Web page decay and Journals: How an interactive “ESI” from 2006 was rescued.

In 2006[cite]10.1021/ic0519988[/cite] 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[cite]10.1039/P29950000007[/cite] 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[cite]10.1021/ic0519988[/cite] 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

This entry was posted on Friday, August 12th, 2022 at 8:33 am and is filed under Uncategorised. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.

10 Responses to “Web page decay and Journals: How an interactive “ESI” from 2006 was rescued.”

  1. Angel Herráez says:
    August 12, 2022 at 10:37 am

    Very nice story, Henry. I am so glad to have been able to contribute. As I said, it was a tempting challenge for a holiday pastime, to try and convert these pages without rewriting them completely. Just a single new JS file that makes the conversion upon page loading. This may be used for other pages, so I am leaving the file itself and some comments in the Jmol Wiki [1], for the future.
    One relevant background message is that the syntax of web pages and things embedded into them keeps changing, but the actual scripts of commends that make Jmol render the structures have needed no modification. So 2022 versions of Jmol and JSmol interpret without hesitation the instructions designed for 2006 Jmol and JmolApplet. Long live Jmol!
    I have also added a comment about this revival of Henry’s article at [2]

    1. https://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Legacy
    2. https://wiki.jmol.org/index.php/Journals_Using_Jmol

    Reply
  2. Henry Rzepa says:
    August 12, 2022 at 10:59 am

    Thanks Angel. I did actually record the early history of “interactive” ESI at this post: https://www.ch.imperial.ac.uk/rzepa/blog/?p=701

    This one from 1998 and the Royal Society of Chemistry as publisher is perhaps one of the very first: https://doi.org/10.1039/A805668D with the ESI at https://www.rsc.org/suppdata/perkin2/1998/2695/index.html It predates Jmol in using the Browser plugin Chime. Now that really is beyond rescue without re-writing the code I fancy.

    The earliest using Jmol from us appears to be https://doi.org/10.1021/ja043819b from a 2005 ACS article and seems rescuable using the script noted above. Please see later.

    Reply
  3. Henry Rzepa says:
    August 13, 2022 at 8:56 am
    1. I noted above that https://doi.org/10.1021/ja043819b from 2005 was the earliest use of Jmol by us using the Applet syntax. The supporting information for this makes for an interesting story. Here I note that a backup copy had been saved at https://doi.org/10.14469/hpc/10856 and has been “rescued” using the method above. The original ESI at the ACS has been “curated” by relocating it to Figshare where you can download a ZIP of the original directory via https://ndownloader.figstatic.com/collections/3200266/versions/1. Had no curation been applied, rescue would have been simple (as performed at https://doi.org/10.14469/hpc/10856 where the original folder was located as backup). Unfortunately, the ACS curation process has renamed all the files. Thus the original name was eg table1.html and this eg references molecular coordinate files as eg RRSS_fm-5-product-thf-anti.mol The new names are e.g. ja043819b_si_076.html and ja043819b_si_049.mol. The consequence is that the invocation within the HTML file and the local filename no longer match and we do not know the algorithm used to rename and so cannot reverse it. Hence the HTML document no longer functions. Remapping all the file names (86 of them) would be arduous and a very manual process certainly involving visual inspection of all the files. But in theory at least the original could be got back to working order and at least the publisher has kept the entire archive.
    Reply
  4. Henry Rzepa says:
    August 14, 2022 at 10:50 am
    1. A further ESI from 2005 has been converted. The article is https://doi.org/10.1039/b510508k with the RSC and the rescued ESI is at https://doi.org/10.14469/hpc/10864 (the original is at http://www.rsc.org/suppdata/CC/b5/b510508k/ ).

    In this example, two types of data were converted to interactive models; molecular coordinates and vibrations and orbital isosurfaces. The JSmol format for these latter is nowadays JVXL, but this predates the availability and another format known as .3dmf was used. This required a browser plugin, much like Chime and so no longer works. Furthermore it is very unlikely that any converter from .3dmf to .jvxl will ever be written.

