Interactive Visualization of Chemical Structures in Biology, Chemistry, and Geology:
Empowering Your Students with a Discovery Learning Tool

Scott A. Sinex
Prince George's Community College

Presented at the Powering Up with Technology Conference at Northwestern High School
in Hyattsville, MD on 15 November 2003.

Examine the mineral corundum given to the left.  Place the cursor on the image, click and move the mouse to rotate the structures.  Click on the red or gray atoms to identify them (watch the status bar at the lower left of the browser).  Right click, select "Display" and vary the mode of display.

We will examine two molecular structure-rendering software packages, Chime from MDL and RasMol by Roger Sayle (see for history).  RasMol is a small application that can run off a 3.5 inch disk and requires no installation.  Chime is a browser plug-in application which works in either Internet Explorer or Netscape.  It must be installed to allow viewing of molecular structures.  Both RasMol and Chime are freeware.  Chime files can operate free-standing in your browser (just open the file) or can be inserted into webpages as a plug-in.  The images then show up on webpages if the computer has Chime installed.  The ability to incorporate molecular images into webpages allows for interactive activities to be developed -- see for example the teacher-created pages from a recent workshop or a growing set of guided-inquiry activities on Structure and Bonding.

Both RasMol and Chime allow for multiple display modes (sticks, ball & stick, spacefill, plus cartoons for proteins and nucleotides) and rotate to view in any position.  The spacefill mode of display gives a realistic view of actual molecule shape and size.  Measurements of bond angles, bond lengths, torsion angles, and molecular dimensions can be accomplished on any molecule.  RasMol displays measurements on the molecule, whereas Chime gives results on the status bar of the browser (lower left of screen).  Chime will identify the atom if you place the cursor on the atom and click.  The details of the menu steps are given in Student Guide to the Use of Chime or Quick Guide to RasMol.

Let's measure the following by menu steps -- place your cursor on ammonia and right click, then click on "Select" followed by  "Mouse Click Action" and finally on "Angle" (or "Distance" or "Torsion").  For a bond angle, click on three consecutive connected atoms; for bond distance, click on two consecutive atoms in the bond (for any general distance, just click on two atoms); and for torsion angle, click on four consecutive connected atoms.

bond angle in NH3            C-O and C=O bond distances            torsion angle in H2O2

               

Students can make measurements to discover how bond lengths shorten with increasing bond order or discover distortion in molecules due to large groups or lone pairs of electrons.  Now to do this you need correct structures -- based on actual measurements or computer computational models.

Collections of molecule files are available at a number of sites -- see the last page of Creating Chime Webpages in FrontPage.  You can also use a search engine with the name or formula of the molecule and the word chime, such as "aspirin chime" or "NO2 chime," to find almost anything.  Beware that not all structures found on the web are correct.  A number of file formats are supported by Chime and RasMol, the most common being pdb.

Chime and Web-based Learning

Chime can handle animation files (.xyz file) of reaction mechanisms or molecular vibrations.  The bending vibration in water is shown to the right.  What is changing?  See the vibrations in the DNA molecule and the molecular motion in a protein helix.  The concept of intramolecular motion and interactions can be introduced at an early level.  Molecules are very flexible!  For more examples see Dance of the Molecules.  You can even zoom in to examine structures (press and hold the shift key and move mouse).

The use of interactive buttons on webpages incorporating Chime allows for simplifying actions to one push and not 3-4 menu steps.  This is very useful for multiple comparisons of structures.  Further explanation for using button and writing script is provided in Creating Chime Webpages in FrontPage and a wealth of button example scripts that you can copy and paste.

Chime also has the capability of producing electrostatic potential maps.  The menu steps are given in the Student Guide to the Use of Chime.  These maps show the charge distribution on a molecule.  This is a nice feature for addressing molecular polarity.

Consider some questions using the structures below.  Ponder and answer and then use the buttons.  The reload or refresh button on your browser will restore the original image.

1.    How packed are the ions in lithium iodide?  What is the LiI bond distance?

2.    Does phenol have a hole in the center?  Is phenol a polar or non-polar molecule (red is negative, blue is positive)?

3.    Hemoglobin is a protein.  Does it contain helices or sheets?  How many protein chains?  You may want to zoom in (press and hold the shift key and move mouse).  Can you find the heme groups?

lithium iodide                            phenol                                hemoglobin

               

spacefill  distance         spacefill   electrostatic potential        cartoon     

Webpages using Chime structures offer a powerful tool for the exploration of molecular structures from general chemistry to biochemistry, and crystalline structures to polymers.  Discovery learning through the measurement of bond angle, bond distances, and torsion angles, or comparisons of structures, especially with the electrostatic potential map, is easy with this interactive tool.  For the chemistry of a variety of compounds using Chime, see the Molecules of the Month website.  Click on the "C" next to each name for the Chime version of the page.

For further instructional technology tools -- click here.

http://academic.pgcc.edu/~ssinex/PUT