MacMolecule: Visualizing Molecules with Computers

MacMolecule is a freeware molecular visualization program from the University of Arizona that allows student to view and rotate very colorful models of molecules in several different forms. It provides smooth rotation animation of fully-rendered and shaded color models of molecules. Molecules as simple as water and as complex as DNA can be visualized using this program.

Here is the assigment done by the students using the MacMolecule program. 

Chemistry 121/122           Name______________________________________

Oct. 5, 1994

Molecular Visualization in MacMolecule

This activity must be done in the Chemistry Macintosh Room, Chem 2305, just
one flight up from our laboratory. (The WAM labs don't have the required
software). This computer room is a public facility that you can use anytime
during its open hours (9 am - 5 pm weekdays).  It has word processors and
other common software but not the same software that the WAM labs have.


MacMolecule works only on the computers with color monitors; work in pairs
on the machines that have color monitors.  Open (double-click on)
FileServer 2, open the Public Domain software folder, open the MacMolecule
folder, and open MacMolecule 1.7.  Click on the flash screen to continue.
MacMolecule is a free (public domain) molecular visualization program
developed at the University of Arizona that is used to study the
three-dimensional shapes of molecules.

a. Pull down the File menu and select Open.  Scroll to the Small Molecule
folder, open it, and scroll to Oxygen - B&S, and open this file.  This
shows O2 as a ball and stick model, very much like the plastic model kit we
used in class.  Position the mouse pointer on the model and press the mouse
button, and drag slowly in various directions.  What happens?

b. Pull down the Options men and select Model.  The pop-up side menu gives
three choices; select Space Filling.  Scientists believe that these space
filling models give a more realistic view of the actual shape of a molecule
than the ball and stick. Can you rotate the space filling model?

c.  Close the oxygen model by clicking on the "close box" in the upper left
corner of the window.  Open the model for water and look at it in both ball
and stick and space filling modes.  What colors are used for hydrogen and
oxygen?

d.  Close the water model by clicking on the "close box" in the upper left
corner of the window.  Open the models for methane and for carbon dioxide
and look at these in both ball and stick and space filling modes. Describe
how the space filling model differs in appearance from the ball and stick
model.

e. Open the model for buckminsterfullerene and, before trying to rotate it,
change to a wireframe model.  Wireframe models are the least realistic but
are easier to draw and can be manipulated more quickly that the other
models, especially for large molecules such as this.  Rotate the model and
note how the carbon atoms form rings or 5 and 6 carbons.  How many carbon
atoms are there altogether?  Are there really holes in the center of the
carbon rings?  (View in space filling mode).

f. Open the Small Inorganics folder and by opening and inspecting the
molecules in that folder, determine the colors that MacMolecule uses to
represent the various atoms.  Enter the colors in the table on the next
page.  Based on the molecules in this folder, what atoms does MacMolecule
have that your plastic model kit did not have?

--------------------
atom         color
--------------------
Hydrogen        
Carbon  
Oxygen  
Nitrogen        
Fluorine        
Chlorine        
Bromine 
Iodine  
Sulfur  
Phosphorous     
Silicon 
Xenon   
--------------------

g. Based on the models in the Small Inorganics folder, what do the
following prefixes mean?

----------------
Prefix  Meaning
----------------
    di-     
   tri-    
 tetra-  
 penta-  
  hexa-   
----------------

h. Which of the molecules in the Small Inorganics folder contain nitrogen
atoms?

i. Many chemists were surprised when the xenon difluoride and xenon
tetrafluoride were discovered some years ago.  Why do you think were they
surprised?
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Appendix:  List of models in the "Small Inorganics" folder:

Amide ion
Ammonium ion
Beryllium chloride
Boron trichloride
Bromine pentafluoride
Carbon dioxide
Chlorate ion
Hydrogen cyanide
Hydronium ion
Iodine trichloride
Nitrate ion
Nitrite ion
Phosgene
Phosphorus pentachloride
Silicon tetrachloride
Stannous chloride
Sulfate ion
Sulfur dichloride
sulfur dioxide
Sulfur hexafluoride
Sulfur tetrafluoride
Triiodide ion
Water
Xenon difluoride
Xenon tetrafluoride