CheMagic Editable Worksheet & Virtual Molecular Model Kit


Under Development (ready for play - not use)

This template is an editable webpage designed to bring the power of Jmol and the JSME Molecular Editor to interactive worksheets dealing with general chemistry, organic chemistry, cheminformatics, chemical structure drawing, and molecular modeling. The CheMagic Virtual Molecular Model Kit (VMK), which is powered by Jmol and JSME, interacts directly with auto-feedback questions in the worksheet. The interaction is established with the VMK open in any browser tab or window.

Instructor content for the Exercises section of the page can be created in each of the 5 line-delimted exercise blocks. Clicking on the horizontal bar under an exercise block will display an edit dialog box for that block. Instructor-created content can be saved as a file and distributed to students or other users. Links at the bottom of the page allow adding/deleting exercises. The sample questions below are designed to illustrate possible question types. This Introduction can also be edited. To get started, click the Introduction edit bar below for additional instructions.

When included with an exercise, the More... link offers step-by-step descriptions of the steps involved in creating that exercise.

This exercise template uses HTML5 and Browser Local Storage. Your Browser meets both of these requirements.


1. What is the atomic mass of carbon?

If you open the Exercise Editor, you will see the Answer Format for this example is set to Numeric and the Correct Answer is 12.01. Try entering several answers besides 12.01, e.g. 12, 12.0, 12.013.

How would you change the Answer Format and the Correct Answer if the question were "What is the atomic number of carbon?"
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2. What is the name of the element He?

With the Answer Format set to Text, capitalization is not relevant. Helium, helium, HELIUM, etc. are all acceptable answers.

How would you format the question "What is the symbol of the element helium?"

Try formatting this question: "What are the symbols of the first two elements in the periodic table?"
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3. Draw the structure of butan-2-ol.

This structure must me drawn in the VMK. The VMK can be in any browser tab or window. Any VMK tab or window will communicate with the exercise sheet.

The Answer Format is set to Drawing. The Correct Answer text box contains a character string called a SMILES that corresponds to the structure drawn. The JSME editor generates SMILES "on the fly". Click the More... link for step-by-step instructions for creating this type of question.

Modify this exercise to specify drawing the structure of (2R)-butan-2-ol. Be sure to use the stereochemical bond tool. Click the Load Model button to load the model of your drawing and use the Mark R/S button in the VMK to check the stereochemistry of the model. Click the Get Identifiers button to get the SMILES for this stereoisomer of butan-2-ol.

Here are the steps required to create this question:

1. Go to any tab or window containing the VMK.

2. Click the Draw button. (The single bond tool is selected by default.)

3. Click in the drawing window. (This creates a bond-line drawing of ethane.)

4. Click on one end of the drawing of ethane, then on one end of the resulting drawing of propane to complete the bond-line drawing of butane.

5. Convert butane to 2-methylbutane.

6. Select the O atom tool and click on the C-2 methyl group of 2-methylbutane.

7. Click on the Smiley face emoji, copy the SMILES for butan-2-ol, and paste it into the Correct Answer text field for this problem.

8. Click the Check Your Drawing button to see if the drawing is correct.


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4. In an open VMK tab or window, use the Load Models: Name button to load butan-2-ol. Convert the pre-loaded model of butan-2-ol into a model of butan-2-one.

The Answer Format for this type of exercise is set to Model. The SMILES for the Correct Answer is available via the Get Identifiers button in the VMK.

Try creating an exercise where students convert butan-2-ol into butanoic acid. Or, have them make a model of butan-2-ol starting with the default model of methane in the VMK.

With the Answer Format set to Model, you can convert butan-2-ol into butan-2-one with two clicks:

1. Select the Bond Edit = Double button.

2. Click on the center of the C-O bond.


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5. In an open VMK tab or window, use the Load Models: Name button to load butane-2-one. What is the m/z value of the base peak in the mass spectrum of butane-2-one?

This exercise illustrates the cheminformatics capabilities of the VMK. The Exercise Answer Format is set to Integer even though the exercise involves the use of the VMK. The Correct Answer is entered as 43. The image of the mass spectrum was copied from the NIST website and is included to demonstrate the use of the Image URL feature of the exercise sheet.

Try creating an exercise that involves retrieving information about butan-2-one from the PubChem data base.

You can determine the answer to this exercise with just 3 VMK button/link clicks :

1. Click NIST Google button.

2. Click the yellow Open Data link.

3. Click the image of the mass spectrum.

Enter the m/z value (43) into the Correct Answer text box.


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