
High-resolution images of a molecule as it breaks and reforms chemical bonds - samlittlewood
http://phys.org/news/2013-05-first-ever-high-resolution-images-molecule-reforms.html
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ck2
Fantastic.
[http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteve...](http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteverhig.jpg)

Not sure how they "feel" the interactions without disturbing them but that's
why they are the physicists.

~~~
csense
> how they "feel" the interactions without disturbing them

They can't. I don't know if there are quantum complications at that scale that
change this picture, but my basic idea from classical physics is that Newton's
Third Law says the probe can't have a force exerted on it by the sample
(action) without also simultaneously itself exerting a force on the sample
(reaction).

> The single-atom moving finger of the nc-AFM

The mass of the detector particle being deflected by the fields is small
compared to the mass of the molecule being measured. So a force large enough
to move the probe by a lot might still be small enough to only move the sample
by a little.

The bottom line is, you can't measure a sample without disturbing it, but as
the ratio of probe mass to sample mass shrinks, the level of that disturbance
also shrinks. In this case they're using a single atom probe to measure a
large organic molecule, apparently the ratio is small enough.

> Resulting movements of the stylus are detected by a laser beam

I guess in order to engineer a system this small, you need a probe to measure
the probe. Again I'm guessing the momentum of the photons from the laser that
are used to measure the probe atom is small enough not to appreciably deflect
the probe.

~~~
gus_massa
Well, there are a lot of quantum complications in this scale, the structure of
the bounds is totally a quantum effect. And there are some problems with the
Newton's Third Law when you consider the electromagnetic field. Anyway the
general idea of force-reaction still holds, so it's a good approximation for
this experiment. If the tip "see" the molecule, then the molecule "see" the
tip.

The problem with your explanation is that the probe is much much bigger than 1
atom. It's a whole macroscopic tip, with a mass of a few grams. The tip of the
tip use a single CO molecule, so the prove ends in a single atom, but the atom
is attached to a big structure. If the tip were thicker, they would measure an
average of the surface under the tip, with a very sharp tip they measure a
small area.

The molecules are attached to a silver surface, so they are relatively fixed.
The O atom in the CO molecule in the tip is approached to measure the force at
each point of the surface. I couldn't find the exact distance but Wikipedia
says that in similar experiments the distance is between 10A and 100A. For
comparison, a bound between two Carbons in a molecule is approximately 1.5A.
So the CO molecule is far away and the force is very small (in the absolute
and the relative sense), and the system must use an incredible amount of
amplification.

But the force in the sample molecule is also relatively small, so it isn't
disturbed too much, and the data that you get are very similar to the data of
the unperturbed molecule.

I suppose that it's possible to tweak the setting to decrease the distance so
the interaction between the molecule in the tip and the sample molecule is
smaller. I suppose that it's possible to use this to make some reactions
happen, but I don't remember an experiment with this phenomenon. Anyway a
usual problem is to crash the tip against the surface. It's bad for the tip,
you need to pick another CO molecule and if it hit the sample molecule it
could be interesting. With a similar microscope that use the tunnel effect
it's possible to move atoms from one place to another, so it's possible to do
things on the surface using the correct settings. You can even do a movie!
<https://news.ycombinator.com/item?id=5637150>

~~~
csense
> the probe is much much bigger than 1 atom

I guess I didn't clearly state an additional assumption of my explanation. I
assumed the oxygen atom has an electric charge, the rest of the probe
structure is electrically neutral, and the electrostatic attraction/repulsion
of charges is the mechanism by which the oxygen atom on the probe reacts to
the sample [1].

So while the rest of the probe structure does exist, it's effectively [2]
electrically neutral.

[1] I think we can agree that the gravitational attraction of the probe and
sample to each other is way too small to matter.

[2] I think the large probe structure is close enough to neutral and/or far
enough away from the sample to have an effect which is smaller than the effect
of the oxygen atom. The structure may contribute some nontrivial amount of
noise due to being neither exactly neutral nor infinitely far away, but not
enough to totally drown out the signal from the oxygen atom.

~~~
gus_massa
I've found a previous article with more information and the full article
available: "The chemical structure of a molecule resolved by atomic force
microscopy" <http://www.sciencemag.org/content/325/5944/1110>

In this article, they explain that to get a good image, the distance between
the tip and the molecule should be only ~1A. It's similar to the distance
between atoms in the molecule, so the force is (relatively) big. Another
important point is that using simulations to fit the data, they found that the
main contribution to the force is not electrostatic, it's the Pauli repulsion
(that is a quantum effect). Nevertheless if the tip "see" the molecule, then
the molecule "see" the tip.

