Imperial College London

Henry Rzepa

In 1953, the model of the DNA molecule led to what has become regarded
as the
most [famous](http://www.ch.ic.ac.uk/rzepa/blog/?p=3235){target="_blank"
rel="noopener"} scientific diagram of the 20th century. It had all
started 93 years earlier in 1860, at a time when the tetravalency of
carbon was only just established (by William Odling) and the concept of
atoms as real entities was to remain controversial for
another [45](http://dx.doi.org/10.1002/andp.19053220806){target="_blank"
rel="noopener"} years (for example Faraday, perhaps the most famous
scientist alive in 1860 did not believe atoms were real). So the idea of
constructing a molecular model from atoms as the basis for understanding
chemical behaviour was perhaps bolder than we might think. It is shown
below, part of a set built for [August Wilhelm von
Hofmann](http://en.wikipedia.org/wiki/August_Wilhelm_von_Hofmann){target="references"
rel="noopener"} as part of the lectures he delivered at the
Royal College of Chemistry in London (now Imperial College).

::: {#attachment_3474 .wp-caption .aligncenter style="width: 266px"}
[![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2011/02/molmod.jpg "molmod"){.size-full
.wp-image-3474 loading="lazy" decoding="async"
aria-describedby="caption-attachment-3474" width="256" height="341"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2011/02/molmod.jpg 256w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2011/02/molmod-225x300.jpg 225w"
sizes="(max-width: 256px) 100vw, 256px"}](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2011/02/molmod.jpg)

The original August Wilhelm von Hofmann molecular model, located in the
archives at the Royal institution, London and used by Hofmann in his
1865 lecture there
:::

This grand-daddy of all molecular models does have some interesting
features. The most obvious is that the carbon atom at the centre is
square planar (tetrahedral carbon was still 14 years in the future).
What HAS survived to the present day is the colour scheme used
(black=carbon, white=hydrogen, and not shown here, red=oxygen,
blue=nitrogen, green=chlorine).  But another noteworthy aspect is the
relative size of the white hydrogen, which is larger than the black
carbon. This deficiency was however very soon rectified in 1861 by Josef
Loschmidt, who published  [a famous
pamphlet](http://www.ch.ic.ac.uk/rzepa/loschmidt/){target="_blank"
rel="noopener"} in which he set out his ideas for the structures of more
than  270 molecules (many of which by the way were cyclic, and this some
four years before Kekule's dream!). An example (#239) is shown below,
which gets the relative sizes of the atoms more or less correct (OK,
chlorine is shown with rather an odd shape). To get an idea of how good
Loschmidt's model actually was, click on the diagram to load a modern
model, and compare the two! Even more impressive, these diagrams
pre-date [van der
Waals](http://en.wikipedia.org/wiki/Johannes_Diderik_van_der_Waals){target="_blank"
rel="noopener"} work on the finite sizes of atoms, first presented in
1873.

::: {#attachment_3476 .wp-caption .aligncenter style="width: 307px"}
![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2011/02/0-1.jpg "0-1"){.size-full
.wp-image-3476 loading="lazy" decoding="async"
aria-describedby="caption-attachment-3476" width="297" height="171"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2011/02/0-1.jpg 594w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2011/02/0-1-300x172.jpg 300w"
sizes="(max-width: 297px) 100vw, 297px"}

Loschmidt's molecular models. Click for 3D
:::

To conclude, I cannot resist showing one more model. [Hermann
Sachse](https://webspace.yale.edu/chem125/125/history99/6Stereochemistry/Baeyer/Sachse.html){target="_blank"
rel="noopener"} believed cyclohexane could not be planar. To try to
convince people, in 1890 he included a  "flat-packed" model in the pages
of a journal article,  evidently believing that people would cut it out,
and assemble it into a 3D shape.

::: {#attachment_3477 .wp-caption .aligncenter style="width: 402px"}
[![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2011/02/chair.jpg "chair"){.size-full
.wp-image-3477 loading="lazy" decoding="async"
aria-describedby="caption-attachment-3477" width="392" height="136"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2011/02/chair.jpg 392w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2011/02/chair-300x104.jpg 300w"
sizes="(max-width: 392px) 100vw, 392px"}](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2011/02/chair.jpg)

Flat-packed molecular model of cyclohexane
:::

You might have noticed a theme in the present blog of presenting 3D
models for many of the molecules I discuss (include the Loschmidt one
above). For the historians amongst you, I note our [1995
article](http://www.ch.ic.ac.uk/rzepa/RSC/P2/4_05970K.html){target="_blank"
rel="noopener"} in which we updated\[cite\]10.1039/P29950000007\[/cite\]
Sachse's origami with an article featuring how to incorporate
interactive models into journals (still sadly only too rare). Perhaps a
history of the molecular model, and how it has been presented over 150
years might be an interesting one to trace!

------------------------------------------------------------------------

#### Acknowledgments

This post has been cross-posted in PDF format at
[Authorea](https://doi.org/10.15200/winn.144224.42394){rel="noopener"
target="_blank"}.

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


In 1953, the model of the DNA molecule led to what has become regarded as the most famous scientific diagram of the 20th century.

A short history of  molecular modelling: 1860-1890.

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

A short history of molecular modelling: 1860-1890.

On the importance of Digital repositories in Chemistry