ChemDraw and Chem3D Exercises

Background

The ability to represent chemical structures and to produce reaction mechanisms is an important part of modern chemistry, especially organic chemistry.  In this exercise you will use ChemDraw and Chem3D to show chemical structures and some reaction mechanisms.  You will also use these computer programs during the semester so that you can include chemical structures in your written reports.

The following reactions or reaction mechanisms are from Experiment I.  These diagrams were originally drawn using ChemDraw.  Using this computer program, you can adequately represent the chemical pathways and show mechanisms to understand reactions better.  You will use these programs to draw structures and to include structures in your written reports.

First Day:

1. For this exercise, you will use ChemDraw to display each* of the following:
  • cyclohexanol
  • trans-1,2-cyclopentanediol
  • benzenesulfonic acid
  • D- & L-Alanine (in Fischer projection)
  • p-xylene
  • adenosine

2. Draw reaction mechanisms (show entire reaction, including reactants and products) for:

3. Using Chem3D, show energy minimized drawings for trans- and cis-2-butene.  (It is best to draw these structures in ChemDraw and transfer the image to Chem3D.  Minimize the structure and show a perspective that is pleasing to your eye and shows clearly the structure of the molecule.  Then, select this image, which would print as a full page from Chem3D, and copy it back to the ChemDraw page.  You can size the image to make it smaller.  Follow the same procedure for the other structure.  This way, you can label your structures and put your names on the printed page, from ChemDraw, which you cannot do from Chem3D.)

Second Day:

During the second day of this lab, you will individually do a short quiz using ChemDraw and Chem3D. You will work alone, and will have 30 min to finish this quiz. Students will draw a number (or be assigned times) indicating the time that they will be admitted back into the lab to do this exercise. This exercise will count as a regular quiz, not as a lab score.

*If you need a structure or formula, you should look in the text, in a reference book, or you can obtain the information online.  You can use ChemFinder Online at http://www.chemfinder.com and follow the prompts.  If you need a username and password, you can use donrobertson@miracosta.edu as the username and organic as the password.

iBook printing protocol: If you are using one of the Mac iBook computers, in order to print you need to do the following to connect to the server:

  1. Click on any part of the desk top
  2. Click on the thing that looks like radio waves on the top tool bar
  3. Use the drop down menu to go to “OTHER”
  4. Type in “MCC-WPA” (do not include quotation marks in any field)
  5. Then, go to the drop down menu right below that and click on "WPA Enterprise"
  6. Then type in the name of your computer (listed on the top of the computer; e.g., Avogadro)
  7. As your pass word type in "12345"
  8. Click OK
  9. Click on “try again”
  10.  Click on “Show certificate”
  11. Click the little box that says “Always trust”
  12. Then click OK

 You should be ready to print at this time.  If you have any questions, please ask your instructor or lab-support personnel.

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Copyright © Donald L. Robertson (Modified: 01/24/2007)