Chemistry Labs

Emerging interdisciplinary directions

Atomic-resolution microscopy (AFM, STM, imaging single bonds)

How scanning probe microscopes map surfaces atom by atom and, under carefully controlled conditions, reveal molecular structure and bond contrast.

IntuitionFeeling a surface atom by atom

A scanning probe moves a sharp tip over a surface and records how the tip–sample interaction changes with position. The instrument does not simply photograph atoms: an image is a map of a measured signal, and its appearance depends on the tip, the surface, and the measurement conditions.

Compare constant-height and feedback-controlled scans to see how tip motion and interaction contrast shape a scanning-probe image.

SchoolTwo common scanning probe methods

Definition: Scanning tunneling microscopy (STM)

STM measures a tunneling current between a conductive tip and a conductive or suitably supported sample. The current depends very strongly on their separation and also on the electronic states available near the Fermi level, so bright contrast is not a simple height map.

Definition: Atomic force microscopy (AFM)

AFM senses forces or force gradients between a probe and a surface, often by tracking the deflection or oscillation of a cantilever. In frequency-modulation AFM, shifts in resonance frequency report changes in the tip–sample force gradient; the signal depends on the chosen operating mode.

UndergraduateFrom interaction signal to atomic contrast

I(z)∝e−2κz,κ≈2mΦ/ℏI(z)\propto e^{-2\kappa z},\qquad \kappa\approx\sqrt{2m\Phi}/\hbar

In a simple tunneling model, current falls approximately exponentially with tip–sample separation z; κ depends on the effective barrier height Φ. Thus small changes in separation can cause large current changes. Real STM contrast also reflects the local density of electronic states and tip structure, making interpretation more subtle than topography alone.

Atomic-resolution imaging requires stability against vibration and drift, a clean and well-characterized surface, and a suitable tip. Low temperatures and ultrahigh vacuum often reduce contamination and thermal motion. A convincing assignment compares images or signals across controlled tip conditions and with structural or spectroscopic evidence.

AdvancedImaging individual bonds

Definition: Bond-resolved AFM contrast

A flexible molecule attached to the tip apex can sharpen contrast in noncontact AFM. The apparent lines between atoms can arise from short-range forces and relaxation of the tip-attached molecule; they are not a direct photograph of electron density or a literal image of a bond object.

Functionalizing the tip, often with a CO molecule, can provide submolecular contrast but also introduces mechanical relaxation and chemical sensitivity. Simulations that include tip flexibility and the force channel help distinguish a robust structural feature from imaging artifacts.

ResearchResearch frontier

A defensible atomic-scale interpretation identifies the measured channel and scan mode, documents surface preparation and tip state, tests alternative tip structures, and compares data with simulations or complementary spectroscopy. Reproducibility across preparations is stronger evidence than a single striking image.

References

  • The chemical structure of a molecule resolved by atomic force microscopy · L. Gross, F. Mohn, N. Moll, P. Liljeroth, G. Meyer, 2009
  • Bond-order discrimination by atomic force microscopy · L. Gross et al., 2012
  • Mechanism of high-resolution STM/AFM imaging with functionalized tips · P. Hapala et al., 2014