In 2006[1] we published an article illustrating various types of pseudorotations in small molecules. It’s been cited 20 times since then, so reasonable interest! We described rotations known as Lever and Turnstile as well as the better known Berry mode. Because the differences between these rotations are quite subtle, we included an interactive electronic supporting information to illustrate them. That ESI was written in HTML and used Jmol to animate the rotations. Now, 16 years is a long time in the Web ecosystem (some early wag suggested, like dogs, that one year in normal time approximates to about 7 years in Web time) and inevitably, like e.g. both Rasmol[2] and Chime before it, Jmol no longer works when invoked from a Web browser; Java applets are very much dead and we are now on the fourth generation of molecule viewer, JSmol. Two days ago I was contacted by someone (thanks Peter!) who had noticed that the journal landing page did not seem to point to any ESI. Here I tell the story of what happened next.
Thus the landing page[1] does not mention any method for accessing any ESI. But since the page is paywalled, you have to login to see more. When you do this, you get a reference to “enhanced objects”, so I should explain what these were.
The norm nowadays seems to be that ESI is expressed as a PDF file, but that allows interactivity only with extreme difficulty. In 2006, if you wanted this feature, you used HTML. The publisher (ACS) coined the expression of WEO, or Web-enhanced object. We produced perhaps 50 or so of these for various publishers and in those days they were hosted on publishers’ own sites. At some stage since 2006, these pages have been moved and the enhanced object for this article has been (temporarily?) “lost”. It is perhaps easy to understand why, since changes to the publishers publication workflows would need to factor in such pages and probably there were not enough of them to merit inclusion in the workflow.
So on to 2022, when I was contacted by Peter about this issue. Whenever we submitted such interactive ESI, we always kept a local copy, and indeed this was quickly located at DOI: 10.14469/hpc/10849, now of course allocated its own DOI. By now the ESI had lost its interactivity, but more worryingly, was lacking any error messages. Why? This was the HTML code then used:
<applet width="300" name="ClF5-gsA"
height="250" archive="JmolApplet.jar" code="JmolApplet"
mayscript="true">
<param name="progressbar" value="true" />
<param name="progresscolor" value="blue" />
<param name="boxmessage"
value="Downloading JmolApplet.jar" />
<param name="boxbgcolor" value="black" />
<param name="boxfgcolor" value="white" />
<param name="load" value="ClF5-gsAC2vpTZ.mol" />
<param name="script"
value="select all; labels off; spacefill 0.25;
wireframe 0.1; center atomno=2" />
</applet>
In modern web browsers this is simply ignored. So the solution is to rewrite this code into modern syntax, and for this I turned to a long time hero and expert, Angel, who is one of the active maintainers of JSmol, the successor to Jmol. A few hours later a conversion script came back.‡ It is just 55 lines long! It is invoked in the header of the HTML document as:
<script type="text/javascript" src="JSmol.min.js"></script>
<script type="text/javascript" src="convertJmolApplets.js"></script>
and hey presto, all works as originally. I transclude a small snippet here to give a flavour, although the original is formatted for wide pages, so go see all the ESI there.
So what is the take home message? Well, it turns out that the Java/Jmol syntax developed for the Web more than 20 years ago has actually proved pretty resilient. And so pages where technology has overtaken them can sometimes be quite easily rescued and restored back to life. A number of those WEOs from the early naughties have indeed been rescued by expedients such as described above. And perhaps in 10 years time when Javascript and JSmol have themselves moved on, further rescues will be needed. But had I been asked back in 2006 or earlier whether I expected those interactive ESI pages to still be working 16+ years later, I may well have replied that it seemed unlikely. So it is a very pleasant surprise to find that they (now) are. All we need is for the journal itself to point to a working version; for that, keep your eyes peeled.
On a more general point, a history of “ESI” as used in chemistry would be an interesting topic. Although generally thought of as having its roots around 1996, it may well go back further. Any historians around?
‡Available at https://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Legacy and 10.14469/hpc/10852
References
- H.S. Rzepa, and M.E. Cass, "A Computational Study of the Nondissociative Mechanisms that Interchange Apical and Equatorial Atoms in Square Pyramidal Molecules", Inorganic Chemistry, vol. 45, pp. 3958-3963, 2006. https://doi.org/10.1021/ic0519988
- O. Casher, G.K. Chandramohan, M.J. Hargreaves, C. Leach, P. Murray-Rust, H.S. Rzepa, R. Sayle, and B.J. Whitaker, "Hyperactive molecules and the World-Wide-Web information system", Journal of the Chemical Society, Perkin Transactions 2, pp. 7, 1995. https://doi.org/10.1039/p29950000007
