Imperial College London

Henry Rzepa

[Previously](https://www.ch.imperial.ac.uk/rzepa/blog/?p=20679){target="_blank"
rel="noopener noreferrer"}, I explored (computationally) the normal
vibrational modes of Co(II)-tetraphenylporphyrin (CoTPP) as a
"flattened" species on copper or gold surfaces for comparison with those
recently imaged\[cite\]10.1038/s41586-019-1059-9\[/cite\]. The initial
intent was to estimate the "flattening" energy. There are six electronic
possibilities for this molecule on a metal surface. Respectively
positively, or negatively charged and a neutral species, each in either
a low or a high-spin electronic state. I reported five of these earlier,
finding each had quite high barriers for "flattening" the molecule. For
the final 6th possibility, the triplet anion, the SCF
(self-consistent-field) had failed to converge, but for which I can now
report converged results.^†^

[![](https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/flat.svg){.aligncenter
.size-large .wp-image-20781 decoding="async"
width="300"}](https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/flat.svg)

<table data-border="1">
<colgroup>
<col style="width: 20%" />
<col style="width: 20%" />
<col style="width: 20%" />
<col style="width: 20%" />
<col style="width: 20%" />
</colgroup>
<tbody>
<tr class="header">
<th>charge</th>
<th><p>Spin</p>
<p>Multiplicity</p></th>
<th>ΔG, Twisted Ph,<br />
Hartree</th>
<th>ΔG, “flattened”,<br />
Hartree</th>
<th><p>ΔΔG,</p>
<p>kcal/mol</p></th>
</tr>
&#10;<tr class="odd">
<td rowspan="6">-1</td>
<td rowspan="3">Triplet</td>
<td rowspan="3">-3294.68134 (C<sub>2</sub>)</td>
<td>-3294.64745 (C<sub>2v</sub>)</td>
<td><strong>21.3</strong></td>
</tr>
<tr class="even">
<td>-3294.616684 (C<sub>2v</sub>)</td>
<td>40.6</td>
</tr>
<tr class="odd">
<td>-3294.37012 (D<sub>2h</sub>)</td>
<td>195.3</td>
</tr>
<tr class="even">
<td rowspan="3">Singlet</td>
<td rowspan="3">-3294.67713 (S<sub>4</sub>)</td>
<td>-3294.39418 (D<sub>4h</sub>)</td>
<td>175.6</td>
</tr>
<tr class="odd">
<td>-3294.39321 (D<sub>2h</sub>)</td>
<td>178.2</td>
</tr>
<tr class="even">
<td><span style="color: #ff0000;">-3294.56652
(D<sub>2</sub>)</span></td>
<td><span style="color: #ff0000;">69.4</span></td>
</tr>
<tr class="odd">
<td colspan="5">FAIR data at DOI:<a
href="https://doi.org/10.14469/hpc/5486" target="data"
rel="noopener noreferrer">10.14469/hpc/5486</a> FAIR data version of the
tables in this and previous post at DOI:<a
href="https://doi.org/10.14469/hpc/5561" rel="noopener noreferrer"
target="_blank">10.14469/hpc/5561</a></td>
</tr>
</tbody>
</table>

I am exploring the so-called "flattened" mode, induced by the voltage
applied at the tip of the STM (scanning-tunnelling microscope) probe and
which causes the phenyl rings to rotate as per above. This rotation in
turn causes the hydrogen atom-pair encircled above to approach each
other very closely.^‡^ To avoid these repulsions, the molecule buckles
into one of two modes. The first causes the phenyl rings to stack
*up/down/up/down*. The second involves an all-up stacking, as shown
below. Although these are in fact 4th-order saddle points as isolated
molecules, the STM voltage can inject sufficient energy to convert these
into apparently stable minima on the metal surface.

::: {#attachment_20787 .wp-caption .aligncenter style="width: 410px"}
![](https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/all-up-1024x335.jpg){.size-large
.wp-image-20787 decoding="async"
aria-describedby="caption-attachment-20787"
onclick="jmolApplet([450,450],'load wp-content/uploads/2019/04/triplet-anion-alt-394.log;frame 44;spin 3;vectors on;vectors 4;vectors scale 8.0;color vectors green;vibration 6;','c1');"
width="400"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/all-up-1024x335.jpg 1024w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/all-up-300x98.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/all-up-768x251.jpg 768w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/all-up.jpg 1921w"
sizes="(max-width: 1024px) 100vw, 1024px"}

All syn mode, Triplet anion
:::

The *up/down/up/down* "flattened" form (below) shows a much more modest
planarisation energy than all the other charged/neutral states reported
in the [previous
post](https://www.ch.imperial.ac.uk/rzepa/blog/?p=20679){target="_blank"
rel="noopener noreferrer"}, whereas the *all-up* isomer (which on the
face of it looks a far easier proposition to come into close contact
with a metal surface) is far higher in free energy.

The caption to Figure 3 in the original
article\[cite\]10.1038/s41586-019-1059-9\[/cite\] does not explicitly
mention the nature of the metal surface on which the vibrations were
recorded, but we do get "*The intensity in the upper right corner of the
320-cm^−1^ map is from a neighbouring Cu--CO stretch"* which suggests it
is in fact a copper surface. Coupled with the other observation that *in
"contrast to gold, the Kondo resonance of cobalt disappears on Cu(100),
suggesting that it acquires nearly a full electron from the metal (see
Extended Data Fig. 2)*," the model below of a triplet-state anion on the
Cu surface seems the most appropriate.