    Reply
  5. Henry Rzepa says:
    August 14, 2022 at 3:19 pm
    1. The legacy library provided by Angel continues to be useful. Thus https://doi.org/10.1021/ja061400a dating from 2006 now has working ESI at https://doi.org/10.14469/hpc/10865 The translation also finds small errors undetected at the time of creation but which can be corrected now.
    Reply
  6. Henry Rzepa says:
    August 14, 2022 at 4:11 pm
    1. Here is another set of ESI from 2007 and again from Inorganic Chemistry, DOI: https://doi.org/10.1021/ic062473y) which has misplaced the ESI sent to the journal. This one was good value for money, containing six “WEOS”. Rescued versions of all six can now be found at https://doi.org/10.14469/hpc/10866 By now, the applet form had been abandoned and replaced with Javascript syntax, but still using Jmol rather than JSmol. A different converter script is now used to rescue these examples.
    Reply
  7. Henry Rzepa says:
    August 14, 2022 at 7:08 pm
    1. This one from ACS Organic Letters, DOI: https://doi.org/10.1021/ol0518333 in 2005 for which the ESI is at https://ndownloader.figstatic.com/collections/3183106/versions/1 and a functional version is now at https://doi.org/10.14469/hpc/10868

    What one learns from this it that during the period 2005 – 2007, when the concept of author-provided interactive ESI (IESI ?) was evolving, many different styles and expressions were being experimented with in something of a time capsule for that era. Of course, the genre did not stop this process then – the period 2008-2022 continued to show much evolution.

    Reply
  8. Henry Rzepa says:
    August 15, 2022 at 1:57 pm
    1. On to 2008, and another ACS organic letters article where the ESI has mysteriously vanished (DOI: https://doi.org/10.1021/ol703129z ) The rescued version is now at https://doi.org/10.14469/hpc/10871
    2. This is an ACS Natural Products article,https://doi.org/10.1021/np0705918 with ESI available on the original location at https://pubs.acs.org/doi/media/10.1021/np0705918/ and revitalised at https://doi.org/10.14469/hpc/10947
    3. This is an JACS article, https://doi.org/10.1021/ja710438j for which the relocated ESI at https://ndownloader.figstatic.com/files/4631845 appears to be wrong. There were four “WEOs” there, rescued at WEO1: DOI https://doi.org/10.14469/hpc/10948, WEO2: DOI https://doi.org/10.14469/hpc/10949, WEO3: DOI https://doi.org/10.14469/hpc/10950
      WEO4: DOI: https://doi.org/10.14469/hpc/10951

