A Melange of Molecules

Molecules can come in a variety of shapes and sizes. We will look at examples of four categories of molecules. The Chime plugin is used to display these molecules in such a way that you can manipulate them. Let's first learn to use the basic control features for this plugin. You can also download more detailed instructions on "Using the Jmol molecule viewer".

Using Jmol to Visualize Molecules

WATER

There are many molecules which consist of only a few atoms or perhaps several dozen atoms. Here is an example of two important ones - water and beeswax.

You can manipulate these molecules by following the instructions below:

To adjust size, location, and orientation:

Size: Hold down the shift key and drag over the molecule. (Try this on the Beeswax molecule to the left.)
Location: Hold down the shift key, double-click, and drag the molecule. (Reset by shift-double-clicking away from the molecule.)
Orientation: Drag the mouse around inside the molecule window.

To bring up a popup menu:

Click on the Jmol in the lower right corner or
"Right click" for anywhere in the molecule window .
The menu options will allow you to display the model several different ways. You should experiment with as many of these menu commands as you like, but make sure to try every option under the "Render->Scheme" menu. If you choose "Stereo Display->cross-eyed" you will see two molecules. If you make them overlap by either crossing your eyes or looking "through" the monitor you can see a 3D version of the molecule.

Beeswax (sometimes used in candles)

There are many ways to categorize molecules. Let's look at four common types of these molecules:

Small Molecules - These molecules consist of a small number of atoms strongly bonded together.
Polymers - These molecules consist of repeating small molecules bonded together to form larger molecules.
Large Molecules - These molecules consists of a large number of atoms strongly bonded together. Polymers fall into this category. However, not all large molecules are made of repeating smaller groups of atoms.
Network Molecules - All previous examples involved molecules that were somewhat linear or sequential, with one atom bonded to the next and so on. Sometimes a network of bonds can form between many neighboring atoms.