Studies of self assembled monolayers on highly oriented pyrolytic graphite using scanning tunneling microscopy and computational simulation 2

EXPERIMENTAL
CHAPTER 2
EXPERIMENTAL

2.1 Scanning Tunneling Microscopy (STM)
There are many modern instruments for surface structural and chemical analysis
such as the Field Ion Microscope (FIM), the Field Emission Microscope (FEM),
Low-Energy Electron Diffraction (LEED), Scanning Electron Microscope (SEM),
Electron Spectroscopy for Chemical Analysis (ESCA), Transmission Electron
Microscope (TEM), etc. The development of these techniques has played an
important role in the field of surface science. However, each of these techniques has
certain strengths and limitations. LEED and X-ray diffraction techniques rely on
large-scale order of the surface, and can at best give averaged information about local
and defect structures; SEM requires samples with strong corrugation or mass contrast
and its resolution is not high enough to resolve surface atoms. High-resolution TEM
can in some cases resolve features with atomic dimensions of specially thinned
samples. However this can be accomplished only by aligning the electron beam with
the rows of atoms in a crystalline lattice. FEM and FIM are only able to probe the
two-dimensional geometry of the atomic structure on the surfaces of sharp tips with
radii less than 100nm. In addition, sample preparation is rather complicated. For FIM
the samples must be stable in high fields, thus limiting its general usefulness. Other
surface analytical techniques, such as X-ray Photoemission Spectroscopy (XPS),
Ultraviolet Photoemission Spectroscopy (UPS) and Electron Energy Loss
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EXPERIMENTAL
Spectroscopy (EELS), can only provide spatially averaged information of the
electronic structures of the surfaces. Moreover, some of the techniques mentioned
above require high-vacuum environment and can only provide indirect results or
strongly rely upon model systems for data interpretation. Until the Scanning
Tunneling Microscope (STM) was introduced, it still remained a dream to directly
observe geometric and electronic surface structures at the atomic level at ambient

pressure and room temperature [1-3].
Compared to other surface analytical techniques, there are several reasons for the
diversity of STM and STM-based technological applications: STM can achieve lateral
and vertical resolutions of 0.1nm and 0.01nm, respectively, i.e., individual atoms and
molecules can be resolved. The higher vertical resolution of STM relative to other
microscopes also offers advantages with regard to qualitative analysis of surface
roughness on a nanometer scale. STM can be performed in different environments,
such as vacuum, air, low or high temperature, etc. Samples can even be immersed in
water or other solutions under potential control. In most cases, special techniques for
sample preparation are not required, and samples remain mostly free of damage. With
these advantages, STM is especially suitable for in-situ electrochemical studies,
biological studies, and the evaluation of sample surface under various experimental
conditions.
The other unique feature of the STM is its truly local interaction with the surface
under study at the atomic scale rather than the averaged properties of the bulk phase
or of large surface area. This allows the study of individual surface adsorbates, surface
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EXPERIMENTAL
defects, surface reconstructions, and adsorption-induced surface reconstructions at
unprecedented resolution. Three-dimensional images of the surface and the solid-fluid
interface in real space can be obtained in real time, independent of the sample’s
periodicity. This capability allows in-situ imaging of some dynamical processes taking
place on surfaces and at the solid-fluid interface. Local surface electronic properties
such as charge-density waves, the changes of surface barrier and energy gap, as well
as spectroscopic images, can be provided by STM.
STM can be employed for the modification of a surface and for the manipulation
of atoms and molecules through tip sample interactions, opening up the prospects of
constructing atomic or molecular scale devices.

2.1.1 Principle of the Scanning Tunneling Microscopy (STM)

Scanning tunneling microscope (STM) is a powerful technique for viewing
surfaces at the atomic level. It probes the density of states of a material using
tunneling current. The basic design of the STM is shown in Fig 2.1.
Based on the concept of quantum tunneling, when a sharp conducting tip is
brought very close to the metallic or semiconducting surface ( 10Å), the wave
functions of the sample will overlap with the wave function of the tip. If a bias
voltage V between the tip and surface is applied, the electrons can travel through the
energy barrier via a quantum-mechanical mechanism called tunneling to give rise to a
current.
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EXPERIMENTAL


