Lab Course STM

Advanced Lab Course: Scanning Tunneling Microscopy
- 1 -
Universit de Strasbourg
Chimie Physique des Molcules et des Interfaces

Scanning Tunneling Microscopy of 2D-Molecule Crystals
at the Solid / Liquid Interface

Vers. 1.0, jan 2011 A.Cadeddu

Persons in charge: Andrea Cadeddu, Artur Ciesielski
cadeddu@unistra.fr ciesielski@unistra.fr
Room 126 Nanochemie, Isis

1. Topic

In this experiment, two-dimensional organic molecular crystals will be generated at the solid /
liquid interface on graphite and imaged time dependently in situ with a scanning tunneling
microscope (STM) with sub-molecular resolution. The unit cell of the molecular lattice and its
orientation relative to the graphite lattice will be determined. If domain boundaries are visible
in the molecular lattice, their structure and dynamics will be studied additionally.

2. Duration: 1 day

The protocol is due after one week at the latest!

3. Literature

/1/ J.P. Rabe, S. Buchholz, Commensurability and Mobility in Two-Dimensional Molecu-
lar Patterns on Graphite, Science 253 (1991) 424-427

/2/ J.P. Rabe, S. Buchholz, Direct Observation of Molecular Structure and Dynamics at
the Interface between a Solid Wall and an Organic Solution by Scanning Tunneling
Microscopy, Physical Review Letters 66 (1991) 2096-2099

/3/ L. Askadskaya, J.P. Rabe, Anisotropic Molecular Dynamics in the Vicinity of Order-
Disorder Transitions in Organic Monolayers, Physical Review Letters 69 (1992)
1395-1398

Create PDF files without this message by purchasing novaPDF printer (http://www.novapdf.com)
- 2 -
4. Introduction

4.1. The scanning tunneling microscope (STM)

4.1.1. Basic principle

Historically the scanning tunneling microscope (STM) is the first representative of the family
of scanning probe microscopes (other representatives are e.g. the scanning force microscope
and the near-field optical microscope). The
basic principle of these microscopes is to raster
scan a probe with small lateral dimensions and
a distance-dependent interaction with the sam-
ple surface in close proximity over the surface.
The interaction with the sample and therefore
the distance of the probe over a homogenous
sample can be kept constant with a feedback
loop. The output of the feedback loop, plotted
as a function of the xy-position of the probe,
gives a contour image of constant interaction.
For homogenous samples this corresponds in
good agreement with the sample topography.

In STM, the probe consists of a fine wire tip (tunneling tip): an atomically sharpened metallic
Probe usually produced by cutting or chemical etching of a Pt/Ir or W wire, and the interac-
tion is the tunneling current.
Classically it is impossible for an electron to
overcome a potential barrier which is higher
than its own energy. However, quantum me-
chanically there is a finite possibility that this
will happen (Fig. 2).
The STM can provide an image of the tunnel-
ing current in a plane across a conductive
sample which, in a first approximation, corre-
sponds to the topographical map of the sam-
ple. More accurately, the tunneling current im-
ages give evidence of the electronic density of
states (LDOS) at the surface. 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.
Rather than measuring physical topography, it
measures a surface of constant tunneling probability. The (semi-)conducting sample is electri-
cally contacted and a tunneling voltage ranging from a few millivolts to a few volts is applied
between the tip and the sample. Reducing the distance between sample and tip leads to an on-
set of the tunneling current below distances on the order of 1 nm. The magnitude of the tun-
neling current is in the nanoampere range and decays exponentially with increasing tip-
sample distance, as the amplitude of the electron wave decays exponentially inside the poten-
tial barrier.

Fig. 2:
The difference between classical physics and quan-
tum mechanics, demonstrated with the example of a
potential barrier.

Fig. 1: Schematic design of an STM. Inset: atomi-
cally resolved graphite in air, 60C, scan length 1.4
nm. Taken from /3/
- 3 -

= 1 0 / ( )
V = bias potential between tip and sample;
s = gap width;
u = average barrier height between the two electrodes (~4 eV).

Roughly, a variation of the gap of one ngstrm 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 ngstrm can be reached.

When the tip is brought into close proximity of the sample surface (few ngstrms), 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.
(See Fig. 4). 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 .

