Imperial College London

Henry Rzepa

The bimolecular nucleophilic substitution reaction at saturated carbon
is an icon of organic chemistry, and is better known by its mechanistic
label,
**[S~N~2](http://en.wikipedia.org/wiki/SN2_reaction){target="references"}**.
It is normally a slow reaction, with half lives often measured in hours.
This implies a significant barrier to reaction (\~15-20 kcal/mol) for
the transition state, shown below (X is normally both a good nucleophile
and a good nucleofuge/leaving group, such as halide, cyanide, etc.  Y
can have a wide variety of forms).

::: {#attachment_784 .wp-caption .aligncenter style="width: 257px"}
![The Sn2 transition
state](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2009/09/sn2.jpg "sn2"){.size-full
.wp-image-784 loading="lazy" decoding="async"
aria-describedby="caption-attachment-784" width="247" height="185"}

The Sn2 transition state
:::

This transition state is normally regarded as the only situation in
which carbon can sustain penta-coordination (there are some exceptions),
and this is often contrasted with the analogous situation for silicon,
which demonstrates an abundance of stable penta- (and hexa-)coordinate
(crystal) structures. Perhaps inevitably therefore, chemists have set
themselves the goal of capturing a penta-coordinate carbon, not as a
transition state with fleeting lifetime, but as a stable (and perchance
crystalline) species.  The best strategy is to explore potential systems
computationally, and the latest report of such an exploration has some
suggestions for synthesis (Pierrefixe, S. C. A. H.; van Stralen, S. J.
M.; van Strale, J. N. P.; Guerra, C. F.; Bickelhaupt, F. M.,
"Hypervalent Carbon Atom: "Freezing" the SN2 Transition State," DOI:
[10.1002/anie.200902125](http://dx.doi.org/10.1002/anie.200902125){target="references"}).
Their suggestion corresponds to Y=CN and X=At (Astatine), a rather
esoteric combination it has to be said.  In the manner of the
blogosphere, Steve Bachrach has noted this report in his own
[blog](http://comporgchem.com/blog/?p=385){target="references"}, where a
discussion has opened up on the origins of why carbon can be regarded as
*abnormal* (at least compared to silicon), and more particularly whether
such a species should be regarded as merely *hypercoordinate*, or as
Bickelhaupt and co-workers suggest, *hypervalent*.

In fact, such reports are not new. As I note in the discussion of
Steve's blog, a crystalline structure of a **hexa-coordinate** carbon
compound was reported in 2008 (DOI:
[10.1021/ja710423d](http://dx.doi.org/10.1021/ja710423d){target="references"}
(below), and it is also tentatively described as possibly hexavalent
near the end of the article! I shall return to this compound in the
second part of this post.

::: {#attachment_787 .wp-caption .aligncenter style="width: 205px"}
![Hexa-coordinate
carbon](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2009/09/hexa.jpg "hexa"){.size-full
.wp-image-787 loading="lazy" decoding="async"
aria-describedby="caption-attachment-787" width="195" height="172"}

Hexa-coordinate carbon
:::

The astatine system reported above is unusual, and it really only
contains three carbon-carbon bonds surrounding the pentacoordinate
carbon. The compound above contains only **two** such C-C "bonds". It
would be perhaps more interesting to ask if one could design a compound
with **five** C-C bonds surrounding the putative pentacoordinate atom.
Whilst mulling over Steve's post, and pondering my contribution to that
blog, a colleague in my department wandered into my office (my door is
almost always open) and without saying a word, he wrote a structure on
my blackboard (yes, I really do have such).  He then walked out (almost;
 I believe he did mutter perhaps two words before leaving). He had
sketched the key feature of an article by Ethan L. Fisher and Tristan H.
Lambert entitled *Leaving Group Potential of a Substituted
Cyclopentadienyl Anion Toward Oxidative Addition*
(DOI: [10.1021/ol901598n](http://dx.doi.org/10.1021/ol901598n){target="references"}).
This triggered the following question in my mind: **could the aromatic
cyclopentadienyl anion act as the X group in the pentacoordinate carbon
example above**? The essential property of group X is that it must be
big!  Well, cyclopentadienyl can be made big! It would also achieve the
purpose of forming a penta-coordinate carbon with  five  C...C bonds.

