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You can explore the relationship between bond strength and separation in the covalent bonding interactive tutorial
In the tutorial on states of matter you can change ice to water and steam

Hydrogen bonds can be displayed as seen in this mixture of octanol and water

Acetic acid. The electrostatic poential map shows the polarity of the molecule

Sodium Chloride dissolving in water
Stereo and Structural isomerism are explained using 3d models
A 3d strand of RNA from one of the biochemistry tutorials. In Odyssey molecules vibrate and move according to their structural properties
The Simple Ionic Solids topic allows instructors and students to systematically build up crystal lattices by adding unit cells. 3-D Visualization and manipulation of crystal structures is available for an assortment of ionic solids, including NaCl, CsCl, ZnS, and CaF2
Individual molecules can be traced as seen here in the mean free path tutorial
Carbon Models include a sampling of various forms of naturally occuring and synthetically prepared molecular carbon. The models can be displayed in a variety of model styles including wire, ball and wire, tube, ball and spoke, and space filling. Note that the green background colour can be customised