Exercise 8 Return to Index

Introduction

In Exercise 7 we stopped in alanine and took a look around. We had our first taste of the JME Structure Drawing Applet and saw how it could be used in combination with the Molecular Editor. We also saw that the VMK can invert stereochemistry at a chiral atom. Using the Problem Clipboard: and Compare: tools allowed us to evaluate the stereochemical relationship between two models. Now it's time to get back on the road and drive to L-tyrosine. Before we arrive, we will call upon three additional features of the VMK, the Append: tool, the Optimize (Opt:) tool, and the Formal Charge (FC:) tool to help us along the way.

Instructions

1. Make a model of L-alanine, or, if you stored it during Exercise 7, use the Problem Clipboard:Paste command to load your model into the Jmol window.

2. Append a model of benzene using the Append:benzene option in the Molecular Editor.

Note that the Atom:C option is active at this point.

3. Click on C-3 of the L-alanine and drag the cursor onto one of the C atoms of the benzene ring.

4. Optimize your model using either the Opt:Jmol or the Opt:NIH link.

The Jmol option performs a simple molecular mechanics calculation that is very fast. The NIH computation uses a more sophisticated algorithm, which takes a bit longer and is not available when the NIH server is down.

5. Activate the Atom:O option and click on C-4 of the aromatic ring of phenylalanine.

6. Use Query:name to check that the name of the compound is L-tyrosine.

7. Use the Image control panel to verify that the stereochemistry at the chiral carbon is S.

We are nearly at the end of our journey. One detail remains; amino acids exist as zwitterions, which is to say that the amino group is protnated while the carboxylic acid OH group is deprotonated. In other words, the nitrogen atom has a formal charge (FC) of +1 while the oxygen atom has a formal charge of -1.

8. Select the FC:inc option and click on the N atom of your model.

9. Select the FC:dec option and click on the O atom of of the OH group.

That's it. Congratullations! Now that you know how to drive the VMK there's no limit to the places you can go. Let's take a quick trip down "Route 9" to norepinephrine. That'll get your adrenaline flowing.