- Chemistry, Structure, and 3D molecules: A-Z Index The Molecule of the Month website from the University of Oxford, now updated to make use of Jmol, showing hundreds of small molecules, inorganic polyhedra and protein structures - Karl Harrison, Oxford, UK.
- Gallery of Inorganic Molecules, Polyhedra and Bioinorganic Structures Karl Harrison, Oxford, UK.
- 3D-Structures in Organic Chemistry Models and structures related to teaching basic organic chemistry (DE) - PD Dr. Stefan Immel
- 3D-Structures of Achiral and Chiral Molecules Structures visualizing different types of chirality (DE) - PD Dr. Stefan Immel
- 3D-Structures and Animations in Vibrational Spectroscopy Structures and animations used to visualize vibrational frequencies in IR spectroscopy (DE) - PD Dr. Stefan Immel
- Atlas of Macromolecules is a browsable list of over 150 3D protein or nucleic acid structures, many with snapshots, and each with links for viewing in FirstGlance in Jmol.
- ChemEdDL's Molecules 360 A collection of small inorganic molecules and their properties. Hosted at the Chemical Education Digital Library
- CoolMolecules - St. Olaf College, USA.
- Periodic Table Live! - allows you to explore a broad range of information about the elements, their reactions, their properties, their structures and their histories. Hosted at the Chemical Education Digital Library
- Stereochemistry - Learn how to name organic molecules using the IUPAC system; learn how to recognize, draw and name stereoisomers (E/Z, R/S, M,P).
- The Virtual Museum of Minerals and Molecules - Previously implemented on Chime, the VMMM is now fully converted to Jmol (applet + JavaScript), with over 100 molecules and minerals in its galleries
- Comparison of structure of inorganic compounds and minerals - Theoretical and X-ray structures
Specific Examples
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Chiral Organic Molecules: Pick Tetrahedron
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Thalidomide: Background | Jmol
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E. Coli Ribosomal Termination Complex 1mL5 MW approx 2.1 million