::: {#attachment_20798 .wp-caption .aligncenter style="width: 410px"}
![](https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/udud.jpg){.size-full
.wp-image-20798 decoding="async"
aria-describedby="caption-attachment-20798"
onclick="jmolApplet([450,450],'load wp-content/uploads/2019/04/triplet-anion-284.log;frame 46;spin 3;vectors on;vectors 4;vectors scale 8.0;color vectors orange;vibration 6;','c2');"
width="400"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/udud.jpg 1015w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/udud-300x288.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/udud-768x737.jpg 768w"
sizes="(max-width: 1015px) 100vw, 1015px"}

Syn/anti mode, Triplet anion with C2v symmetry
:::

There is one final remark made in the article worth repeating here:
"*This suggests that the vibronic functions are complex-valued in this
state, as expected for Jahn--Teller active degenerate orbitals of the
planar porphyrin.^26^*" Orbital degeneracy can only occur if the
molecule has *e.g.* D~4h~ point group symmetry, whereas the triplet
anion stationary-point shown in the figure above has only C~2v~ symmetry
for which no orbital degeneracies (E) are expected. Enforcing D~4h~
symmetry on Co(II) tetraphenylporphyrin results in eight pairs of H...H
contacts of 1.34Å,^‡^ which is an impossibly short distance (the
shortest known is \~1.5Å). Moreover this geometry has an equally
impossible free energy 176 kcal/mol above the relaxed free molecule.
Visually from Figure 3, the H...H contact distance looks even shorter
(below, circled in red)! A D~2h~ form (with no E-type orbitals) can also
be located.

<table data-border="0">
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<tbody>
<tr class="odd">
<td><div id="attachment_20816" class="wp-caption aligncenter"
style="width: 235px">
<img
src="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/d4h.jpg"
class="size-large wp-image-20816" decoding="async"
aria-describedby="caption-attachment-20816"
onclick="jmolApplet([250,400],&#39;load wp-content/uploads/2019/04/anion-singlet-d4h-370.log;frame 56;spin 3;vectors on;vectors 4;vectors scale 8.0;color vectors green;vibration 6;&#39;,&#39;c3&#39;);"
width="225" />
<p><strong>Singlet, Calculated with D<sub>4h</sub> symmetry. Click for
vibrations.</strong></p>
</div></td>
<td><div id="attachment_20828" class="wp-caption aligncenter"
style="width: 235px">
<img
src="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/d2h-singlet-1024x1022.jpg"
class="size-large wp-image-20828" decoding="async"
aria-describedby="caption-attachment-20828"
onclick="jmolApplet([250,400],&#39;load wp-content/uploads/2019/04/anion-singlet-d2h.log;frame 55;spin 3;vectors on;vectors 4;vectors scale 8.0;color vectors green;vibration 6;&#39;,&#39;c4&#39;);"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/d2h-singlet-1024x1022.jpg 1024w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/d2h-singlet-150x150.jpg 150w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/d2h-singlet-300x300.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/d2h-singlet-768x766.jpg 768w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/d2h-singlet-144x144.jpg 144w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/d2h-singlet.jpg 1255w"
sizes="(max-width: 1024px) 100vw, 1024px" width="225" />
<p><strong>Singlet, Calculated with D<sub>2h</sub> symmetry. Click for
vibrations.</strong></p>
</div></td>
</tr>
<tr class="even">
<td colspan="2"><div id="attachment_20808"
class="wp-caption aligncenter" style="width: 310px">
<img
src="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2019/04/D4h-article.jpg"
class="size-full wp-image-20808" decoding="async"
aria-describedby="caption-attachment-20808" width="300" />
<p><strong>Taken from Figure 3 (Ref 1).</strong></p>
</div></td>
</tr>
</tbody>
</table>

These totally flat species are calculated to be at 13 or 12th-order
saddle points, with the eight most negative force constants having
vectors which correspond to up/down avoidance motions of the proximate
hydrogen pairs encircled above and the remaining being buckling modes of
the entire ring.

So to the mystery, being the nature of the "flattened" CoTPP on the
copper metal surface, as represented in Figure 3 of the
article.\[cite\]10.1038/s41586-019-1059-9\[/cite\] Is it truly flat, as
implied by the article? If so, the energy of such a species would be
beyond the limits of what is normally considered feasible. Moreover, it
would represent a species with truly mind-blowing short H...H contacts.
Or could it be a saddle-shaped geometry, where the phenyl rings are not
lying flat in contact with the metal but interacting *via* the phenyl
para-hydrogens? That geometry has not only a much more reasonable energy
above the unflattened free molecule, but also acceptable H...H contacts
(\~2.0.Å) However, would such a shape correspond to the visualised
vibrational modes also shown in Figure 3? I have a feeling that there
must be more to this story.

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

^†^These convergence problems were solved by improving the basis set
*via* adding "diffuse" functions, as in (u)ωB97XD/6-311+G(d,p).
Convergence to the lowest energy electronic state (^3^B~2~) is achieved
using a Huckel initial guess rather than the default Harries, which
gives the higher energy ^3^A~2~. ^‡^If the crystal structure for these
species is flattened without geometry optimisation, the H-H distance is
around 0.8Å ^♥^This blog has a DOI:
[10.14469/hpc/5559](https://doi.org/10.14469/hpc/5559).

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


Previously, I explored (computationally) the normal vibrational modes of Co(II)-tetraphenylporphyrin (CoTPP) as a “flattened” species on copper or gold surfaces for comparison with those recently imaged[cite]10.1038/s41586-019-1059-9[/cite]. The initial intent was to estimate the “flattening” energy. There are six electronic possibilities for this molecule on a metal surface.

Rogue Scholar Beiträge

Imaging normal vibrational modes of a single molecule of CoTPP: a mystery about the nature of the imaged species.