Samorí , Paolo : Self-assembly of conjugated (macro)molecules: nanostructures for molecular electronics


Kapitel 2. Scanning Probe Microscopies

In this chapter Scanning Probe Microscopies are described in detail, focusing particularly on Scanning Tunneling Microscopy and Atomic Force Microscopy.

2.1 The techniques

The Scanning Tunneling Microscope (STM) [Bin82a, Bin82b], developed in the laboratories of IBM in Zürich in 1981, represents just the first of the family of the Scanning Probe Microscopies (SPM)s, which are a class of surface science instruments that introduced a new simple approach in the investigation of conducting, semiconducting and insulating samples [Wie92,Wie98]. They are based on few common principles:

  1. A sharp probe (tip) interacts with the sample surface;
  2. The tip probes local physical properties of the sample. The tip-sample interaction is very sensitive to small changes in the distance tip-sample;
  3. A piezoelectric circuit allows to perform displacements of the tip and/or the sample in the X, Y, and Z directions with a precision of a fraction of an Ångström;
  4. A feedback system controls the distance tip-sample.

They exhibit:

  1. High vertical resolution (le 0.1 nanometer for AFM and STM);
  2. High lateral resolution (le 1 nanometer for AFM and STM);
  3. Possibility to measure at solid-liquid interfaces, i.e. at surfaces in their native environments;
  4. Possibility to explore non-crystalline samples;
  5. Not or mildly invasive technique.

One of the biggest advantages of SPMs, if compared to Scanning Electron Microscopies (SEM) or Transmission Electron Microscopies (TEM), is the possibility to investigate a


sample outside vacuum, i.e. in air or in a solution. This renders feasible the visualization not only structures, but also dynamic processes that occur on a time scale that spans from few milliseconds to several days.

The STM became the ancestor of all Scanning Probe Microscopies (SPM) that have been developed in the following years. They differ from the type of physical property that governs the interaction tip-sample:

Table 2.1: Main Scanning Probe Microscopies.


Physical interaction tip-sample

Type of samples



Max. lateral resolution

Inventors and year



Electron tunneling

Conductors, semiconductors

W, Pt/Ir

1 Å

Binnig, Rohrer et al. (1981)






Conductors, semiconductors, insulators

W, Si, Si3N4

1 Å

Binnig, Gerber, Quate (1986)



Magnetic forces

Ferromagnetic materials

Ni AFM coated tips

5 Å

Martin, Wickra-masinghe (1987)



Optical properties under the diffraction limit

Conductors, semiconductors insulating adsorbates and biological films

Optical fiber

10 Å

Pohl et al. (1984)



Photon emission from electrons in STM

Conductors, semiconductors

STM tip + photodiode

5 Å

Coombs, Gimzew-ski et al. (1988)



Heat transfer

Conductors, semiconductors insulating adsorbates and biological films


30 Å

William, Wickra-masinghe (1986)



Ion transfer

Conductors, semiconductors insulating adsorbates and biological films

Electrode in a ionic solution

1000 Å


Bard et al. (1986)


SECM = scanning electrochemical microscopy


The SPM is basically composed of 3 parts:

The last two can be controlled by a personal computer or workstation through an analog/ digital converter and a Digital Signal Processing (DSP) card. In all Scanning Probe Microscopes, a piezoelectric scanner behaves as an extremely fine positioning stage able to move the probe over the sample (or the sample under the probe). The SPM electronics drives the scanner in a type of a raster pattern, as shown in Figure 2.1.

Figure 2.1. Scanner motion during data acquisition

The scanner moves across the first line of the scan, and back. It then steps in the perpendicular direction to the second scan line, moves across it and back, then to the third line, and so forth. While the scanner is moving across a scan line, the image data are sampled


digitally at equally spaced intervals. The data recorded is the tip-sample interaction that varies from SPM to SPM. The scan length of the image (L) spans from tens of Ångström to over 100 microns, and from 128 to 512 data points per line. The image is a square grid of measurements (data points).

2.2 Scanning Tunneling Microscopy

The STM can provide an image of the tunneling current in a plane across a conductive sample which, in a first approximation, corresponds to the topographical map of the sample. More accurately, the tunneling current images give evidence of the electronic density of states (LDOS) at the surface [Lan85, Gim87]. STMs can in fact sense the number of filled or unfilled electron states near the Fermi surface, within an energy range determined by the bias voltage [Han87]. Rather than measuring physical topography, it measures a surface of constant tunneling probability.

Figure 2.2: Scheme of the STM junction.