Fig 2.1 Schematic view of scanning tunneling microscope (Copyright: Michael Schmid, TU Wien).
It consists of scanning tip, piezoelectric controlled scanner, sample-to-tip control, and data
processing component.
The direction of the electron flow depends on the sign of the applied bias on the
sample. For a positive bias, electrons flow from occupied states of the tip to
unoccupied states of the sample and the direction is reversed for the opposite polarity.
By keeping the tunneling current constant with an electronic feedback circuit, a fixed
tip-sample gap distance can be maintained as the tip is scanned laterally across the
sample. Plots of the tip height z versus lateral positions x and y can then be generated
and such images yield information about the electronic structure and topography of
the surface being analyzed.
The tunneling current is proportional to the local density of states (LDOS) near
the Fermi level. The current is also proportional to the exponential of the separation d
between the tip and the sample: . Such relationship gives STM the ability to
d
eI


2

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EXPERIMENTAL
study surfaces with high sensitivity to height changes due to individual atoms.
Even though the principle of a scanning tunneling microscope is not very
complicated, many factors must be taken into consideration in the design to ensure a
stable and reliable performance. Optimum functioning of an STM device requires
tip-to-sample position control with picometer precision, a fine positioning capability
in three dimensions, high scanning speed, and simplicity of operation. These
requirements have to be satisfied in the presence of building vibrations with up to
micrometer-size amplitudes, electric noise, thermal drift, creep and hysteresis of the
piezoelectric translation elements and other perturbations [1, 2].
In our experiment we use the commercial available product Nanoscope IIIa
provided by Veeco Asia. This microscope system has both AFM and STM functions
which can be operated in air or organic solutions [4].

2.1.2 Vibration Isolation of the STM
The frame of the instrument is always subjected to vibrations transmitted from
the ground or the air. Since the tunneling current depends exponentially on the gap
between tip and sample, even the smallest vibrations can affect the stability of the
instrument. For many materials, especially metals, the atomic corrugations observed
in the constant current STM mode will typically be 0.01 nm. Therefore, a good
vibration-isolation system is very important for a well-functioning STM. In the
process of minimization of the sensitivity of an STM to vibrations from the building,
ventilation ducts and people’s motion, primary attention has to be given to the
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EXPERIMENTAL
frequency range between 1 and 100 Hz. Increasing the inherent resonance frequency
of the STM body and employing a vibration damping system are two major ways to

isolate vibrations. In our STM system, the vibration isolation is achieved by a massive
platform rest on inner tubes which are supported by the compressed air as shown in
Fig 2.2.

Fig 2.2 Picture of a typical working platform of STM in our lab: the scanner is placed on a
vibration-isolated platform. The metal cover was used to block the electromagnetic wave. The
floating platform was supported by high pressure air gas.
On the platform there is a small plate which is supported by the spring, where the
scanning tunneling microscope base is located. The base and the STM head are
covered with a metal bell to isolate electromagnetic field from the environment.
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EXPERIMENTAL
Furthermore the whole working platform is covered by a huge and heavy acoustic
hood. By all these means the vibrations from building and air can be minimized as
much as possible [1, 2, 4].

2.1.3 Preparation of the STM Tips
The reliable fabrication of tunneling probe tips is critical for the proper operation
of STM. The size, shape and chemical identity of the tip influence not only the
resolution and shape of an STM scan, but also the measured electronic structure. The
microstructure of the tip is the key to atomic resolution because the tunneling current
depends exponentially on the gap distance. It is necessary to have a single site of
closest atomic approach for stable operation, as anomalous imaging artifacts will
appear when simultaneous tunneling occurs through multiple atoms on the tip. This is
commonly referred to as double-tip imaging.

STM tips are typically fabricated from metal wires of tungsten (W),
platinum-iridium (Pt-Ir), or gold (Au) and sharpened by mechanical grinding, cutting
with a wire cutter or razor blade, “controlled” crashing, field emission/evaporation,
ion million, fracture, or electrochemical etching [1, 2].

Preparation of Tungsten Tips
The preferred method for preparing tungsten STM tips is the electrochemical
etching method. There are two ways by which this can be done: Alternating-Current
(AC) or Direct-Current (DC) etching according to the applied potential. Each
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EXPERIMENTAL
procedure gives a different tip shape; the AC etched tips have a conical shape and
much larger cone angles than the DC etched tips. The hyperboloid-shaped DC etched
tips are much sharper than AC etched tips and are preferable for high-resolution STM
imaging.