4.1.2. Feedback loop and piezo elements

The tunneling current is kept constant by an electronic feedback loop in order to keep the dis-
tance between tunneling tip and the sample surface constant. The feedback loop measures the
actual tunneling current and compares it with the value given by the operator (set point or ref-
erence input). If these differ from each other, the feedback loop tries to eliminate the differ-
ence with its output (actuating signal). The speed of the feedback loop can be influenced with
two parameters, the integral part (I-gain) and the proportional part (P-gain). The I-gain pri-
marily determines the speed with which the feedback loop reacts to deviations: high I-gains
mean high speed. The P-gain determines how strongly proportional the feedback loop reacts
to deviations: a high P-gain means a strong reaction of the feedback loop.

The feedback parameters strongly depend on the tip and the sample and on the mechanical
stability of the STM and can not be set arbitrarily high. In addition, the feedback loop is in it-
self an oscillatory system with a limiting frequency, above which the feedback loop oscillates
at its resonance frequency. These oscillations can lead to damage of the tip and the sample. If
the feedback loop cannot be set fast enough to image the sample topography satisfactorily for
a given scanning speed, then the scanning speed must be reduced accordingly. In that way, the
data rate that must be processed by the feedback loop is reduced and can be made processable

Fig. 4
Schematic energy diagram for the tun-
neling contact between a metallic tip
and an adsorbate-covered metal sur-
face. Left tunneling contact: negative
sample potential; right tunneling con-
tact: positive sample potential.

- 4 -
at the lower scanning speed. In that sense, the scanning speed can be viewed as a further feed-
back parameter.

The changes made by the feedback loop are transmitted to the tunneling current via the piezo
elements (actuators, control elements), which move the tunneling tip in xyz-direction. Piezo
elements are made out of piezoelectric ceramics, which can change their outer dimensions if a
bias is applied (piezoelectric effect). With suitably dimensioned piezo elements, mechanical
movements ranging from the sub-ngstrm regime up to many tens of microns can be real-
ized. On the one hand, the piezo elements keep the tunneling tip at a constant distance over
the sample surface, on the other hand they simultaneously raster scan the tip over the surface.

4.1.3. Topography images and current images
During the measurement two signals are plotted on the monitor in dependence of the xy-
position of the tunneling tip: the first is the feedback loop output, i.e. the voltage applied by
the feedback loop to the piezo elements in order to keep the tip at a constant distance over the
sample surface. This corresponds to the sample topography. The second is the actual tunneling
current, which can be interpreted as the error signal of the feedback loop. If the feedback loop
were ideal, i.e. arbitrarily fast, the tunneling current would be constant at all times and no con-
trast would be visible in this image. Any deviations of the actual current value from the set
point are visible in the current image. If, however, the feedback loop is set considerably too
slow, the tip is unable to follow the topographical contours and contrast is lost in the topogra-
phy image. At the same time the error signal of the feedback loop is accordingly larger, i.e. the
contrast increases in the current image.

These two extreme cases are called constant current mode (feedback loop as fast as possible,
contrast completely in the topography channel) and, somewhat misleading, constant height
mode (feedback loop extremely slow, contrast entirely in the current channel, no z-movement
of the tip constant height). The constant height mode has the advantage over the constant
current mode in that it enables much higher scanning rates, because the feedback loop no
longer poses a limitation. Since the tunneling current signal is always superimposed with a
frequency dependent noise signal that declines at higher frequencies (1/f-noise), a shift of
the measuring signal to higher frequencies through faster scanning speeds leads to an im-
provement in the signal to noise ratio. In addition, the influence of temperature drifts is re-
duced by the faster image acquisition. A disadvantage is that the constant height mode can on-
ly be used at sufficiently small scan lengths and flat surfaces, because the tip would otherwise
hit the surface.

For the STM used here, typical P and I gain values for the constant current mode are between
1 and 2.

4.2. Physisorption of (macro)molecules at a solid-liquid interface

The interplay between enthalpy and entropy governs the process of self-assembly at solid-
liquid interfaces. Molecules tend to physisorb into a tightly packed monolayer on a solid sur-
face such as HOPG since upon adsorption the system gains an amount of enthalpic energy,
which is roughly proportional to the chain length and number of the adsorbed molecules, thus
to the overall number of building blocks adsorbed at the surface. The acquired enthalpy must
compensate for the loss in entropy upon formation of a tightly packed 2d-crystal. Indeed two
different types of entropy play a role during the adsorption process: (a) an internal entropy,
related to intra-molecular degrees of freedom and (b) an external entropy, namely the trans-
- 5 -
lation entropy. While (a), similarly to the enthalpic gain, is proportional to the overall number
of building blocks adsorbed to the surface, (b) is a constant contribution for each single chain,
independently from the chain length. According to this, in the case of the adsorption of a mix-
ture of molecules possessing different lengths, namely a polydisperse system, (b) favors the
adsorption of longer chains because they lose less amount of translational entropy per unit
mass.
Nevertheless, in the present advanced lab course, a monodisperse molecular system will be
studied.