So in it goes for a B3LYP/6-311+G(2df) calculation. Surely, the life of
a computational chemist is an easy one; all one  has to do is wait a few
hours (or, with a large basis set, days) for an answer. The result is
shown below.

::: {#attachment_794 .wp-caption .aligncenter style="width: 207px"}
![The SN2 reaction captured with cyclopentadienyl
anion](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2009/09/sn2-vib.jpg "sn2-vib"){.size-full
.wp-image-794 loading="lazy" decoding="async"
aria-describedby="caption-attachment-794"
onclick="jmolInitialize('../Jmol/');jmolSetAppletColor('green');jmolApplet([450,450],'load wp-content/uploads/2009/09/cpd-penta-184.xyz; frame 1; zoom 100;connect (atomno=21) (atomno=5) PARTIAL;connect (atomno=21) (atomno=12) PARTIAL;vectors on;vectors 4;vectors scale 5.0; color vectors black; vibration 20;animation mode loop;');"
width="197" height="156"}

The SN2 reaction captured with cyclopentadienyl anion
:::

The key vibrational mode (which you can see animated if you click on the
image above) has a wavenumber of 194 cm^-1^ (B3LYP/6-311+G(2df); other
basis sets show similar values). It corresponds to the S~N~2 mode,  and
is what we normally think of as the  transition or reaction normal mode
for this reaction. But  in this case, it is not an imaginary mode, but a
real mode!  The S~N~2 has been (virtually) captured for a
penta-coordinate carbon with five C...C interactions. How does it
compare with the astatine system noted in
[10.1002/anie.200902125](http://dx.doi.org/10.1002/anie.200902125){target="references"}?
Well, unfortunately, the umbrella-mode for that system  is only reported
as a force constant without mass weighting, so it cannot be compared to
the mass-weighted value we have here. The calculation is digitally
archived (e.g. as
[10042/to-2407](http://hdl.handle.net/10042/to-2407){target="references"}
or
[10042/to-2415](http://hdl.handle.net/10042/to-2415){target="references"})
so you can analyze it for yourself!

An obvious question to ask is what the nature of the  axial bonds for
X=cyclopentadienyl is. Is the central carbon hypercoordinate, or
hypervalent, or both? But this blog is quite long enough already, and so
this will all be discussed in part 2, to follow shortly.

Oh, one final comment. The issue of hypervalency and hypercoordination
of carbon has previously been discussed largely in conventional
scientific publications (for which DOIs are provided above). The forum
moved to Salt Lake  City in the  USA, where some of the results were
presented orally at the ACS spring conference in 2009.  Now that it  has
been formally published, it has been taken up by Bachrach in his blog,
where some of the discussion has continued. So where should I have
presented the present result?  In the primary scientific literature? Or
perhaps another ACS meeting? Well, here it is in another blog (I have
been variously told I am either brave or very foolish for doing
so!). And as I write this, of course it is not peer reviewed (but there
is nothing to stop people from commenting on this of course, as has
happened in Bachrach's blog). Will it "count" here -- in other words,
does it (yet) have any scientific respectability? Should  blogs report
new scientific results, or merely be reserved for commenting on such
results which have been reported in the "proper scientific manner"? Will
indeed this result appear in the future in the scientific literature
under different authorship, but with no accreditation for this blog? If
I do choose to "write it up properly" (assuming the journals now let
me), can I cite this blog in the way one can cite the ACS conferences? I
do not suppose many people know what the answers are to all these
questions. Perhaps the appearance of this post might provide some?

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


The bimolecular nucleophilic substitution reaction at saturated carbon is an icon of organic chemistry, and is better known by its mechanistic label,
<strong>
 S
 <sub>
  N
 </sub>
 2
</strong>
. It is normally a slow reaction, with half lives often measured in hours.

Messaggi di Rogue Scholar

Capturing penta-coordinate carbon! (Part 1).