MOLÈVISION

Welcome to the Molèvision (ryhmes with television) site at University College Dublin.  The purpose of these pages is to demonstrate key concepts in structure and bonding in organic molecules.  The site also showcases a variety of important organic compounds, such as biomolecules and pharmaceuticals, and illustrates their great diversity, and their importance in our lives.

Using this site

First check that the visualisation software used (a Java applet called Jmol) is working properly, if it is you will see molecules spinning in the windows below.  Jmol allows the viewer to interact with the molecular structures in many ways, e.g. to rotate or zoom the model and change the display style.  This powerful visualisation tool will help you to see and understand concepts that are difficult to convey with static images.  The ability to change between different model styles, e.g. "ball and stick" and "spacefilling", and to manipulate 3D representations of atomic and molecular orbitals is a very useful aid to understanding structure and bonding in organic molecules.  'Playing' with molecular structures in this way is an excellent complement to the use of plastic molecular model kits.  If you haven't used Jmol before, please read the "Using Jmol" section below.

 If the applet is working properly, choose the aspect of organic chemistry that interests you from the menu below, and enjoy!

Explore the structure and geometry in some simple organic molecules, and understand the bonding by visualising the atomic and molecular orbitals.

See the structures of drug molecules that had a profound effect on our health, from Aspirin to Viagra, and read about their discovery and mode of action.

Explore the structures of the molecules of life, including fats, sugars and proteins, and read about their biological functions.

Take a look at some of the thousands of molecules that are essential to our way of life, from sunscreens to superglues, and read about how they work.

Using Jmol

Jmol is a Java application and should run on just about any personal computer (Windows, Apple and Linux) and in most browsers. The only requirement is that a Java plugin is installed. Java will already be installed in the great majority of PCs, and if it is installed and working correctly on your machine you will see images of four molecules spinning in dark blue windows above. You may have to give the browser permission to display the "active content" - this is OK.  If no Jmol windows appear, try installing the free Java plugin, available here.

If you haven't used Jmol before, take a few moments to learn some of its basic features.  You can rotate the molecules by left clicking anywhere in the windows and dragging in the desired direction. You can zoom in and out using the mouse wheel. Right cicking in the windows will bring up a menu that offers many more options for changing the display,etc. Try some of these to get an idea what can be done.


Links

There are many excellent sites containing related material. For example, try: ChemTube3D;   3Dchem.com;  Cool Molecules;   3-D structures of Biological molecules;   Mol4D;   MolecularModels.ca;   The Molecule of the Month;   DCU CHIME and Jmol Pages.


Acknowledgements

Software that is free for academic use was used as much as possible in creating this site. A big thanks to the creators of the excellent software that was employed:

  • Jmol: an open-source Java viewer for chemical structures in 3D.
  • Bob Hanson's Jmol pages at St Olaf College were indispensable in creating this site.
  • MOPAC input files were created using ACDChemSketch with ACD/3DViewer.
  • Molecular orbital calculations were carried out using MOPAC.
  • Most of the molecule data files were created from the MOPAC output using OpenBabel.
  • Conformational searches were carried out using PCMODEL from Serena software.

 

Mike Casey,  School of Chemistry & Chemical BiologyUCD,  2009