4.3. Moir patterns

The aim of the experiment is
to determine the lattice param-
eters of a 2D molecular crystal
relative to the graphite sub-
strate. An in situ calibration of
the STM with the graphite
substrate with known lattice
constants (a = 246 pm) can be
used to determine the lamella
width AL and the orientation of
the molecule axis A and the
lamella axis L relative to a
graphite axis C.

In order to determine these
values with a higher accuracy
than is possible with a direct
STM measurement, due to its
intrinsic problems such as e.g.
image distortion, Moir pat-
terns stemming from the adsorbate and substrate lattices will be exploited. These patterns, in
conjunction with the graphite lattice parameters known extremely precisely from x-ray dif-
fraction, allow the lattice parameters of the molecular crystal to be determined with an en-
hanced accuracy.

Molecular rods tend to pack in lamella (fig. 5) with a main axis L and widths AL. The inter-
molecular distances AA are determined perpendicular to the main molecular axis A. In the
STM images, the contrast of the molecules can vary along L due to the molecular distance as
well as with a period AM, which is markedly larger than the molecular distance AA. This vari-
ation of contrast results from a beating between adsorbate and substrate lattice frequencies. It
is also called intralamellar Moir pattern. A similar interlamellar variation can also be seen
between neighboring lamellae (interlamellar Moir pattern). Here we will only be interested
in the intralamellar Moir pattern.

Fig. 5:
Clarification of the used no-
menclature for an arbitrary
molecular crystal:
A: main molecule axis
L: lamella axis
C: graphite axis (zigzag)
AA: intralamella molecular
distance
AL: lamella width
AM: Moir period
: lamella angle between
L and C

- 6 -
The Moir pattern is due to a beating caused by a mismatch between the adsorbate and sub-
strate lattice. As indicated in fig. 6, long chain alkanes form a commensurable packing on
graphite, i.e. the alkane separation is a multiple of the graphite lattice constant. The alkane
chains occupy every second carbon row of
the graphite (intralamellar distance AA =
426 pm). For end-functionalized alkyl
chains, however, often a not simply com-
mensurable packing relative to the graphite
lattice is observed (AA > 426 pm). This is
due to the increased space requirements of
functional groups compared to a simple me-
thyl group or to the directed interaction of
the end groups among each other. Therefore,
the single molecules cannot occupy identical
adsorption sites any more, and an equivalent
adsorption site is available only after a cer-
tain number of molecules. Since only equiv-
alent adsorption sites lead to the same tun-
neling contrast, a modulation of the tunnel-
ing contrast results. The period of this modu-
lation is called the Moir period AM or coin-
cidence period and is measured parallel to the lamella axis L. The molecular distance AA can
be calculated from this period with the following formula:

AA
b x
x
=
+ ( ) 2 1
(1)
where x is the number of alkyl chains within AM,
x e 9
+
and b = ( )
1
2
3 246 pm (see fig.7).

Applied to the model depicted in fig. 5, the formula
gives:

Fig. 7:
Graphite lattice with the lattice constant a =
246 pm and the distance
between parallel graphite axes.

Fig. 6:
Reason for the intralamellar Moir pattern. Model
of a simply commensurable and not simply com-
mensurable packing of alkyl chains on graphite. b
denotes the distance of parallel graphite axes, MA
denotes the Moir period.
- 7 -
5. The experiment

5.1. Mixing of the organic solution

The organic molecule arachidic acid (CH
3
-(CH
2
)
18
-COOH) will be used. If the experiment
goes very well, two further molecules can be used, namely octadecanol (CH
3
-(CH
2
)
16
-
CH
2
OH) and dotriacontane (C
32
H
66
). First of all, a saturated stock solution must be made. For
that purpose, 20 mg of the molecules are dissolved in 0.5 ml phenyloctane. 0.2 ml of this
stock solution are then further diluted by 10%, i.e. 20 l phenyloctane. This second solution
will be used for the experiment.