    4. From J. Org. Chem., https://doi.org/10.1021/jo801022b The link to the WEO is active but nees to be converted from Java to JSmol; a functioning WEO is now at https://doi.org/10.14469/hpc/10955
    5. From Chem. Theory. Comp, https://doi.org/10.1021/ct8001915 The link to the WEO is active but nees to be converted from Java to JSmol; a functioning WEO is now at https://doi.org/10.14469/hpc/10956
    6. From Dalton Trans in 2008, https://doi.org/10.1039/b810147g this is the first instance when a re-activated version of the ESI has already been updated on an earlier occasion on the publisher’s own site, http://www.rsc.org/suppdata/dt/b8/b810147g/Table1.html
    7. On to 2009, and another from PCCP, https://doi.org/10.1039/B810301A with the ESI at https://www.rsc.org/suppdata/cp/b8/b810301a/Table/Table1.html which had already been updated on an earlier occasion.
    8. From the ACS Org. Lett in 2009, DOI: http://dx.doi.org/10.1021/ol901172g the ESI is still available at https://pubs.acs.org/doi/media/10.1021/ol901172g/ but invoking Jmol. A JSmol version is now available at https://doi.org/10.14469/hpc/10957
    9. From ACS J. Phys. Chem. in 2009, DOI: https://doi.org/10.1021/jp902176a, the original WEO is at https://pubs.acs.org/doi/media/10.1021/jp902176a/index.html and invokes non-functional Java. The active version is at https://doi.org/10.14469/hpc/10958
    10. Again from Phys. Chem. Chem. Phys., DOI: https://doi.org/10.1039/B911817A the publisher version was rescued several years ago by direct contact with them; http://www.rsc.org/suppdata/cp/b9/b911817a/Table/Table1.html
    11. Another previously rescued version from Nature Chem., https://doi.org/10.1038/nchem.373 at http://www.nature.com/nchem/journal/v1/n7/media/nchem.373_jmol.html
    12. From RCS Chem. Commun, DOI: https://doi.org/10.1039/B913295C the interactive ESI is at https://www.rsc.org/suppdata/cc/b9/b913295c/table/tables_index.html and contains this statement in the HTML header: 
      Table updated 6 June, 2017 by H. S. Rzepa 
(orcid.org/0000-0002-8635-8390) to replace invocation 
using Java with one based on Javascript alone. 
Published in association with
doi: https://dx.doi.org/10.1039/B913295C
    13. Tetrahedron letters from 2009, https://doi.org/10.1016/j.tetlet.2009.02.228 This journal declined to host the IESI themselves, and so it was straightforward to update our hosted version at https://10.14469/hpc/10961
    14. From 2010, ACS and J. Chem. Ed, DOI: https://doi.org/10.1021/ed800058c the IESI was located at https://pubs.acs.org/doi/media/10.1021/ed800058c/ interestingly behind the paywall. The rescued version can be found at https://doi.org/10.14469/hpc/10962
    15. Science is anther publisher that hosted provided IESI, from article DOI: https://doi.org/10.1126/science.1181771 at http://www.sciencemag.org/feature/data/1181771/ This link no longer works, but the backup has been rescued at https://doi.org/10.14469/hpc/10967
    16. This from ACS Org. Lett in 2010, DOI: http://dx.doi.org/10.1021/ol9024259 where the WEO is available at https://pubs.acs.org/doi/media/10.1021/ol9024259/index.html (but its behind the paywall) as a non-functioning Jmol applet. The ZIP archive of the WEO is held at https://ndownloader.figstatic.com/collections/2657143/versions/1 where it can be downloaded and indeed then rescued. Such a rescued version is at https://doi.org/10.14469/hpc/10968
    17. From J. Org. Chem in 2010 comes https://doi.org/10.1021/jo100920e with a Java-version of the IESI at https://pubs.acs.org/doi/media/10.1021/jo100920e/ converted to JSmol at https://doi.org/10.14469/hpc/10969
    18. ACS J. Org. Chem, https://doi.org/10.1021/jo1002906 with Java-WEO at https://pubs.acs.org/doi/media/10.1021/jo1002906/ files at https://ndownloader.figstatic.com/files/4465477 and rescue at https://doi.org/10.14469/hpc/10977
    19. From Nature Chem in 2010, DOI: https://doi.org/10.1038/NCHEM.596, the article already has a pointer to https://doi.org/10.14469/hpc/10978 with the comment added to the HTML: 
      Table updated 28 February, 2018 by H. S. Rzepa 
(orcid.org/0000-0002-8635-8390) to replace 
invocation using Java with one based 
on Javascript alone. Published in association 
with doi: https://dx.doi.org/10.1039/C2CC33676F
This version uses the Jmol to JSmol 
mapping script Jmol2.js, which allows 
the original Java syntax to be retained
    20. From Che, Euro J. in 2010, DOI: https://doi.org/10.1002/chem.201001087 with access to the Java version of the IESI at https://application.wiley-vch.de/contents/jc_2111/2010/chem.201001087/Figure9/ and the updated JSmol version at https://doi.org/10.14469/hpc/10980
    21. From ACS J. Chem. Theory. Comp, DOI https://doi.org/10.1021/ct100470g the IESI files themselves are archived at https://ndownloader.figstatic.com/files/4375201 and the Java version is at https://pubs.acs.org/doi/media/10.1021/ct100470g/. The JSmol version is at https://doi.org/10.14469/hpc/10983
    22. From RSC Chem. Commun in 2010, https://doi.org/10.1039/C0CC04023A the IESI is https://www.rsc.org/suppdata/CC/c0/c0cc04023a/Table1/ and carries the comment in the HTML: 
      Table updated 5 June, 2017 by H. S. Rzepa 
(orcid.org/0000-0002-8635-8390) to replace invocation using
Java with one based on Javascript alone. 
Published in association with 
doi: http://doi.org/10.1039/C0CC04023A
    23. From 2011 and ACS Org. Lett, https://doi.org/10.1021/ol2001705 with the Java based IESI at https://pubs.acs.org/doi/media/10.1021/ol2001705/ and the file archive at https://ndownloader.figstatic.com/collections/2589874/versions/1 The JSmol version is now at https://doi.org/10.14469/hpc/10989
    Reply
  9. Henry Rzepa says:
    August 23, 2022 at 8:39 am