Fig 2.3 Schematic view of the etching machine: it consists of ring-shape Pt electrode, power
supply, and wire holder where the sample being etched is fastened. The etchant surface just touchs
the Pt-ring.
Fig 2.3 illustrates the details of the electrochemical cell used in DC etching,
which contains 100 mL of 2M NaOH or KOH. The W wire to be etched is placed in
the center of the cell and serves as the anode. It is mounted on a micrometer so that its
position relative to the surface of the electrolyte can be precisely adjusted. The
counter electrode (or cathode) consists of a Pt ring which surrounds the anode.
When a DC voltage of 13V is applied to the anode, bubbles can be observed
emerging at the cathode/solution interface. The overall electrochemical reaction is
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EXPERIMENTAL
Cathode: 6H
2
O + 6e
-
 3H
2

(g) + 6OH
-
SRP = -2.45 V
Anode: W(s) + 8OH
-
 WO
4
2-
+ 4H
2
O + 6e
-
SRP = +1.05 V
W(s) + 2OH
-
+ 2H
2
O  WO
4
2-
+ 3H
2
(g) E
0
= -1.43 V
where SRP stands for standard reduction potential. The above reaction involves the
oxidative dissolution of W to soluble tungstate (WO
4
2-
) anions at the anode, and the

reduction of water to form bubbles of hydrogen gas and OH
-
ions at the cathode.
Actually, the reaction mechanism is much more complex than indicated by the above
equations and the potential required to drive an electrochemical reaction is usually
higher than that calculated from standard electrode potentials [1, 5, 6, 7].
Several factors affect the etching process. Due to the surface tension of the
aqueous solution, a meniscus is formed around the wire once it is placed into the
electrolyte. It is primarily the shape of the meniscus which determines the aspect ratio
and overall shape of the tip. The shorter the meniscus is, the smaller the aspect ratio
becomes. A low aspect ratio is important in reducing vibration in the tip during
scanning. As the reaction proceeds, the change in the surface area of the wire and in
the fluid disturbances may result in the variation of the meniscus height. To avoid
oddly shaped tips, the meniscus height should be kept at the same position by
adjusting the micrometer during etching.
Usually, a quick automatic cutoff circuit is used to cut off the potential to avoid
over-etching. The cutoff time of the etching has a significant effect on the radius of
curvature of the tip: the faster the cutoff time, the sharper the tip. Because OH
-
is
consumed in the reaction, it is necessary to replace NaOH solution periodically. The
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EXPERIMENTAL
tip-drop-off time increases with the decrease of the OH
-
concentration.
The chemically etched tungsten tips are very sharp but can be oxidized easily in
air to form tungsten-oxide layer that has much higher resistance than the desired
tunneling gap resistance. It leads to tip crashing sometimes. Thus the tungsten tips are
not the most suitable tips for our experiment conducted in air, although they work

perfectly in our UHV STM system. The etching system we used here is W-TEK
purchased from Omicron Technology.

Preparation of Pt-Ir Tips
Platinum, although a soft metal, is a material preferred over tungsten because it is
inert to oxidation. The addition of Ir to form a Pt/Ir alloy adds stiffness while
maintaining a chemically inert material. Pt-Ir tips are widely employed, too,
particularly in atmospheric and electrochemical environments.
Mechanical shearing is the most common approach for fabricating Pt-Ir tips. In
spite of the variation in shape, many experiments had proven that atomic resolution
can be achieved using the mechanically fabricated Pt-Ir tips. Although resolution
requirements are usually not as stringent for highly topographic samples, wide-area
scans place unique restrictions on the tip morphology. For such samples, symmetric,
controlled-geometry tips with small radii of curvature and high aspect ratios are
necessary to minimize the convolution of the tip shape into the acquired image.
However, asymmetric or double tips are often formed during mechanical shearing of
the Pt-Ir wire, resulting in misleading sample topography. To make the tip as sharper
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EXPERIMENTAL
as possible, we usually cut the Pt-Ir wire with very large seizers, with the angle 
equals to 45°. At the end of cutting, we pull the seizers away from the Pt-Ir tip along
the wire. This step helps to form a sharper tip at the moment when the tip is broken
into two pieces. Usually the tips cut by this method are always quite sharp, and can be
readily used in STM experiments.


Fig 2.4 Illustration of the tip cutting procedure: the vertical line represents Pt-Ir wire; the crossing
line represents the seizers. Angle  equals to 45. When the tip is nearly dropping off from the
wire, the seizers should move along the arrow so that a sharp tip could be produced.
Meanwhile several in-situ tip treatments were already used at the birth of STM by

the inventors: by gently touching the tip with the sample surface, the resolution can be
improved; or by exposing the tip to high electric fields, of the order of 10
9
V/cm, the
tips become sharpened. There are additional methods to improve the tip sharpness
when the experiment is carried out in air. The freshly prepared STM tips are always
washed with absolute ethanol to remove the possible organic contents either from the
seizers or environment. The tip is engaged onto surface and then withdrawn from
surface for several times. Such movements help to remove the possible contaminants
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EXPERIMENTAL
on the tip. Applying a high voltage (~5V) pulse in milliseconds to the tip can also
sharpen the tip. However, the control of the voltage is critical and the high electric
field at the tip also leads to a high temperature at which the tip may melt and becomes
blunter.

