.....Among the more difficult concepts that high school chemistry
students tackle are those dealing with atoms and how they bond. Learning
the difference between predominantly ionic and predominantly covalent bonds,
though, lays the foundation for understanding and predicting many chemical
properties. Visualizing chemical bonding can be made much easier for the
beginning student by taking advantage of chemistry web resources and programs
such as CHIME, RASMOL, and VRML. In addition, there are commercial programs
such as SPARTAN, which give the teacher a powerful teaching tool to help
students "see" molecules in topics such as bonding, polarity, periodic
trends. The 3D rendering of shapes and electron density in introducing
dipoles even outpaces hands-on handling of physical models by showing via
color the high and low electron density regions of molecules.
....."Webbed" teachers have available online a wide range of high-content web sites on which to draw for visualizing atoms, molecules, and bonding. Sites range from those appropriate for use with older elementary students to computation-heavy sites more appropriate for college students. This page collects links to several visualizing/modeling sites selected for their potential in helping high school students visualize atoms and the bonding process.
.....If you maintain or know of a site that would also be a good teaching resource, kindly email the URL to me (email address at the bottom of the page).
MATHMOL --K-12 Mathematics and Molecules..A starting point for modeling, including models of water, ice, carbon allotropes, hydrocarbons, as well as GIF, PDB, and VRML images of molecules, including nucleic acids and common pharmaceutical molecules.
Chemistry Visualization...Probably one of the best sites available to teachers is the Chemistry Visualization (ChemViz) project housed at the National Center of Supercomputing Applications (University of Illinois, Urbana-Champaign). Teachers may apply to the National Computing Center to use the Supercomputer for atomic and molecular visualization projects! The site permits you to generate both stills and movies of selected atoms bonding. The site also contains curricular materials for teachers to use in their classrooms with on-line materials! The application is available through the email address on the page.
Modes de representations en infographie moleculaire les differentes techniques d'estompage..A molecular modeling site in French, maintained by Francois Savary, University of Geneva. An English page link is provided, although it did not work as this page is written. Two links lead to GIF tables of 48 linked thumbnail images (in French, but still decipherable for the non-French speaking). In addition, one link permits downloading of compressed RGB format images.
An index of Amino Acids...From Berlin, this index of amino acids links to pages providing the German name and the properties, as well as ball and stick models.
Chime home page...from MDL, Chime (the ch is pronounced like _ch_erry) is available for free download from this page. This plug-in is an invaluable asset for looking at molecules and rotating them in 3D in several formats. Unfortunately, Internet Explorer no longer supports this plug in. You must use Netscape 4.6 or 4.7 (Netscale 6.x will not work).
Protein Explorer Home page Eric Martz. This is a GREAT program for visualizing protein molecules. The page has links to a step-by-step tutorial on the use of the program. It requires Chime and Netscape 4.6 or 4.7. Internet Explorer no longer supports Chime, so does not support this utility.
FrontDoor to Protein Explorer A quick start tutorial for Protein Explorer.