Studies of self assembled monolayers on highly oriented pyrolytic graphite using scanning tunneling microscopy and computational simulation 1

INTRODUCTION
CHAPTER 1
INTRODUCTION

1.1 The Highly Oriented Pyrolytic Graphite (0 0 1) Surface

The highly oriented pyrolytic graphite (HOPG) (0 0 1) surface has been a subject
of continued interest for more than decades. Since the observation of self-assembled
monolayers (SAMs) at the liquid/graphite interface [1, 2], a large number of SAMs
studies have been carried out.
The HOPG is a highly ordered form of pyrolytic graphite with an angular spread
of the c axis of less than 1 degree. It can be synthesized by heat treatment of pyrolytic
graphite under compressive stress at temperatures above 3000K [3]. As a new form of
graphite, the structure of HOPG is now well understood. The flatness and
conductivity of the HOPG make it one of the best substrates for probe microcopies,
such as scanning tunneling microcopy (STM).

1.1.1 Atomic Arrangement of HOPG crystal
Graphite is one of the stable forms of pure carbon in nature. Other allotropes of
carbon include diamond, amorphous carbon, fullerenes, etc. The physical properties
of carbon vary widely with the allotropic form. The atomic arrangement of the HOPG
crystal is shown in Fig 1.1 [4]. The graphite crystal is built up by layers with the
honeycomb arrangement of carbon atoms being strongly covalently bonded to one

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INTRODUCTION
another. The nearest-neighbour distance AA’ is 1.42Å. The in-plane lattice constant a
0

is 2.46Å. The layers are spaced 3.35Å apart and are held together by van der Waals
forces. The most abundant form of graphite in nature is the hexagonal graphite in

which the neighboring layers are shifted and result in an ABAB stacking sequence.
This stacking sequence gives rise to two non-equivalent carbon atom sites within the
surface unit cell: carbon atoms in white are on top of carbon atoms of the second layer,
whereas the carbon atoms in black are located above the center of the six-fold carbon
rings of the second layer [4].

Fig 1.1 Crystal structure of HOPG [4]: The graphite crystal is built up by layers with the
honeycomb arrangement of carbon atoms being strongly covalently bonded to one another. The
neighboring layers are shifted and result in ABAB stacking sequence

1.1.2 Electronic Structure of Graphite
STM studies of the graphite (0001) surface have revealed images showing a
triangular lattice (Fig 1.2). The spacing between the neighbouring bright dots

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INTRODUCTION
observed in the STM images is 2.46Å, suggesting that only every other surface carbon
atom appears as a protrusion. As shown in the graphite model in Fig 1.1, there are two
types of carbon atoms on the top layer: the ‘white’ carbon atoms and the ‘black’
carbon atoms. The ‘black’ carbon atoms exhibit a higher local electronic density of
states near Fermi level and are therefore expected to appear as protrusions in STM
images, whereas the ‘white’ carbon atoms appear as saddle points.


Fig 1.2 STM image of a freshly cleaved HOPG surface (V
bias
=80mV, I
set
=30pA). Only every other
surface carbon atom appears as a protrusion, hence the unit cell is triangle.

1.1.3 Interaction between HOPG Surface and Adsorbates
Since HOPG consists of layers held together by van der Waals forces, the layers
can be easily cleaved, providing atomically flat terraces of up to several micrometer

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INTRODUCTION
grain size. The cleavage of the graphite layer does not create dangling bonds and
therefore a freshly cleaved surface is able to stay clean for a long time.
The interaction between the inert HOPG surface and adsorbates is considered
very weak in general [5, 6, 7, 8]. Only when the adsobates contain aromatic fragments,
the - interaction will be present between the organic compounds and graphite
surface [9, 10, 11]. - interaction is a noncovalent interaction between aromatic
moieties caused by intermolecular overlapping of p-orbitals in -conjugated systems.
The strength of the interaction rises as the number of -electrons increases. It is
usually slightly stronger than other noncovalent bondings including van der Waals
forces, or dipole-dipole interactions [9]. For example, it acts strongly on flat
polycyclic aromatic hydrocarbons such as anthracene, triphenylene, and coronene
because of great number of delocalized -electrons. The - interaction is also
orientation dependent [10].
Therefore HOPG has been considered as one of the best substrates to study SAMs
as its conductivity, flatness, and inertness provide us a suitable environment for STM
experiments. Last but not least, the structure of the HOPG is well understood and
relatively simple and any possible interactions between adsorbates and substrates will
not involve fairly intricate processes.

