Displaying Molecules and Spectra For Electronic Conferences in Organic Chemistry

Henry S. Rzepa

Department of Chemistry, Imperial College, London, SW7 2AY.

This short poster demonstrates1 how 3D molecule and IR and NMR spectral data can be inserted into an article or poster designed for discussion at an electronic conference, using downloadable programs called Java applets.

1. Molecules displayed using the ChemSymphony Applets

  1. HTML Code to display a molecule
  2. Display the Molecule
  3. Size of download: Code 339505 bytes, Molfile 933 bytes

1.1 Discussion

There is much debate whether molecular information should be displayed using so-called plug-ins, which in effect chemically enhance your browser, or whether an alternative procedure based on Java should be used. Whereas the former requires the user to go through the actions of installing software on their computer, the latter makes no such demand on the user. To a large extent, it depends what the user expects to do with the information. If they wish to have the best possible performance, and to perhaps save 3D molecule coordinates on their own computer, then plug-ins are the way to go. If they wish the convenience of not having any local software to install or de-install, the Java route is preferable. It may also be the only route available if an appropriate (platform specific) version of the plug-in is not available for your favourite computer (e.g Unix systems).

Note in the above example that whilst the code size is significant, the actual molecule coordinate file size is trivial. Thus on a slow Internet link, the user will have to wait significantly for the display of a small molecule. For this reason, this page has been designed not to force such download upon loading the page, but to specifically request the use to invoke the action themselves at their convenience. This page itself contains no images or other download-intensive data, and so should be displayed rapidly even when the Internet connection is a relatively slow one.

2. Spectra displayed using the jSPEC Applet

  1. HTML code to display a spectrum
  2. Display the Spectra: UV/IR-Netscape | UV/IR-Internet Explorer |NMR (p-tolualdehyde)-Netscape | NMR (p-tolualdehyde)-Internet Explorer
  3. Size of download: Code 32153 bytes, UV, 2508, IR, 48162, 1H NMR 262972, 13C NMR, 131908 bytes.

2.1 Discussion

Spectral display is a much less CPU intensive procedure than 3D molecule display and rotation. This in turn means that the code for invoking such display can be kept very small and compact. In this case, it is the spectral data that is far larger in size than the jSPEC code used to display it. In this case as well, we have chosen to keep the Applet displaying the spectra quite separate from the mechanism used to display molecules. Some programs (e.g. Chime V 2.0) can support both types of display, as well as other properties such as molecular surfaces. The jSPEC code can in fact be also used to communicate with Chime-based objects, although introducing this feature also makes the Java-based jSPEC code much more browser specific; one of the undesirable features that the use of Java was meant to avoid. Thus the Netscape version of the jSPEC viewer contains Java classes that are only supported in Netscape, and hence will fail using Internet Explorer. These classes are the ones that support communication with Netscape plug-ins, a feature not (yet) supported in Internet Explorer.

3. The Future of Internet-based Chemical Object Display

The current HTML standard widely implemented is level 3.2. Data destined for display using a plug-in is invoked using an <embed src=molecule.mol> style tag. In contrast, data which will be displayed using a Java applet must be invoked using <applet code=Visua2.class ...><param value="Fluor.spc"></applet>. In effect, its the author who is apparently deciding how the data will be displayed, in making a choice between these two methods. Ideally, that choice should be left to the reader, not the author. The proposal for HTML 4.0 will replace both these methods with a single method <object data="molecule.mol" type="chemical/x-mdl-molfile"></object> which could be passed to either a plug-in or a Java applet.

4. Conclusions

This poster illustrates some of the ways in which structured and high value chemical information can be displayed using Internet technologies developed over the last five years. One issue facing us over the next two years is whether we should now move directly to the use of a higher level of markup such as CML (Chemical Markup language), rather than using what are described as the legacy files that current generations of plug-ins and applets support (e.g MDL Molfiles). Some two million Internet-based documents contain chemical information, and the task of migrating this chemistry to more highly structured forms will be one of the challenges facing us in the near future.


  1. H. S. Rzepa, "A History of Hyperactive Chemistry on the Web: From Text and Images to Objects, Models and Molecular Components", Chimia, 1998, to be published in November issue.

(c) ECHET98. May 1998