    I have been steadily curating old instances of Jmol diagrams submitted to journals, and had reached 28. Now I come to one which represents a change. Read on to find out why

    1. This next article, published by BioMedCentral in 2011 in the journal of Cheminformatics, DOI: https://doi.org/10.1186/1758-2946-3-46 and was entitled “The past, present and future of Scientific discourse”. The current article is conventional, and especially Figures 3 and 4 are static. In the author-original version, at https://doi.org/10.14469/hpc/10990 you can see the HTML version, now converted to use JSmol. Originally the journal hosted this version at eg http://www.jcheminf.com/content/supplementary/1758-2946-3-46-s1/ but that has now vanished. Instead the journal has replaced it with https://static-content.springer.com/esm/art:10.1186/1758-2946-3-46/MediaObjects/13321_2011_230_MOESM1_ESM.zip I suspect the reason it was so archived by the journal was the decay of the Java-original. But at least this original can be rescued in the manner being described here. This article is noteworthy for two other observations:

      1. The article described how the static presentation in all journals could be enhanced with an interactive data-based version. Ironic then that after a few years, the interactive version had transformed into a ZIP archive of files (although now recovered to again be interactive by suitable curation).

      2. These lines appear “We may also speculate at this point on other forms of rendering data. Jmol was written in Java, and requires the browser to support a Java virtual environment. New generations of mobile information devices, which are primarily designed for long battery life, may not continue with this approach. Instead, one favoured alternative is to interface the browser directly to the graphical hardware using e.g. WebGL, and to implement the functionality of something like Jmol using the emerging HTML5 standard and appropriate scripts [20, 21].” This is the first statement in print of the potential appearance of a non-Java implementation. The “appropriate scripts” of course soon became JSmol! WebGL did not really make it!

    2. From 2012, in Chem. Euro, DOI: https://doi.org/10.1002/chem.201200547 the original Java-IESI is at https://application.wiley-vch.de/contents/jc_2111/2012/chem.201200547/Webtable1/ and the JSmol version at https://doi.org/10.14469/hpc/10993
    3. From ACS Macromolecules in 2012, DOI: https://doi.org/10.1021/ma300803b comes seven sets of IESI, all downloadable using https://ndownloader.figstatic.com/files/4131244 and available as JSmol versions at
      10.14469/hpc/10998, 10.14469/hpc/10999, 10.14469/hpc/11000, 10.14469/hpc/11001,
      10.14469/hpc/11002 and 10.14469/hpc/11003
    4. From RSC, Chem. Comm in 2012, DOI: https://doi.org/10.1039/C2CC33676F we have the IESI at https://www.rsc.org/suppdata/cc/c2/c2cc33676f/dyotropic/ and the note in the HTML: 
      Table updated 9 June, 2017 by H. S. Rzepa 
(orcid.org/0000-0002-8635-8390) to replace invocation 
using Java with one based on Javascript alone. 
Published in association with doi: https://doi.org/10.1039/C2CC33676F
    5. From 2013 in Chem. Euro, DOI: https://doi.org/10.1002/chem.201102942 the original IESI is at http://www.wiley-vch.de/contents/jc%5f2111/2012/chem.201102942/Webtable/ using Java and the files for it are downloadable at https://chemistry-europe.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fchem.201102942&file=chem_201102942_sm_micellaneus-information.zip
      A functioning JSmol version is now at https://doi.org/10.14469/hpc/10991
    6. This from 2013 and the J. Cheminformatics, DOI: https://doi.org/10.1186/1758-2946-5-6 The files comprising the IESI have been archived by the publisher at https://static-content.springer.com/esm/art:10.1186/1758-2946-5-6/MediaObjects/13321_2012_363_MOESM1_ESM.zip
      https://static-content.springer.com/esm/art:10.1186/1758-2946-5-6/MediaObjects/13321_2012_363_MOESM2_ESM.zip
      https://static-content.springer.com/esm/art:10.1186%2F1758-2946-5-6/MediaObjects/13321_2012_363_MOESM3_ESM.zip
      https://static-content.springer.com/esm/art:10.1186%2F1758-2946-5-6/MediaObjects/13321_2012_363_MOESM4_ESM.zip

      whilst the non-Java versions can be seen at https://doi.org/10.14469/hpc/10997

      This collection also breaks new ground in using not just JSmol, but also ChemDoodle and GLMol, two alternative script-based systems for molecular rendering introduced around that time. These last two have subsequently not been as successful as has JSmol in this regard.