2.1.4 Preparation of the STM Samples
A small piece of highly oriented pyrolytic graphite (HOPG) crystal was cut and
mounted onto a metallic plate with conducting silver paste. The conductivity between
the top of the graphite and the bottom metal plate was tested to ensure that the whole
piece of sample is conductive. The metal plate must be magnetic so that it can be
secured onto the scanner. The top several layers of graphite were removed by
adhesive tapes. The solution containing the molecules to be studied was heated up to
around 60ºC. Then one drop of the warm solution was added onto the freshly cleaved
graphite surface. The crystallization of molecules was allowed to take place at room
temperature before the sample was studied using STM.

Fig 2.5 Diagram of a prepared sample: black part is the HOPG crystal adhered to metal plate using
conductive silver paste. On top of the graphite there is a drop of depositing sample solution.

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EXPERIMENTAL
2.1.5 Chemicals
The chemicals used consist of 29H,31H-phthalocyanine (Aldrich), copper
phthalocyanine (Aldrich), cobalt phthalocyanine (Aldrich), zinc phthalocyanine
(Aldrich), heneicosanoic acid (TCI), lignoceric acid (TCI), stearic acid (TCI), and
oleic acid (Aldrich), which are all research grade chemicals (98-99% purity) and were
used without further purification. 1-phenyloctane (Merck, >98%), 1-heptanol (Aldrich,
98%), 1,2,4 trichlorobenzene (HPLC grade, Aldrich) and toluene (HPLC grade,
Aldrich) were used as solvent without further distillation.
Samples of 3-(decyloxy)-benzenamine, 3-(tetradecyloxy)-benzenamine, 3-
(dodecyloxy)-benzenamine, 1-(hexadecyloxy)-2-nitrobenzene were synthesized by
the research group under Prof Hardy Chan Sze On of Department of Chemistry,
National University of Singapore (NUS). The samples were purified by column
chromatography.
SU-CY4F, SUCYBB, SU1876 and SU-DT were synthesized and purified by Dr
Shu Lijin. Their structures are attached in Scheme 2.1 at the end of this chapter.
The osmium organometallic compound Os
3
H(CO)
10
S(CH
2
)
10
CO
2
H was provided by
Prof Leong Weng Kee of Department of Chemistry, NUS.
Polymer samples and porphyrin derivatives were provided by Prof Lai Yee Hing’s

group. The structures of the polymers are listed in Scheme 2.2.
Samples provided by Prof Valiyaveettil Suresh’s group are listed in the Scheme
2.3.
The standard HOPG crystals are of the ZYB grade and were provided by the
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EXPERIMENTAL
Veeco Asia Pte Ltd, Singapore. The silver conductive paint was purchased from R.S
Components, Northants, UK.

2.2 Computational Studies - Forcite
The Forcite program packages in Materials Studio (version 4.0) of Accelrys Inc
were employed for the computational works in the current project. This is a molecular
mechanics module for potential energy and geometry optimization calculation of
arbitrary molecular and periodic systems using classical mechanics. It offers support
for the COMPASS, UFF, and Dreiding forcefields. With this wide range of forcefields,
Forcite can handle essentially any material. The geometry optimization algorithm
offers steepest descent, conjugate gradient, quasi-Newton, and full Newton-Raphson
Methods, in addition to the Smart algorithm, which uses these methods sequentially.
This allows very accurate energy minimization to be performed [8].
As the most molecular clusters in our project contain several layers of graphite,
the number of atoms in each module is usually more than 300. The construction and
calculation of the adsorption energies of the molecules on the graphite (0001) surface
are based on the clusters having a planar molecule positioned above the surface with a
distance larger than a C-C single bond (>1.54 Å). In most cases the distance was set at
2.0 Å. The way of positioning molecules on the graphite is based on the STM results.
All carbon atoms of the graphite were constrained to represent the bulk-like
environment.
The adsorption energies, E
ad
, for different configurations were calculated by

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EXPERIMENTAL
subtracting the energies of the cluster comprising the adsorbate molecules and the
substrates from the total energies of the free substrate cluster and the gas-phase
adsorbates as shown in Equation 2.1:
E
ad
= E(surface) + E(adsorbate) - E(adsorbate/surface) (2.1)
With this definition, a positive E
ad
corresponds to stable adsorption on the surface.
For the calculations, the Condensed-phase Optimized Molecular Potentials for
Atomistic Simulation Studies (COMPASS) forcefield was employed for both
geometry optimization and dynamics. For the convergence tolerance, the Medium
quality was chosen with energy at 0.001 kcal/mol and force of 0.5 kcal/mol/Å. In the
dynamics calculation the temperature was set at room temperature 298K.