1.2 Self-Assembled Monolayers (SAMs)
The concept of the self-assembled monolayers (SAMs) is primarily
introduced by Zisman in 1946 [12, 13]. The traditional SAMs is an organized layer of

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INTRODUCTION
amphiphilic molecules in which one end of the molecule is designed to have a
favorable and specific interaction with the solid surface of the substrate. A stable
monolayer film can be formed when the designed molecules are deposited onto the
substrate surface from either vapor or liquid phase. A typical example is that the
formation of thiolate monolayers on the gold (111) surface (Fig 1.3).


Fig 1.3 Schematic of an n-dodecanethiolate monolayer self-assembled on an atomically flat gold
substrate [14]. The assembly is held together by the bonds between the sulfur headgroups and the
gold surface as well as van der Waals interactions between neighboring hydrocarbon chains.

1.2.1 Chemisorbed SAMs
Much research has been focused on the SAMs because of their potential
applications in materials design, nano-devices development, and biological process.
Works of thiols adsorbed on gold surfaces by Nuzzo and Allara [13, 15] in the early
1980s and trichlorosilanes on silicon oxide by Maoz and Sagiv [13, 16] introduced the
two most popular SAMs systems. Alkanethiol molecules consist of saturated
hydrocarbon chains terminated by a thiol group, which can chemisorb onto gold and

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INTRODUCTION
other metal surfaces [17]. The chemisorption process usually involves the breaking of
the S-H bond and formation of the S-Metal bond. Organosilane molecules can
assemble onto silicon dioxide substrates through the reaction with the surface
hydroxyl groups [14] to form a monolayer of siloxane at the interface (Fig 1.4).


Fig 1.4 Schematic of an organosilane self-assembled on a SiO

2
substrate [14]. The silane groups
condense with surface hydroxyl groups to form a thin layer of polysiloxane.
The formation of thiolate SAMs and silane SAMs is primarily determined by the
covalent bond strength between the adsorbates and substrates, the weak interactions
which include hydrogen bonding, electrostatic forces and van der Waals forces do not
have a significant effect on the process [18]. One proposed sequence of the formation
of such SAMs is shown in the Fig 1.5 [13]. The adsorbates are randomly distributed
on the surface at low surface coverage, where the molecule either stands or lies on the
surface with its head covalently bonded to the substrate. As the surface coverage

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INTRODUCTION
increases, the adsorbed molecules will form a close-packed matrix with uniform
molecular orientation.

Fig 1.5 Schematic of the formation of the traditional SAMs [13]. The adsorbates randomly
distribute on the surface at low surface coverage, where the molecule either stands or lies on the
surface with its head covalently bonded to the substrate. As the surface coverage increases, the
adsorbed molecules will form a close-packed matrix with uniform molecular orientation.

1.2.2 SAMs at the Liquid/HOPG Interface: Current Research Status and Our
Objective
SAMs at the Liquid/HOPG interface have attracted more and more research
attentions in the last two decades with the development of the STM technology.
Through the years a large number of SAMs formed by organic molecules at the
Liquid/HOPG interface have been studied [1,2,19-28]. Opposite to the traditional
SAMs, the organic molecules deposited at the Liquid/HOPG Interface do not form