    7. From Nature Chem in 2013, https://doi.org/10.1038/nchem.1751 the Java-IESI is at https://springernature.figshare.com/articles/dataset/The_Vinylcarbene_Cyclopropene_Equilibrium_of_Silicon_an_Isolable_Disilenyl_Silylene/744825/1 as a downloadable fileset and the JSmol version at https://doi.org/10.14469/hpc/11005
    8. From BMC Chem in 2013, https://doi.org/10.1186/1752-153X-7-94 from which the files for the Java-IESI are available at https://static-content.springer.com/esm/art%3A10.1186%2F1752-153X-7-94/MediaObjects/13065_2013_638_MOESM1_ESM.zip and the JSmol version at https://doi.org/10.14469/hpc/11006
    9. From ACS Org. Chem in 2013, FOI: https://doi.org/10.1021/jo401146k has the JAva-IESI files at https://ndownloader.figstatic.com/files/4031107 and the old Java-based display at http://pubs.acs.org/doi/media/10.1021/jo401146k/ (behind paywll) The functional JSmol display is at https://doi.org/10.14469/hpc/11007
    10. From RSC Chem. Comm., in 2013, https://doi.org/10.1039/C3CC46720A the IESI is at https://www.rsc.org/suppdata/cc/c3/C3CC46720A/C3CC46720A/ and carries the statement 
      Table updated 9 June, 2017 by H. S. Rzepa 
(orcid.org/0000-0002-8635-8390) to replace invocation
using Java with one based on Javascript alone. 
Published in association with 
doi: https://doi.org/10.1039/C3CC46720A
    11. Something new now. From ACS, J. Org. Chem., in 2013 https://doi.org/10.1021/jo401316a with downloadable files at https://ndownloader.figstatic.com/collections/2146827/versions/1 and the IESI itself at https://pubs.acs.org/doi/media/10.1021/jo401316a/index.html This appears to be the first IESI that used native JSmol rather than Java, and so in theory needs no updating. BUT: 
      [Warning] [blocked] The page at http://pubs.acs.org/doi/media/10.1021/jo401316a/index.html 
 was not allowed to run insecure content from 
http://pubsapp.acs.org/iapps/jsmol/jsmol-1.0/JSmol.min.js?.
      [Warning] [blocked] The page at http://pubs.acs.org/doi/media/10.1021/jo401316a/index.html 
was not allowed to run insecure content from 
http://pubsapp.acs.org/iapps/jsmol/jsmol-1.0/JSmol-init.js?.

      The http request (rather than https) is probably a mis-configuration at the publisher’s site.
      A functional version (which has not been updated during this rescue and is original JSmol) is at https://doi.org/10.14469/hpc/11008

    12. This one from 2014 was the first deployment of native JSmol, although you will see it hedged its bets by also including the option to use Java-Jmol; DOI: http://doi.org/10.1039/C3SC53416B The IESI have been archived by the journal at 
      https://figshare.com/ndownloader/files/6055467
https://figshare.com/ndownloader/files/6055443
https://figshare.com/ndownloader/files/6055455
https://figshare.com/ndownloader/files/6055461
https://figshare.com/ndownloader/files/6055464
https://figshare.com/ndownloader/files/6055470
https://figshare.com/ndownloader/files/6055473

      an the journal also offers the IESI as a set of links

      https://figshare.com/articles/dataset/Table_1_Transition_state_energies_R_Ph_calculated_using_the_Houk_List_method/832533
https://figshare.com/articles/dataset/Table_2_Basis_set_superposition_errors_for_R_Ph_/832532
https://figshare.com/articles/dataset/Table_3_Calculated_transition_state_properties_for_R_Ph_scheme_2_/840483
https://figshare.com/articles/dataset/Table_4_Calculated_transition_state_properties_for_R_iPr_scheme_2_/840484
https://figshare.com/articles/dataset/Table_6_Passive_explicit_solvation_of_the_Houk_List_transition_state_R_Ph/832534
https://figshare.com/articles/dataset/Table_7_Proton_relay_mechanism_R_Ph/840485
https://figshare.com/articles/dataset/Table_8_Houk_List_Transition_state_analogues/832543