An important detail is that the Oxygen atom is small and it's not possible to
measure how it is moved by the forces. The molecule applies a small force to
the Oxygen atom that is attached to the Carbon atom that is attached to the
big tip. The tip resonates like a tuning fork, and the small force on the
Oxygen atom changes slightly the resonating frequency of the whole system.
They measure this frequency shift and use it to calculate the force on the
Oxygen atom.

------
kumar_navneet
Amazing stuff, feels really good to see that it is exactly the same as we read
in textbooks.

~~~
andy_ppp
When I looked at chemical symbols before seeing this I had always assumed them
to be a sort of vague outline of what was really happening. It's amazing to
think that the way chemicals bond is the same in reality as drawn in
textbooks.

~~~
marcosdumay
They choosed a molecule that was similar to its diagram, but that's not always
the case.

the main difference is that the diagram is 2D, and molecules are usualy 3D.

~~~
jcrites
I think you can see some slight 3D effects in the picture:
[http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteve...](http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteverhig.jpg)

In the two variants on the right, their edges seem to be curling upward making
a bowl shape. Their edges are also brighter, which perhaps means they are
closer to the probe than parts that are farther away. Additionally, the
hexagons are also not all the same shape. I assume that's due to the curling.

I would be interested to know if my interpretation of the image is correct, or
if the molecule is really flat and what I'm seeing is an artifact.

~~~
bsg75
I am curious as to the mathematical properties (definitions?) of the hexagonal
shape that make it common in natural structures
([http://www.space.com/3611-bizarre-hexagon-spotted-
saturn.htm...](http://www.space.com/3611-bizarre-hexagon-spotted-
saturn.html)).

I probably learned it in some chem course, and later forgot as all my math and
science got applied to business :(

~~~
jfarmer
You don't really need much math to see why this is happening. First, the bonds
in a benzene ring aren't discrete like we draw them, alternating between
single bonds and double bonds. It's also important to realize that although we
typically represent benzene in 2D all molecules really have a 3D geometry.

Electron orbitals can overlap in different ways depending on the geometry of
the atom and its electronics. See this for a picture:
[http://en.wikipedia.org/wiki/File:Benzene_Representations.sv...](http://en.wikipedia.org/wiki/File:Benzene_Representations.svg)
So, the electrons in a benzene ring really form more of a cloud around the
entire ring. You'd expect this to pull the atoms into a perfect circle with
the carbon atoms all being equidistance from each other, all else being equal.

However, each carbon atom also has a hydrogen atom attached to it. So now you
have a sort of a circle with 6 "strings" attached at points equidistant around
the circle all pulling outward, perpendicular to the circle.

Imagine a perfectly circular piece of string with 6 strings attached
equidistantly around the circle. You apply an equal force perpendicular to the
surface of the circle.

Hopefully you can see how this would result in the original circular string
being "deformed" into a hexagon.

It's a far leap from there to say why hexagons are "so common in nature." Are
they? Relative to what? I don't know that any of this has anything to do with
the shape of that storm you linked to.

~~~
bsg75
> It's a far leap from there to say why hexagons are "so common in nature."

I was thinking of things (compared to other geometric shapes) like the storm,
honey bee cells (honeycombs), basalt columns [1], turtle shells (although
irregular), and a common snowflake shape.

[1] <http://en.wikipedia.org/wiki/Giants_Causeway>

~~~
jfarmer
There are three regular polygons you can use to tile a plane: triangles,
squares, and hexagons. The regular hexagonal packing is the densest sphere
packing in the plane, so any time you have objects constrained to a plane
which for the sake of maximizing or minimizing some force want to be
equidistant from each other you'll get something close to a hexagon.

~~~
jfarmer
I'll add that sometimes a shape like that might result from a more
evolutionary process. In a 2D plane a circle is the structure which most
equally distributes force, so it's the shape most able to hold up under
pressure.

But a tile of circles isn't so fortunate. Of all the possible tilings, the
hexagonal tiling holds up the best precisely because it's the densest sphere
packing in the plane.

Other arrangements might appear, but over the course of time you're more
likely to see hexagonal tilings since those are the ones that best survive
external forces.

------
alexholehouse
Original paper here

[http://www.sciencemag.org/content/early/2013/05/29/science.1...](http://www.sciencemag.org/content/early/2013/05/29/science.1238187)

------
da_n
Incredible stuff, seems essentially (to a layman) like a stylus on vinyl
records.

