High-resolution images of a molecule as it breaks and reforms chemical bonds

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

> 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.

>Rings with fewer than 6 members are uncommon in chemistry

In chemistry, or in nature? five membered rings show up all over the place, both aromatic and otherwise. Granted, cyclobutyl (4 member, square) and cyclopropyl (3 membered, triangle) suffer from ring strain and are uncommon, but 5, 6, 7, (or higher) rings show up all over the place.

Examples off the top of my head are the cyclopentadienyl ion pervasive in inorganic chemistry (see ferrocene, et al) and amino acids tryptophan, tyrosine, histidine, and phynylalanine all feature cyclic aromatics 5 and 6 membered, as well as proline with a non-aromatic 5 member ring.

The takeaway point is that although ring-strain (having non ideal angles (120 or 109.5 degrees)) increases the internal energy of the molecule (destabilizing it), other factors, such as aromaticity, which decrease internal energy (stabilizing it) may balance or exceed the ring-strain, still giving a stabilized, if non-ideal geometry.

(But yeah, 3, 4 membered rings, ugh. Look up platonic alkanes for some really crazy strain angles.)

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.

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.