The technique is based on the quantum-mechanical effect of electron tunneling. The tunneling occurs between two conductors separated by a gap (or insulating layer), that acts as a potential barrier for the electrons. The tunneling current decays exponentially with the gap width. This causes the current signal to be determined by the tip apex as shown in Fig. 2.2 and it permits a lateral resolution of ~1 Ångström to be achieved [Gim87]. The tunneling current can be estimated by:



V = bias potential between tip and sample;

s = gap width;

phi-gr = average barrier height between the two electrodes (~4 eV).

Roughly, a variation of the gap of one Ångström gives rise to a variation of the tunneling current of one order of magnitude. Because of this reason a vertical resolution of fractions of an Ångström can be reached.

Figure 2.3: Energy diagram explaining tunneling in STM experiments

In the STM apparatus the two electrodes are the sample and an atomically sharpened metallic probe; this latter one is usually produced by cutting or chemical etching of a Pt/Ir or W wire. When the tip is brought into close proximity of the sample surface (few Ångströms), applying a bias voltage (< 1.5 V) between the two electrodes causes the electrons from the sample to tunnel through the gap into the tip or vice versa, depending upon the sign of the bias voltage [Ter83]. (See Fig. 2.3). The resulting tunneling current varies with the tip-to-sample spacing, and it is this signal which is used to create an STM image. A big limitation of STM is that it cannot image thick insulating layers. Having the possibility to probe currents in the picoampere range, the thickness of an insulating layer can be at maximum ~ 15 - 20 Å.


2.2.1 STM modes

The STM can be constructed to scan a sample in either of two modes: constant-height or constant-current mode, as shown in Fig. 2.4.

Figure 2.4: Comparison of constant-height and constant-current mode for STM.

In constant-height mode, the tip scans in a horizontal plane above the sample and the tunneling current changes depending on the topography and the local surface electronic properties of the sample. The tunneling current measured at each point on the sample surface represents the data set.

In constant-current mode, the STM uses a feedback loop that enables the tunneling current to be constant by adjusting the height of the scanner at each measurement location. For example, when the system detects an increase in tunneling current, it adjusts the voltage applied to the piezoelectric scanner in order to enhance the distance between the tip and the sample. In constant-current mode, the motion of the scanner constitutes the data set. If the system keeps the tunneling current constant to within a few percent, the tip-to-sample distance


will typically be constant to within a few hundredths of an Ängström.

Each mode has advantages and disadvantages. Constant-height mode is faster because the system does not have to move the scanner up and down, but it provides useful information only for relatively smooth surfaces. Constant-current mode can measure irregular surfaces with high precision, but the measurement takes more time and the lateral resolution that can be achieved is usually smaller due to the difficulty in setting a proper feedback loop which allows contemporary the tip to follow the surface prosperities and not to introduce a periodic noise in the dataset.

The STM offers the possibility to perform a spectroscopical investigation of the sample down to a sub-nanometer scale using the Scanning Tunneling Spectroscopy, (STS) mode [Wie98,Fee94,Sta95b]. The tip is “frozen“ at a well specific distance to the sample surface (position) and at an increasing voltage (U) (between a selected range within -10 V and 10 V) dI/dU is sampled The resulting curve ((dI/dU)=f(U)) can usually be attributed to structure in the electronic density of states.

2.2.2 Applications of STM

The STM had a big success due to the high resolution imaging that can be achieved.


The first samples that have been studied with this technique were metal surfaces. Binnig and co-workers observed the reconstruction of the Au(110) surface [Bin83a]. Later the structure of several other metals have been monitored such as Pt(100) and (110), Pd(100), Ir, Au(100), Ag(111) [Wie92]. These investigations have been carried out either in UHV or air environments.

Inorganic semiconductors:

A breakthrough for the high resolution imaging with STM was the observation of the 7x7 reconstruction of Si (111) according to the model of Takayanagi [Iss91]. Another compound


deeply investigated is GaAs [Fee87]. Because of the fast oxidation of this surfaces, these studies have been executed in UHV ambient.

Organic adsorbates:

The STM has been used to monitor the structure of thin organic layers at the solid-liquid interface and in dried films, produced both from solution and from UHV sublimation.

The investigations at the solid-fluid interfaces started from the pioneering work of J.S. Foster and J.E. Frommer on liquid crystals [Fos88, Smi89, Spo89]. It was continued with investigations of small molecular systems at the interface between an almost saturated solution and a crystalline conductive substrate by J. P. Rabe and coworkers on alkanes, alcohols, fatty acids [Rab91a], didodecylbenzene [Rab91b], conjugated oligomers [Bäu95] and a variety of other chemical species. In this environment the resolution in space and in time made it possible to monitor dynamic processes such as coarsening of molecular interfaces [Sta95a], photodecompositions [Hei94] and photopolymerizations [Gri97]. With the same set-up the electronic properties of single molecules have been measured by means of STS [Sta95b].

