Exercise 7 Return to Index

Introduction

Before we continue forward, let's take a look back. Up to this point we have seen two ways of making a model of propanoic acid-using the three tools Start with:, Atom:, and Bond: from the Molecular Editor, as well as loading a pre-assembled model from the Pre-Assembled MM Library Menu in the Model Tools control panel. This exercise will demonstrate yet a third method the VMK offers for making models; the JME Structure Drawing Applet. Perhaps more importantly, it will then illustrate one of the most powerful features of the VMK, its ability to deal with stereochemistry. Let's continue.

Instructions

If you are not familiar with the JME Structure Drawing Applet, there is a tutuorial available on the O=CHem website. Figure 7.1 provides images of typical results for those steps marked with an *.

1. Activate the Draw control panel.

2. Draw the structure of propanoic acid.

3. Click the Load 3D:NIH link to load a model of your drawing into the Jmol window.

This command loads a 3-dimensional model of the 2-dimensional structure in the JME window into the Jmol window through a process that involves a server at the National Institutes of Health. In the event that the NIH server is down, the PubChem option provides an alternative method for loading the model. The Jmol option is Plan C, if you will.

4*. Select Atom:N in the Molecular Editor and replace one of the two H atoms on C-2 with an NH₂ group.

5. Query:name

The name of the stereoisomer of the amino acid alanine that you have made will appear in the Jmol window as well as in the Molecular Editor below the Feedback Area & Script Command Field.

6. Use the Problem Clipboard:Copy command to save a copy of your model.

7*. Activate the Image control panel and click the NIH 2D Capture link

This command loads a 2D image of alanine with the stereochemistry at C-2 labeled as R or S depending upon which H atom you replaced in step 4.

8*. Rotate the model in the YZ plane until it looks like the image in the third panel of Figure 7.1.

9. Select Atom:invert and click on C-2 of the model.

10. Repeat step 7.

The stereochemical designator, R or S, should have changed to reflect the inversion at C-2.

11*. Append your original model to the Jmol window with the Problem Clipboard:Append command.

12*. Use the Compare: compare option to determine the stereochemical relationship between the two models.

Figure 7.1