Looking Inside Molecules

Imaging with Scanning Tunneling Hydrogen Microscopy

  • Fig. 1: Scanning tunneling hydrogen microscopy image of a monolayer of PTCDA (3,4,9,10-perylenetetracarboxylic-dianhydride) adsorbed on Ag(111) surface.Fig. 1: Scanning tunneling hydrogen microscopy image of a monolayer of PTCDA (3,4,9,10-perylenetetracarboxylic-dianhydride) adsorbed on Ag(111) surface.
  • Fig. 1: Scanning tunneling hydrogen microscopy image of a monolayer of PTCDA (3,4,9,10-perylenetetracarboxylic-dianhydride) adsorbed on Ag(111) surface.
  • Fig. 2: (a) dI/dV(V) spectrum measured in the center of PTCDA  adsorbed on Au(111) in the presence of D2.  G0=(12.9 kΩ)-1 is the quantum of conductance. (b) STM (top) and STHM image (bottom) of PTCDA on Au(111): 1.3x0.7nm2, constant height, recorded with D2 in the junction, V=316mV (STM) and V=-5mV (STHM). The chemical structure formula of PTCDA is shown for comparison. APS 2010, taken from [5].
  • Fig. 3: STHM image of a Au dimer on Au(111) (constant height, V=2mV, D2) (bottom panel) and schematic sketch of contrast generation. APS 2010, taken from [4].
  • Fig. 4: (a-d) Herringbone phase of PTCDA molecules on Au(111). (a) Structure model of the film unit cell. Conventional STM image in constant height mode. (c) STHM image. A two-colour palette has been used. (d) Superposition of the image from (c) with the structure of the herringbone phase in (a). White lines mark possible hydrogen bonds. ACS 2010, taken from [5].
  • Fig. 5: (a) STHM image of a monolayer of PTCDA on Au(111) doped with potassium. (b) The same as in a), but with structure formulas of PTCDA superimposed. White lines indicate O-K bonds visible in b). (c) Structure model of the K/PTCDA/Au(111) phase following from the STHM images. ACS 2010, taken from [5].

Molecular hydrogen (H2) or deuterium (D2) condensed in a low-temperature STM results in a new type of imaging resolution - scanning tunneling hydrogen microscopy (STHM). The microscope operated in the STHM regime images the inner structure of large organic flat lying molecules as well as intermolecular interactions in organic monolayer films.

Scanning tunneling microscopy (STM) is among the few techniques that initiated the nanotechnological revolution. The history of the STM started with the determination of the atomic structure of the famous 7x7 reconstruction of the Si(111) surface. Nowadays the STM is increasingly often applied to the studies of chemically complex systems. One of the examples of such systems are organic molecular films [1]. Fundamental understanding of the structure of such films is a key problem in a variety of research fields ranging from organic electronics to catalysis and biophysics. In general, however, this task remains a challenging problem as, due to their complex chemical structure, the molecules experience numerous types of interactions, a delicate interplay of which finally determines the structure of a molecular film. In such circumstances, an effective microscopy tool resolving the atomic-scale architecture and visualizing the interactions between the individual atomic and molecular species, is indispensable.

Unfortunately the conventional STM does not generally reach the desired imaging conditions since it only images electronic states located in a narrow energy interval close to the Fermi level [2]. Because these states are quite loosely bound to the nuclei, STM micrographs often only vaguely resemble the underlying structure defined by the positions of the atomic cores. To overcome this limitation the STM must become sensitive to another property of the sample, one that closer follows the structure. One of the ways to do that is to add an extra element, a sensor perceptive to the chosen property. To allow readout of the sensor, a transducer, converting the sensor state into the junction conductance, must be employed.

It turns out that the "sensor-transducer" scheme described above is realized when H2 or D2 condenses in the junction of an ordinary STM operating in ultra-high vacuum (UHV) at temperatures below 10K [3].

The gas deposited at such conditions physisorbs on cold parts of the STM, including the sample and the tip. When the gas coverage reaches a certain level, the junction's dI/dV(V) spectra develop characteristic conductance spikes at voltages of ±Vinel (fig. 2a). Such a spectrum means that the junction has a bias dependent structure and can be reversibly switched between two structurally different states. Scanning with the junction in the low-bias state at |V|<<Vinel, we observe a new type of resolution (fig. 1 and the middle panel of fig. 2b) - the scanning tunneling hydrogen microscopy or simply STHM contrast [4]. Strikingly, the STHM images closely resemble the chemical structure of imaged molecules (bottom panel, fig. 2b). The STHM contrast does follow a property different from the density of states (DOS) typically imaged by the conventional STM. Clearly, the observed change is due to the gas molecules present beneath the apex of the STM tip. Interestingly, these molecules are excited away from the tip apex by inelastically tunneling electrons at |V|>Vinel. As a result the junction switches back reversibly into the conventional DOS imaging mode (upper panel, fig. 2b). In this way the same junction can be used in two different imaging regimes by simply changing the tunneling bias: the STHM at |V|<<Vinel and conventional STM regime at |V|>Vinel, as shown in figure 2.