Studies of UHV sublimed thin films have been performed on naphtalene [Hal91] and azulene derivatives and later porphyrin moieties adsorbed on metal surfaces [Jun97]. Chemisorbed species as Self-Assembled Monolayers of thiol functionalized molecules have been widely investigated on several metallic substrates (Au, Ag, Pt, Pd, Cu) [Ulm91].

Biological samples:

The possibility to observe molecular systems in their native medium was very appealing and has constituted the main reason why biologists have put a big effort into this technique since the early years. The limitations were due to the small electronic conductivity of these kinds of materials. This problem was partly overcomed either by using an STM able to detect currents in the picoampere range [Guc94] or by coating the sample with a conductive layer (e.g. of gold or amorphous carbon).


2.3 Atomic Force Microscopy

The invention of Atomic Force Microscopy (AFM) [Bin86, Rug90] in 1986 also by Binnig and co-workers has solved the problem of imaging samples with a low electrical conductivity. In fact the physical properties that are measured with this apparatus, namely the interaction forces between a sharp conical tip and the sample surface, allow investigations to be performed on electrical conductors as well as on semiconductors, on organic and also on biological materials.

Figure 2.5: The beam-bounce detection scheme.

AFM probes the surface of a sample with a sharp tip, with a terminal radius often less than 100 Å. The tip is located at the free end of a ~ 100µm long cantilever that has got an elastic modulus that can reach tenths of N/m. Forces of a few piconewton between the tip and the sample surface cause deflections of the cantilever in the Ångström spatial scale. A laser beam bounces off the back of the cantilever onto a position-sensitive photodetector (PSD). As the cantilever bends, the position of the laser beam on the detector shifts. The PSD itself can measure displacements of light beams as small as 10 Å. The ratio of the path length between the cantilever and the detector to the length of the cantilever itself produces a mechanical amplification. As a result, the system can detect sub- Ångström vertical movements of the cantilever tip. The measured cantilever deflections enable the computer to generate a map of surface topography. This apparatus can be called also Scanning Force Microscopy, that is its suitable name in particular for studies carried out in a micrometer and sub-nanometer scale.

The interaction forces in the AFM are often quite complex due to several factors:

Even if the tip apex should be monoatomic, the number of atoms from the tip involved in the interaction is not one, due to the contribution of rather long range forces;


The forces are dependent on the environment (gas, liquid or vacuum);

The scan is a dynamic process, which means that velocity dependent forces need to be considered;

The tip can deform the sample.

2.3.1 Classification of forces

It is important to distinguish the type of forces between the tip and the sample in order to separate the contributions and correctly interpret the experimental results. [Isr92]

Long range forces

van der Waals forces: exist between every types of atoms or molecules; they are proportional to 1/r6 where r is the distance between them. The role of these forces in AFM have been discussed by Moiseev [Moi88] and Hartmann [Har90]. They are important in the range from one to tens of nanometers.

  1. Electrostatic forces: they are due to coulombic interactions; in the present case they can occur between an electrostatically charged tip and a charged area of an insulating surface. They are important in the range from one to thousands of Ångström.
  2. Capillary forces: the curvature at the contact between the tip and the sample causes the condensation of vapor from the ambient including water from the air. Also surfaces exposed to the air environment are typically coated by a layer of water, whose thickness depends on the relative humidity (RH) of the atmosphere and on the physico-chemical nature of the object. It results in a strong attractive capillary forces (about 10-8 N) that hold the tip in contact with the surface. To avoid capillary forces the ambient humidity must be at RH=0%, although Thundat and co-workers demonstrated that below RH=10% they could not detect decays any further of the capillary forces [Tun93]. Two simple experimental procedures can minimize the effect of this kind of forces:


  1. flood a sealed chamber for the measurements with a dry inert gas such as N2 , He or Ar;
  2. make use of a fluid cell, that means to perform measurements with both the tip and the sample immersed in a liquid medium [Wei92].