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References
[1] Wiesendanger, R. Scanning Probe Microscopy and Spectroscopy Methods and
applications, Cambridge University Press, 1994.
[2] Bai, C.L., Scanning tunneling microscopy and its application, Scientific Technical
Publishers, 1995.
[3] Drake, B.; Sonnenfeld, R.; Schneir, J.; Hansma, P.K.; Slough, G.; Coleman, R.V.
Rev. Sci. Instrum. 1986, 57, 441.
[4] Digital Instrument Veeco Metrology Group, MultiMode
TM
SPM Instruction
Manual, Version 4.31ce, 1996.
[5] Zhang, B.L.; Wang, E.K. Electrochimica Acta, 1994, 39, 103.
[6] Nagahara, L.A.; Thundat, T.; Lindsay, S.M. Rev. Sci. Instrum. 1989, 60, 3128.
[7] Kazinczi, R.; Szöcs, E.; Kálmán, E.; Nagy, P. Appl. Phys. A 1998, 66, S535.
[8] Forcite - Materials Studio Online Help Manual









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Scheme 2.1
Chemical structures of SUCYBB, SU-CY4F, SU1876 and SU-DT (by Dr Shu Lijin):
SU-CYBB

SU-CY4F
F
FF
F
F
F
F
F

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EXPERIMENTAL
C
12
H
25
Si
SU-1876
triisopropyl(2-(4-(4-(4-(tetradec-1-ynyl)phenyl)buta-1,3-diynyl)phenyl)ethynyl)silane

Si Si
SU-DT
1,4-bis(4-(2-(triisopropylsilyl)ethynyl)phenyl)buta-1,3-diyne

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EXPERIMENTAL
Scheme 2.2
Molecules provided by Prof Lai Yee Hing’s group:
O
O
OC
6
H
13
C
6
H
13
O
x
y
n

x y
Sample 1 3 3

Sample 2 3 4
Sample 4 3 5


N
NH
N
HN
Br
Br

N
NH
N
HN
Br
Br










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EXPERIMENTAL
Scheme 2.3

Derivatives of hexabenzocoronene by Prof Valiyaveettil Suresh’s group
C
12
H
25
C
12
H
25
C
12
H
25
C
12
H
25
N
C
12
H
25
CPAH

C
12
H
25
C
12

H
25
C
12
H
25
C
12
H
25
N
C
12
H
25
CHBC


Br
Br
C
12
H
25
C
12
H
25
N
C

12
H
25
CHBC2

N
N
N
C
12
H
25
C
12
H
25
C
12
H
25
TCC

34
EXPERIMENTAL
N
N
N
R
R
R

SCH
3
H
3
CS
SCH
3
R=CH
2
C(CH
3
)C
4
H
9
TCC2

N
N
N
R
R
R
NN
N
R=CH
2
CH(C
2
H

5
)C
4
H
9
TCC1 TpA


N
N
N
N
N
N
R
R
R
R=CH
2
CH(C
2
H
5
)C
4
H
9
TCC4 TpA

S

S
S
N
N
N
R
R
R
R=CH
2
CH(C
2
H
5
)C
4
H
9
TCC5

N
C
12
H
25
SivaCyc2
N
N
C
12

H
25
C
12
H
25

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EXPERIMENTAL
C
12
H
25
C
12
H
25
C
12
H
25
C
12
H
25
N
N
C
12
H

25
C
12
H
25
CHBC3

Derivatives of perylene by Prof Valiyaveettil Suresh’s group
N
N
O
Br
Br
O O
O
C
12
H
25
C
12
H
25
DDPER

N
N
O
O O
O

C
12
H
25
C
12
H
25
S171

N
N
O
O O
O
C
12
H
25
C
12
H
25
S
S
S170


N
N

O
O O
O
C
12
H
25
C
12
H
25
OMe
MeO
S169

N
N
O
O O
O
C
12
H
25
C
12
H
25
OMe
OMe

OMe
OMe
MeO
MeO
S172

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EXPERIMENTAL
N
N
O O
OO
C
12
H
25
C
12
H
25
S
S
SIV233

N
N
O O
OO
C
12

H
25
C
12
H
25
OCH
3
OCH
3
OCH
3
OCH
3
H
3
CO
H
3
CO
SIV236


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