Developed and maintained by Albert Pratt, School of Chemical Sciences, Dublin City University
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Chemists require an ability to visualise molecules, and reactions involving them, in 3-dimensional space. Installation of the CHIME software plug-in within a web browser permits 3D interactive visualisation of on-screen molecular models. More recently analogous visualisation using the Jmol Java applet, which does not require the use of an additional plug-in, has been developed.
This Dublin City University website was initially developed (1997/99) to exploit the potential of the CHIME plug-in for teaching 3-dimensional aspects of organic chemistry using Netscape. It is being redeveloped (2006) to take advantage of the added convenience which the Jmol Java applet (pre-installed on the website) provides in not requiring anything additional from the website visitor. All updated material will be made accessible from this page as it becomes available and will be compatible with Netscape and Firefox browsers.
For CHIME visualisation a software plug-in needs to be downloaded from the MDL website. Originally developed for use with earlier versions of Netscape and Internet Explorer browsers the plugin file (npchime.dll) also functions with other browsers, such as Firefox, when placed in their "plugins" folder (detailed instructions are available here). Its development involved extensive collaboration between MDL, Glaxo Wellcome, and Roger Sayle and has grown out of RasMol, a particularly useful molecular viewer which Roger Sayle had earlier developed. The chemistry community owes them a major debt of gratitude for having so generously made the technology so widely accessible.
A variety of conventions to represent 3-dimensional molecules on a 2-dimensional surface (paper/board/screen) are in use. A Perspective Drawing tutorial which reviews some of these is available, supported by CHIME-enabled 3D-models.
Also available is a Conformational Analysis tutorial which uses on-screen interactive CHIME enabled models to illustrate the basic principles. The .pdb and .mol files used for the models have been obtained by editing the output files from commercial modelling programmes.
A page illustrating the separation of a racemic mixture into its component enantiomers is available, supported by both Jmol and CHIME visualisation.
A gallery of Molecules of Irish Interest, under development on behalf of The Institute of Chemistry of Ireland, uses the Jmol Java applet to display the interactive 3D-structures.
Tutorials (click to load)
CHIME (requires CHIME plugin) Jmol (no plugin required)
|Perspective drawing||Perspective drawing (not yet Jmol enabled)|
Conformational Analysis (not yet Jmol enabled)
|Molecular Viewing Galleries||Molecular Viewing Galleries|
|Molecules of Irish Interest (Jmol visualisation only) ð||Molecules of Irish Interest|