Molecular imaging, using STM and AFM technologies, appear so far to visually prove most of what we already know about chemical structures, such as VSEPR theory. For instance, here are the ideal structures and AFM of a couple of cyclization reactions:
We've also taken single-atom imaging to pretty scary levels. Behold a field emission electron microscope image of the s and p orbitals of carbon, long relegated to conceptual mathematical images in textbooks:
The question is, have there been any surprises to be had from these images, where something we thought was structured one way was in fact radically different? You can see in the AFM image that some of the bond angles deviate from the ideal regular shapes a little, and it may also be that the electrons in the pi bonds, instead of being regularly distributed, seem to prefer the "far" end of the phenyl rings, but the predicted structures are uncannily accurate. Again, with the orbital imaging, the s orbital isn't perfectly spherical and we don't see the full p-orbital shell, just two "lobes", but again, they're powerful evidence that our theories are right so far.
Has this ever not been the case? Have any of these recent images turned chemistry on its head by showing something totally unexpected?