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Atom World
Beautiful space-filling atomic models showing simultaneous polar and covalent bonding. Make any molecule from diamond to DNA; you'll understand chemistry like never before.
http://www.jlc.net/~aretee/atomworld/
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Chemist's Art Gallery
Visualization is a key to understanding how molecules behave and react, and in designing chemicals for particular purposes. The Chemist's Art Gallery contains visualizations and animations in chemistry done at the Center for Scientific Computing, Finland.
http://www.csc.fi/chem/gallery.phtml
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Chemistry Hypermedia Project
On-line educational hypermedia for general chemistry, analytical chemistry, instrumental analysis, optics, and electronics.
http://www.chem.vt.edu/chem-ed/
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Chemistry Visualization Program at NCSA (ChemViz)
Chemviz is a program which uses the power of the World Wide Web in combination with the power of the SGI supercomputer to generate images of atoms, molecules, and atomic orbitals. The user inputs a set of parameters as they are prompted and submits these parameters to the supercomputer. A picture file is generated which the user downloads and views.
http://chemviz.ncsa.uiuc.edu/
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ComChem
A student's site presenting visualizations and animations of organic, inorganic and biochemical molecules.
http://www.comchem.de/
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Molecules from Chemistry at Okanagan University College
1100+ molecular models in .pdb or .mol format.
http://www.ouc.bc.ca/chem/molecule/molecule.html
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Organic Chemistry at Centre College
Tutorials to help organic chemistry students visualize molecules and changes in molecules. Changes covered include conformations and reactions (substitution and elimination).
http://web.centre.edu/muzyka/organic/organic.htm
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The IrYdium Project
Provides a number of simulations (in applet form) as well as other curriculum development tools with the goal of revolutionizing the way chemistry is taught.
http://ir.chem.cmu.edu/irProject/
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X-ray Spectra
Contains x-ray spectra of elements on the periodic table. The spectra are drawn with a java applet.
http://ie.lbl.gov/xray/
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