To answer your question (flat vs. artifact) directly: It's flat. Sorta. Bear with me a moment. If this is confusing, please let me know, and i'll try to clarify. Molecular symmetry isn't my strong point, unfortunately.
The trouble with all of this is the "picture" is not an actual picture-made-with-photons picture, but a visualization via computer. That isn't to say it's a poor reflection on reality, but that the limitations of the techniques should be accounted for. In this case, the electron density of the overall molecule is being measured. The brighter signals correspond to an increase in local electron density.
In such chemical structures as these, the aromaticity [1] is the main force at play. Without getting too technical, the brighter regions are those with increased electron density. (See figure 4 at the IBM Zurich page on pentacene [2])
The hexagons (and square and pentagons) in fact do not have idealized geometry, but not due to any curling. The unique environment of each carbon is more at play. Symmetry plays a large role; imagine a symmetric vs. unsymmetrical tug-of-war between the carbons with the electrons as the rope. The left hand side and lower right have a dihedral mirror plane, simplifying the density somewhat, where the upper right has a more muddled situation.
Getting back to the flatness, the target molecule is 'mounted' on a suitably uniform surface, such that only one side is being scanned/read by the probe. In a vacuum, the tug of war in the Z direction (into the plane) will cancel out between the +Z and -Z vectors, giving a 'flat' molecule. (Depending on your point of view, either because of this or due to this, each of these molecules has a mirror plane in the plane of the molecule, bisecting each atom.)
Setting all that aside, the entire process is really #$%*& cool, particularly to a chemist. (Yes, those crazy textbook pictures are often reflected in reality. If only the different atoms were color coded, though!)
True. Even having a decent grasp on the topic (or perhaps, because having a decent grasp), I find it difficult to try to peel apart bond energy, electron density, bond length, etc, from each other; They're all effectively functions of each other and the entire system.
It sounds like you might be more up on this stuff than I am. Since the probe measures force, I was picturing it sort of pushing on the bond and registering the resistance, i.e. the bond energy. But that was just an impression, and I'm certainly no authority on this.
The trouble with all of this is the "picture" is not an actual picture-made-with-photons picture, but a visualization via computer. That isn't to say it's a poor reflection on reality, but that the limitations of the techniques should be accounted for. In this case, the electron density of the overall molecule is being measured. The brighter signals correspond to an increase in local electron density.
In such chemical structures as these, the aromaticity [1] is the main force at play. Without getting too technical, the brighter regions are those with increased electron density. (See figure 4 at the IBM Zurich page on pentacene [2])
The hexagons (and square and pentagons) in fact do not have idealized geometry, but not due to any curling. The unique environment of each carbon is more at play. Symmetry plays a large role; imagine a symmetric vs. unsymmetrical tug-of-war between the carbons with the electrons as the rope. The left hand side and lower right have a dihedral mirror plane, simplifying the density somewhat, where the upper right has a more muddled situation.
Getting back to the flatness, the target molecule is 'mounted' on a suitably uniform surface, such that only one side is being scanned/read by the probe. In a vacuum, the tug of war in the Z direction (into the plane) will cancel out between the +Z and -Z vectors, giving a 'flat' molecule. (Depending on your point of view, either because of this or due to this, each of these molecules has a mirror plane in the plane of the molecule, bisecting each atom.)
Setting all that aside, the entire process is really #$%*& cool, particularly to a chemist. (Yes, those crazy textbook pictures are often reflected in reality. If only the different atoms were color coded, though!)
[1] http://en.wikipedia.org/wiki/Aromaticity [2] http://www.zurich.ibm.com/st/atomic_manipulation/pentacene.h...