Imperial College London

Henry Rzepa

The preceeding blog entries contain stories about chemical behaviour. If
you have clicked on the diagrams, you may even have gotten a Jmol view
of the relevant molecules popping up. But if you are truly curious, you
may even have the urge to acquire the relevant 3D information about the
molecule, and play with it yourself. Even after 15 years of the
 (chemical) Web, this can be distressingly difficult to achieve (or can
it be that it is only myself who wishes to view molecules in their
 *native* mode?).  Thus the standard mechanism is to seek out on journal
pages that disarming little entry entitled  **supporting information**
and to hope that you might find something useful embedded there.
 Embedded is the correct description, since the information is often
found within the confines of an Acrobat file, and has to be extracted
from there.  Indeed, that is what  I had to resort to in order to write
one of the blog entries below. I ground my teeth whilst doing so.   
![blog11](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2009/04/blog11.jpg "blog11"){.aligncenter
.size-full .wp-image-93 loading="lazy" decoding="async"
onclick="jmolInitialize('../Jmol/');jmolSetAppletColor('yellow');jmolApplet([450,450],'load wp-content/uploads/2009/04/42-557.xyz; frame 1; zoom 100;vectors  on;vectors 4;vectors scale 5.0; color vectors orange;vibration 6;connect (atomno=2) (atomno=1) partial;connect (atomno=6) (atomno=1) aromatic;connect (atomno=3) (atomno=2) aromatic;connect (atomno=5) (atomno=4) aromatic;connect (atomno=3) (atomno=4) aromatic;connect (atomno=6) (atomno=5) partial;');"
width="304" height="287"}  
So is there a better way? We think so! The  **digital repository**. If
you click on [this](http://hdl.handle.net/10042/to-2117){target="new"}
you should see the entry directly. What can you do there? Well, if you
have suitable programs, you can download eg a *Checkpoint* file of the
calculation that created the molecule model and re-activate it there. Or
you can download just the **CML** file for viewing in any CML-compliant
program (such as e.g. Jmol). Or you can check up on the **InCHi** string
or the **InChI Key** of the molecule.

What about the specific entry above? Well, it corresponds to the
calculation for the π4 + π2 cycloaddition described in the blog entry
below. You can now verify for yourself the assertions made in that
entry, ie that the rotation mode is disrotatory, or that the bond is
forming antarafacially. You do not need to take my word for it! If the
Digital repository is too much trouble for you, click on the graphic
instead to get a similar result.

We now regularly put such links into journal articles, in the form of
*Web-enhanced* tables and figures, so that it is literally just one
click away from such an article to having a vibrant molecule dancing in
front of you. All (chemistry) journals should do this. If they do not
yet, then contact their editor in chief when you next submit an article
and ask them why not!

See also the blog by [Peter
Murray-Rust.](http://wwmm.ch.cam.ac.uk/blogs/murrayrust/){rel="friend colleague"}

::: {.wp_orcid_field}
[https://orcid.org/0000-0002-8635-8390](https://orcid.org/0000-0002-8635-8390){target="_blank"
rel="author"}
:::


The preceeding blog entries contain stories about chemical behaviour. If you have clicked on the diagrams, you may even have gotten a Jmol view of the relevant molecules popping up. But if you are truly curious, you may even have the urge to acquire the relevant 3D information about the molecule, and play with it yourself.

Messaggi di Rogue Scholar

On the importance of Digital repositories in Chemistry