      But, one component has decayed. We were also introducing a new mechanism to retrieve the original data files from a data repository, using a mechanism which depended only on the DOI of each file and its media type. This depends on making a http://dx.doi.org/… request to retrieve the file. Unfortunately the environment into which the file arrives is deemed secure by virtue of having used a https request, and so http:// content cannot be absorbed. Using https://doi.org/ to try to get the data also now fails, since the server responding to the https request (Tomcat) was deemed to have a security issue and has been disabled. Updating Tomcat to a more recent secure version is also deemed “difficult”. At any rate, functioning versions of these IESI table have now been produced that use local copies of the required files and these can be found at
      https://doi.org/10.14469/hpc/11014
      https://doi.org/10.14469/hpc/11015
      https://doi.org/10.14469/hpc/11016
      https://doi.org/10.14469/hpc/11017
      https://doi.org/10.14469/hpc/11018
      https://doi.org/10.14469/hpc/11019
      https://doi.org/10.14469/hpc/11020
      https://doi.org/10.14469/hpc/11021

      But do not try to use the Java-Jmol version offered, it will not work!

    13. This from 2014, again using JSmol natively and remain functionally interactive; DOI: https://doi.org/10.1021/cs500326e with Figshare downloads at
      http://dx.doi.org/10.6084/m9.figshare.865637
      http://dx.doi.org/10.6084/m9.figshare.865638
      http://dx.doi.org/10.6084/m9.figshare.865639
      http://dx.doi.org/10.6084/m9.figshare.1029169
      http://dx.doi.org/10.6084/m9.figshare.1030188
      and interactive versions hosted by the journal at e.g. https://pubs.acs.org/doi/media/10.1021/cs500326e/table1_index.html
      However, one gets the following error

      [Warning] [blocked] The page at https://pubs.acs.org/doi/media/10.1021/cs500326e/table1_index.html 
was not allowed to run insecure content from 
http://pubsapp.acs.org/iapps/jsmol/jsmol-1.0/JSmol-init.js?.

      This appears to be a systemic error at the ACS server-side; potentially absolutely trivial to fix! I have contacted the AC via their Chat service and a case has been raised CSCSI0088211 Created On: 08-24-2022 12:07:13 PM EDT. Lets see what they say!

      Functioning versions are at
      https://doi.org/10.14469/hpc/11024
      https://doi.org/10.14469/hpc/11026
      https://doi.org/10.14469/hpc/11027
      https://doi.org/10.14469/hpc/11028
      https://doi.org/10.14469/hpc/11029
      and have not required any modification.