Short range forces

  1. Repulsive forces: They are proportional to 1/rn with n>8. The interatomic repulsion forces have two origins:
  1. Repulsion between nuclei: the overlap of two electronic clouds gives rise to an incomplete screening of the nuclear charges; this generates coulombic repulsions.
  2. Pauli repulsion: according to the exclusion principles of Pauli, two electrons with the same spin can not occupy the same orbital. Thus the electrons can only overlap when the energy of one electron is increased, which causes a repulsive interaction.
  1. Forces of covalent bonds: they originate from the overlap of the wave functions of two or more atoms. In this case the density of electric charges is concentrated between the two nuclei. This force decreases abruptly for a separation over a few Ångström. The type of interaction can be also called chemisorption.
  2. Metallic adhesion: they derive from the interaction between strongly delocalized electronic clouds, which cause strong interactions that decay exponentially with distance. They are important when two metallic surfaces approach to the extent that the electronic wave functions overlap [Ban90]. This case can be called also physisorption.
  3. Friction: during the scan, there is a force component parallel to the surface, since the tip is not always oriented exactly perpendicular to the surface. This friction tends to twist the cantilever, and since the torsion angle depends on the composition of the surface, the measurement of the twist provides chemical information [Mat92]. It was also shown that this kind of friction force can be detected on the atomic scale [Mat87].


As a first approximation the forces contributing to the deflection of an AFM cantilever can be considered the Van der Waals and the repulsive forces. These contributions are on the basis of the Lennard - Jones potential:


epsilon0/4 = potential energy at the minimum;

sigma = effective molecular diameter;

r = interatomic distance.

Figure 2.6: Interatomic force vs. distance curve.

The force, which is the negative gradient of the energy, is plotted in Fig. 2.6. Two distance regimes are highlighted: 1) the contact regime; and 2) the non-contact regime. In the contact regime, the cantilever is held less than a few Ångström from the sample surface, and the interatomic force between the cantilever and the sample is repulsive. In the non-contact regime, the cantilever is held on the order of tens to hundreds of Ångström from the sample surface, and the interatomic force between the cantilever and sample is attractive (largely a result of the long-range van der Waals interactions). Both contact and non-contact imaging techniques are described in detail in the following sections.


2.3.2 Contact mode AFM

In contact mode AFM a tip makes soft "physical contact" with the sample. The tip is attached to the end of a cantilever with a spring constant, lower than the effective spring constant holding the atoms of the sample together. As the scanner gently scans the tip across the sample (or the sample under the tip), the contact force causes the cantilever to bend in order to follow the topographic profile. Using very stiff cantilevers it is possible to exert large forces on the sample and the sample surface is likely to get deformed; this may be also used in "nanolithography". The total force that the tip exerts on the sample is the sum of the capillary plus cantilever forces, and must be balanced by the repulsive van der Waals force for contact AFM. The magnitude of the total force exerted on the surface varies from 10-8 N (with the cantilever pulling away from the sample almost as hard as the water is pulling down the tip), to the more typical operating range of 10-7 to 10-6 N.

Similarly to STM, the contact mode AFM can generate the topographic data set by operating in one of two modes - constant height or constant force mode.

In constant height mode, the spatial variation of the cantilever deflection can be used directly to provide the topographic data set because the height of the scanner (consequently also the distance sample surface - tip holder) is fixed as it scans.

In constant force mode, the deflection of the cantilever is used as input to a feedback loop that moves the scanner up and down in Z-direction, responding to the topography by keeping the cantilever deflection constant. In this case, the image is generated from the scanner's motion. With the cantilever deflection held constant, the total force applied to the sample is constant. In constant force mode, the speed of scanning is limited by the time of response of the feedback loop, but the total force exerted on the sample by the tip can be controlled. This mode is usually preferred for most applications because it gives a real topographic map of the sample surface. Constant height mode is often used for recording atomic-scale images of atomically flat surfaces, where the cantilever deflections and thus variations in the applied force are small. This latter mode is also essential for monitoring fast processes in real-time, where high scan rates are essential.


2.3.3 Vibrating Modes

In order to overcome the problem of the friction component during scanning in contact mode, to minimize the forces exerted from the tip on the sample and the effect of the capillary forces, alternative modes have been invented where the AFM cantilever vibrates near (on the order of tens to hundreds of Ångströms) the surface of a sample (Fig. 2.7). Basically, stiff cantilever is forced to oscillate near its resonant frequency (typically from 200 to 400 kHz) with an amplitude of a few hundreds of Ängströms. While the tip scans over the sample the system detects the shift in the phase and the gradient in the amplitude of the swing of the cantilever and keeps it constant with the aid of a feedback system that moves the scanner up and down. By keeping the amplitude constant, the system is expected to also keep the average tip-to-sample distance constant. The sensitivity of this detection scheme provides sub-Ängström vertical resolution in the image, as in contact AFM. Due to the elimination of the shear forces that are applied from the tip to the sample, these modes are particularly useful for studying soft materials such as biological and organic films. As a consequence of the reduction of the overall interaction forces between the tip and the sample surface, these modes do not suffer from tip or sample degradation effects that are sometimes observed after taking numerous scans with contact AFM. Unfortunately, the lateral resolution that can be reached is a few nanometers, which is lower than in the contact mode. Non Contact AFM (NC-AFM)