5.2. Imaging of the clean graphite surface

The steps necessary to get the first tunneling image, i.e. mounting of the tip and sample and
operation of the software, will be performed by the persons in charge.

Before adding the molecule solution, it must be ensured that the tunneling tip has a sufficient-
ly high resolution. This can be demonstrated by imaging the graphite lattice. If the tip cannot
produce a stable image of graphite straightaway, then it must be exchanged. Typical tunneling
parameters are 0.5 1 nA and +10 +100 mV. The feedback gains should be around 1 2,
resulting in the contrast being mainly in the current image.

The sample drift can be estimated by looking at the atomic graphite lattice. If it is too big,
then the lattice appears distorted and drifts with time in a fixed direction. Once the hexagonal
lattice is imaged more or less undistorted, a few images should be saved. They will be needed
later to determine the orientation of the molecular lattice relative to the graphite.

5.3. Imaging of the 2D molecular crystal

In order to apply the molecule solution to the graphite surface, the tip must be withdrawn
slightly from the surface by clicking on the button WITHDRAW. However, it should not be
withdrawn much further, because the solution must make a meniscus between the tip and the
surface. This meniscus makes the solid / liquid interface at which the experiment will be per-
formed.

Take a small amount of solution out of the vial with a syringe. Very slowly, squeeze out a
droplet of solution, so that it is still hanging from the syringe. Approach the syringe very care-
fully to the graphite surface and let the droplet run down the graphite surface. This step is crit-
ical! Lack of caution can damage the tip and the sample! Make sure a meniscus has indeed
been created by looking through the optical microscope. Now put back the Faraday cage and
the glass cover on the STM and reapproach the tip to the sample. Be sure the feedback param-
eters are fast enough, otherwise the tip can be damaged by touching the sample! I- and P-gain
should be at 1 2.

Check that the tip has survived the procedure by imaging graphite again. This is also im-
portant to see if the tip is over a flat part of the sample, because after withdrawing and reap-
proaching the tip is generally at a different sample position than before. The application of the
solution can also reintroduce a higher temperature drift into the system.

- 8 -
If the graphite lattice is again imaged relatively free of distortion, the gap voltage can be in-
creased step-by-step. The gap voltage must be increased in order to image the molecular layer.
At low gap voltages of a few 10 mV the tunneling current flows mainly through the orbitals of
the graphite atoms, whereas at voltages around and above 1 V it flows primarily through the
molecular orbitals. Consequently the graphite lattice is imaged at low gap voltages and the
molecule lattice at higher voltages. Sometimes both lattices can be imaged simultaneously at
intermediate voltages of a few 100 mV. Change the voltages and currents in small steps and
give the system some time to adjust to the new parameters.

The formation of the molecular lattice needs a certain time, which can vary from experiment
to experiment. It is also necessary that the STM be stable and have high resolution in order to
resolve the lamellae. Both can be repeatedly checked by imaging the graphite lattice. This can
be done by reducing the gap voltage back to values around a few 10 mV. One can help to in-
duce the ordering process of the molecules with voltage pulses, starting at low values of 5 6
V and going higher if needed. At some time, the lamellae will vaguely become visible. Often
they are initially only visible in small areas of a few nanometers, but then spread in time over
the entire image. With luck domain boundaries and their temporal fluctuations can be seen!

6. Problems and evaluation

- Image the clean graphite surface. Use different scan widths down to atomic resolution.
Calibrate the STM with the graphite lattice and determine the error margin of the calibra-
tion.
- Make the organic solution and apply a droplet to the tunneling contact. Image the graphite
lattice again for the later analysis of the Moir pattern.
- Image the 2D molecular lattice. Take images at various scan lengths in order to determine
the lamella width, the angle between the lamella axis and the graphite axis and the orienta-
tion of the single molecules within the lamella.
- Make sure the Moir pattern can be clearly seen. By analyzing the Moir pattern, deter-
mine the lattice parameter of the molecular lattice and its orientation relative to the graph-
ite lattice.
- If various domains can be imaged: along what directions do the domain boundaries run? Is
there an interphase between the domains? How stable is it?

7. Acknowledgments
We thank Prof. J.P. Rabe (Humboldt University, Berlin) for sharing with us the instructions
for STM exercises.

Lab Course STM

Uploaded by

Document Information

Original Description:

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Lab Course STM

Uploaded by

Copyright:

Available Formats

Advanced Lab Course: Scanning Tunneling Microscopy

You might also like