The reversible switching of the structure can be used to compare the conductance behavior of the junction with and without the adsorbed gas [4]. The main feature of the STHM imaging mechanism derived from such comparison is the following: a gas molecule caught in the junction plays a dual role of the sensor and transducer (see the upper panel of fig. 3). The position of the gas molecule relative to the tip can be seen as readout of the nanoscopic force sensor detecting interactions of the gas molecule with the sample. This readout is transduced into the junction conductance by another mechanism based on short-range repulsion acting between the tip and the gas molecule. The repulsive force stems from the Pauli exclusion principle prohibiting any overlap between a closed electronic shell of the molecule and electronic states of the tip. When the gas molecule approaches the tip, its molecular orbitals push away the tip states, thus decreasing the tip DOS at the Fermi level and reducing the tunneling conductance.

We demonstrate the STHM imaging mechanism using the example of a gold adatom dimer on the surface of Au(111) (fig. 3) [4]. As in conventional STM, the adatoms appear brighter than the Au(111) surface, because the sample local DOS at tip positions close to adatoms, e.g., at rt2, is increased with respect to the one at rt1, due to a reduced effective tip-sample distance (cf. the top panel of fig. 3). However in contradiction to conventional STM, on top of the adatoms at the point where the tip-sample distance is the shortest (i.e., at the point rt3) the junction conductance decreases. The reason for the darker contrast can be found in the presence of D2 in the junction. As the tip moves from rt2 to rt3, the D2 molecule will have to move to a new vertical equilibrium position closer to the tip because at that position the stronger Pauli repulsion from the adatom is balanced by a stronger Pauli repulsion from the tip. This must lead to a reduction of the junction conductance. According to figure 3 this reduction overcompensates the rise in DOS and leads to the dark areas in the centers of the adatoms. The analysis of the adatom image shows that it can be understood as an inverted map of the short-range Pauli repulsion, superimposed over the conventional DOS contrast.

On the basis of the dimer experiment we can also describe the STHM contrast shown in figure 2b. As in the case of the dimer, the D2 molecule probes lateral variations of the Pauli repulsion from the surface and transforms it into variations of the junction conductance by the following principle: stronger Pauli repulsion leads to lower conductance. According to that in C6 rings the Pauli repulsion between the surface and the D2 is weaker while on top of a carbon atom or a C-C σ-bond the repulsion is larger.

Although in the cases shown above the STHM contrast followed the Pauli repulsion strength, it seems that other types of interactions can also be imaged with the same approach. According to the "sensor-transducer" model, the transducer converts any changes of the sensor readout into variations of the conductance. The sensor state, however, is defined as the balance between all forces acting on the gas molecule from the surface, the tip and other gas molecules located close to the tip apex. Since H2 and D2 are very light molecules, their dynamics may also play a significant role in the imaging process. As a result, the sensor state might be defined by a complicated interplay of many factors. In some situations, as was shown above, the influence of particular factors, e.g. the Pauli repulsion, prevails over the others. We suggest, however, that such prevalence must not be a permanent effect, but instead can be tuned by changing such experimental parameters as, e.g.: the type of adsorbed gas and its coverage, tip-sample distance, temperature during imaging etc. The picture emerging from such considerations seems to indicate that the full and detailed identification of the imaging mechanisms in STHM might be a difficult problem; on the other hand due to its complexity and sensitivity to many factors the STHM should be able to image subtle effects of the structure and weak interactions. To support that we demonstrate that STHM can image hydrogen bonding as well as interactions between organic molecules and metal ions (fig. 4 and 5) [5]. Although the particular mechanism by which these interactions affect the STHM sensor is yet to be indentified, the amount of information gained from such images is significant. This motivates further developments of the STHM approach into an effective and versatile tool of nanoscale imaging.


[1] Rosei M. et al.: Prog. Surf. Sci. 71 95-146 (2003)
[2] Repp J. et al.: Phys. Rev. Lett. 94 026803(4) (2005)
[3] Temirov R. et al.: New J. Phys. 10 053012 (2008)
[4] Weiss C. et al.: Phys. Rev. Lett. 105 086103 (2010)
[5] Weiss C. et al.: J. Am. Chem. Soc. 132 11864-11865 (2010)



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