In this mode the tip-sample interaction is indicated on the force-distance curve of Fig. 2.6 as the non-contact regime. Because the force between the tip and the sample in this regime is low (generally about 10-12 N), the force measurement is more difficult than in the contact regime, where it can be several orders of magnitude larger. Furthermore, cantilevers used for NC-AFM must be stiffer than those used for contact AFM because soft cantilevers can be pulled into contact with the sample surface. The small force values in the non-contact regime and the greater stiffness of the cantilevers used for NC-AFM are therefore both factors that limit the force resolution, and consequently the lateral resolution, that can be achieved.


Figure 2.7: Vibrating modes: the tip-sample interaction affects the amplitude and phase of the swing. Tapping Mode™

Tapping Mode™ (TM-AFM) or intermittent-contact atomic force microscopy (IC-AFM) is similar to NC-AFM, except that for TM-AFM the vibrating cantilever-tip is brought closer to the sample so that at the bottom of its travel it just barely hits, or "taps" the sample [Zho93, Tam96,Bus95]. The intermittent-contact operating region is indicated in the force-distance curve in Figure 2.6. Some samples are best handled using TM-AFM instead of contact or non-contact AFM. In general, it has been found that TM-AFM is more effective than NC-AFM both for imaging larger scan sizes, that may include greater variations in sample topography, and for the slightly higher resolution that can be achieved, due to the stronger tip-sample interaction forces that are sampled. The latest development of the Phase Imaging, where the gradient in phase of the vibrations is detected, made it possible to increase further the spatial resolution [Lec96,Fin97,Sto98a]. This imaging mode provides contrast caused by differences in surface adhesion and viscoelasticity; it is therefore very helpful for detecting different phases coating the sample surface.

2.3.4 Applications of AFM

Layered materials:

They represent a family of substrates which are atomically flat on a micrometer scale, and which are easy to prepare freshly by cleaving the surface with an adhesive tape.

Graphite: Highly Oriented Pyrolitic Graphite (HOPG) was the first material to be resolved with lattice resolution [Bin87]. It is commonly used as standard for the calibration of the scanner in all the 3 dimensions.

Mica: is widely used for deposition of organic and biological samples [Sha93], it is also ordinarily utilized, in place of HOPG, to calibrate scanners on a sub-nanometer scale.


Dichalcogenides are also extremely flat and suitable for studies also with STM (due to their metallic or semiconducting properties that vary with the chemical composition). Well-known examples are MoS2 [Lie91], NbSe2 [Kim91] and ReS2 [Kel94].

Ionic Crystals:

LiF, NaCl, PbS and AgBr are some of the inorganic crystals that have been investigated achieving atomic resolution imaging [Hei92].

Organic molecules:

The structure of films prepared by the "Langmuir Blodgett" technique have been monitored for the case of barium arachidate [Bou93] and stearic acid [Chi93]. Only few studies have been carried out on single crystals, as for example tetracene [Ove91]; one reason being that this type of investigation does not give more information than a typical X-Ray analysis.

The use of SFM is more suitable for the investigation on the self-assembly of (macro)molecules adsorbed at surfaces either by vacuum sublimation [Bis95] or from solution [Sam99a]. The SFM can be also used to probe interactions between functional groups (CH3- CH3, COOH-CH3, COOH-COOH) by functionalizing the SFM tip and measuring the interaction forces between the tip and the substrate [Fri94] or by breaking chemical bonds and gaining insights into the strength of different chemical interactions [Gra99].

Biological samples:

The possibility to visualize the surface of insulating biologic materials in their native physiologic environment renders this technique interesting for biophysical and biomolecular investigations. Research includes investigations on tissues, microorganisms, cells down to nucleic acid molecules and their super-hierarchical organization. An example of dynamic process that has been visualized is the Escherichia coli RNA polymerase (RNAP) transcribing two different linear double-stranded (ds) DNA templates [Kas97]. It was also possible to monitor the modification of the quaternary structure induced by bonding with an enzyme [Eri94].

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