    14. Another experiment, from 2014 and Angew. Chemie as the journal: http://doi.org/10.1002/anie.201405238 The interactive version of the article is not available there, and instead one is redirected to Figshare at http://doi.org/10.6084/m9.figshare.1016980 Here, one downloads the entire IESI object as a ZIP archive, which when expanded allows access via index.html in a Web browser. Then the IESI becomes available and as JSmol, is still functional. An original copy which does not need this treatment can be viewed at https://doi.org/10.14469/hpc/11057 The IESI also introduces a new method of accessing the interactivity, by clicking instead on a figure using the Imagemap method. No modifications on either version were required for functionality.
    15. Here is a sort of recursive example. Dating from 2014 and published by the ACS at DOI: https://doi.org/10.1021/ci500302p, the topic was about data repositories and we wanted to illustrate how IESI could be held not so much at a journal, but on a repository, Figshare in this example. We created two WEOs (https://pubs.acs.org/doi/media/10.1021/ci500302p/ci500302p_weo_002.htm and https://pubs.acs.org/doi/media/10.1021/ci500302p/ci500302p_weo_003.htm) which basically invoked IESIs hosted by Figshare, using eg the links http://doi.org/10.6084/m9.figshare.840483 and http://doi.org/10.6084/m9.figshare.777773 At that time, in 2014,Figshare offered this (experimental) feature. If you click on either of the Figshare links, you will see that all you get now are downloadable ZIP archives which allow you to unpack and recreate the originals. As a result the original WEOs at the ACS no longer work either. These original WEOs are also now relocated and edited so that the download and unpacking steps are eliminated and you can see them at https://doi.org/10.14469/hpc/11058 and https://doi.org/10.14469/hpc/11059 Since Figshare no longer offered this functionality, we decided in due course to create a repository that did. That came in 2016.
    16. Another from Angew. Chemie in 2014 with the same properties. The article DOI: http://doi.org/10.1002/anie.201407751 references an IESI at https://doi.org/10.6084/m9.figshare.1115056.v1 which when downloaded, unpacked and index.html is opened reveals the IESI. A version that does not require this is at https://doi.org/10.14469/hpc/11060
    17. Angew Chemie again, https://doi.org/10.1002/anie.201409672 with download of the IESI at https://doi.org/10.6084/m9.figshare.1167503.v1 When unpacked and index.html is browsed, the object mostly works except in one regard. It has fallen foul of the https:// Tomcat server error noted earlier for http://doi.org/10.1039/C3SC53416B. A version which uses local files can be seen at https://doi.org/10.14469/hpc/11062
    18. In 2015 from ACS organometallics, https://doi.org/10.1021/om501286g with Figshare entry for IESI at providing a functional object after unzipping. The alternative instance-access IESI is at https://doi.org/10.14469/hpc/11063
    19. From ACS J. Chem. Ed., https://doi.org/10.1021/ed500398e and IESI downloadable at https://ndownloader.figstatic.com/collections/2164752/versions/1 and a viewable version at https://doi.org/10.14469/hpc/11064
    20. ACS J. Org. Chem, DOI: https://doi.org/10.1021/jo5022647 with IESI downloadable at http://doi.org/10.6084/m9.figshare.1290772 This is another afflicted by the Tomcat https condition noted above. A version using local files is at https://doi.org/10.14469/hpc/11065
    21. From ACS J. org. chem, http://doi.org/10.1021/acs.joc.5b00205, https://figshare.com/ndownloader/files/6055506 as download, we have an instant IESI at https://doi.org/10.14469/hpc/11066 Mostly no modifications needed, except four files which fell foul of the Tomcat sercurity issue note above.
    22. From the J. Comp. Chem in 2015, https://doi.org/10.1002/jcc.23985 Although the text mentions Full interactive 3D models of all the stationary points, along with animations of the IRCs are available in the interactive version of Table 2.20, pointers to this version seem to have vanished. One can be now found at https://doi.org/10.14469/hpc/11070
    23. From Chirality in 2015, https://doi.org/10.1002/chir.22486, the IESI is downloadable at https://doi.org/10.6084/m9.figshare.1228008 and an interactive version can be found at https://doi.org/10.14469/hpc/11071
    Reply
  10. Henry Rzepa says:
    August 28, 2022 at 7:43 am
    1. Starting in 2016, our new repository came into operation, and files started being deposited there. This first entry from ACS, J. Am. Chem. Soc., https://doi.org/10.1021/jacs.5b13070 had a mixture of Interactive ESI and ESI which purely referenced the data repository. Some of the files can be downloaded from the publisher using https://ndownloader.figstatic.com/collections/2858821/versions/6 but the collection is best summarised at http://doi.org/10.14469/hpc/244 (cited in the article) which contains non-interactive components as well as these two interactive versions: https://doi.org/10.14469/hpc/11080 and https://doi.org/10.14469/hpc/11081 These both use JSmol and needed no curation. As a precaution, new versions of the JSmol scripts have replaced the old ones.
    2. Another from 2016, RSC, Chem. Commun, https://doi.org/10.1039/C6CC06395K with repository data at https://doi.org/10.14469/HPC/442 (supposed to be cited as ref 21 but slipped through the cracks). This article represents a project conducted during migration from the old to the new repository, and so it contains citations from both. No IESI was constructed at this stage.
    Reply

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