by Shane Lewis under a Creative Commons Attribution License (CC-BY 2.0), and is an Open Educational Resource.

Last edited by Shane Lewis on Oct 23, 2008 2:55 am -0500.