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INTRODUCTION
covalent bonds with the substrate. Instead, the physisorbed molecules interact with the
HOPG surface through weak interactions, including van der Waals forces and -
interactions. In addition to the adsorbates/substrates interactions, the intermolecular
interactions also play important roles during the formation of the ordered two
dimensional structures. Hence the formation of the SAMs at the Liquid/HOPG
interface is a rather complicated process in which factors from the intermolecular
interactions, adsorbate-substrate interactions, solvent effect, and others must be
considered.
Some factors which affect the formation of the SAMs at the Liquid/HOPG
interface have been scrutinized. The alkyl chains of adsorbates were found to be able
to enhance adsorbates’ desorption barrier, and the stability of the monolayers is
strengthened as increasing the alkyl chain length [28-31]. The choice of the solution
can affect greatly the SAMs patterns, although the exact pattern is hard to be predicted
[32]. The odd-even effect in the SAMs has also been discussed in details [33-42].
Temperature is another important factor that affects the SAMs patterns, as the
physisorbed molecules are sensitive to the thermal energies [43]. Last but not least,
the molecular structure and its functional groups are also crucial during the formation
of the SAMs [44, 45].
In contrast, very few systematic works towards understanding the mechanism of
SAMs formation at the Liquid/HOPG interface has been carried out. We devised some
simple experiments to provide additional knowledge regarding the SAMs formation
mechanism at the liquid/HOPG interface. In the first experiment a solution consisting

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INTRODUCTION
of two fatty acids deposited on the HOPG surface was studied (Chapter 4). A series of
solutions of perylene derivatives on the HOPG were studied and their results were
compared in the subsequent experiment (Chapter 5). The formation of chiral SAMs is
shown in Chapter 6. However, for the insightful understanding of the SAMs

formation mechanism, theoretical studies employing the Materials Studio programme
were also performed to complement the experimental data. The calculated results
mainly comprised energies of the clusters with different molecular configurations on
HOPG.

1.3 Proposed Mechanism: 2D crystal
Despite decades of study focused on the ordered structures of the SAMs, the
principle guiding the formation of these two-dimensional structures is still to be
established. Previously Steven De Feyter and Frans C. De Schryver discussed the
usefulness of the STM in studying the physisorbed organic monolayers and types of
the SAMs on the HOPG surface [46, 47]. Similar works were performed by Wan and
coworkers [48]. An important phenomenon - odd-even effects in organic SAMs have
also been reviewed by Tao and Bernasek [33]. On the other hand, Matzger et al [44]
classified the ordered two-dimensional monolayers structures according to their
symmetry groups, as an important step to link the formation of SAMs on HOPG to the
crystallization process systematically.
In the context of our proposed mechanism, SAMs are considered as two
dimensional crystals. A crystal is composed of regularly repeating ‘structural motifs’,

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INTRODUCTION
which may be atoms, molecules, or groups of atoms, molecules, or ions [49].
Traditionally the repeating ‘structural motifs’ are reproduced in three spatial directions
(X, Y, Z). However, in SAMs they are restricted on HOPG surfaces. Repeating of
‘structural motifs’ on a plane results in two-dimensional crystals (2D crystals). With
the help of 2D crystal model, the derivation of the equations relating the process of
SAMs formation was carried out. All the factors which affect the SAMs formation
process will be referred and further discussed later (refer to Chapter 7).

1.4 Outlook for the Future Work

SAMs technology has great potential in many fields: such as biology and
nano-electronics. Patterning surface with features on the low end of nano-scale can
efficiently be achieved with SAMs. By understanding the theory behind the formation
of SAMs on HOPG, it is possible for us to design SAMs to meet specific application
requirements. The adsorbates could be synthesized using retrosynthetic methods
developed by Nobel Laureate E.J. Corey [50-51]. Combining these two methods,
SAMs with specific patterns and functions can be grown. In other words, we may be
capable of producing molecular circuit and nano-devices. Furthermore, the SAMs
which can be formed on HOPG have potential to modify the graphene sheets - one of
the hottest ‘future’ materials which might play significant roles in industry and
technology [53, 54].



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INTRODUCTION
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