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Introduction to Molecular Modeling for K-12

The following activity is designed to be performed with two students.


If you don't see two water molecules below youneed the CHIME plug-in --> download chime


Take a carefull look at the two molecules shown above. You probably recognize the molecules as water. You are probably also familiar with the chemical formula for water (H2O).

Chemical formulas are a shorthand way of representing chemical substances. The chemical formula for water is another way of saying that each molecule of water contains two hydrogen atoms and one oxygen atom. In the molecular model shown above each atom (element) is represented by a sphere of different color. Try answering each of the following questions on a separate sheet of paper. Some of the questions allow you to check your answer online. Be sure to click the submit button after you type your answer.

Question 1: In the model of water shown in the boxes above, what color is the oxygen molecule?

Question 2: What colore is the hydrogen molecule?

Notice that the image on the right is moving while the image on the left is much like those found in your textbook. The image on the left is a 2-Dimensional image while that on the right is a 3-Dimensional image.

Question 3: Why do you think it is important to view images in 3-D? __________________________

Without moving the images can you tell if these two molecules are the exactly the same?


From what you can see it looks like the image of the molecule on the left has only 4 atoms (1 carbon and 3 hydrogens) while the molecule on the right has 5 atoms (1 carbon and 4 hydrogens). By viewing molecules in 3-Dimensions it is possible to getter a more accurate perspective of the molecules structure and geometry. Molecular modeling gives us this ability.

Using molecular modeling it is possible to rotate, zoom in and out, and translate molecules in the X-Y axis.

Try these activities with your partner.

Take the mouse cursor and put it over the molecule (above) on the left. Hold the left mouse button down, and slowly move the mouse a little to the left, then a little to the right. Now move the mouse slowly up and down. You can now see that the two molecules are the same.

The molecules are both methane (CH4).

If you want to get a closer look try this. Hold the shift button down and the left mouse key down at the same time. Put the mouse cursor arrow inside the box and move the mouse up and down. The molecule should change size.


Try each of the following commands while moving the mouse cursor over the molecule shown below. The molecule you are moving is aspirin.

(put mouse cursor in box then:)

left mouse button = rotate
Shift Key + left button = ZOOM
Shift Key + right button = X-Y rotate
Control Key + right button = translate

Question 4: How many different atom types (elements) does aspirin have?


There are four ways molecules can be displayed when using molecular models.


Wireframe Model
Stick Model
Ball and Stick Model
Space Filled Model

Each model has its advantages and disadvantages. Discuss with your partner what may be the advantanges and disadvantages in using each model.

To change from one model to the another try the following.

Hold the right mouse key down (over a molecule) ---> Display --->Choose your model (wireframe, stick, ball and stick. For space filled then ---> Van der Waals Radii ---> Click.

Try changing the above structures to other display forms. With your partner identify the different atom types in ethanol.

Question 5: What would you expect the chemical formula of ethanol to be?

You will now use molecular modeling to help you in identifying several hydrocarbons in the Alkane series.


The table shown here gives the chemical formulas for several simple hydrocarbons (compounds containing only carbon and hydrogen). Study the pattern shown in the table.

Do you recognize the pattern?

Question 6: How many hydrogens would the molecule Decane (10 Carbons) would have how?


Can you match the structural formulas above with the 3-D molecular models below? Try rotating and/or zooming in on each molecule to help identify the structure. Choose from the following: methane, ethane, propane, butane, pentane, hexane and octane.


Question 7)

Question 8)

Question 9)

Question 10)

Question 11


Another way to view a molecule is by surrounding the wireframe model with a surface of dots that represent the molecular surface.


Hold down the right mouse button down over the aspirin molecule (inside the box)
--> Options ----->
Dot Surface ---->
Van der Waal Radii


Now let the molecule rotate by itself:

Hold the right mouse button down ---> Rotation

To stop the rotation repeat the above step.

You are now finished with Part I. Click here to go to part II.