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

1.1.1 Atomic Arrangement of HOPG crystal Graphite is one of the stable forms of pure carbon in nature.. Fig 1.1 Crystal structure of HOPG [4]: The graphite crystal is built up by layers

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

another The nearest-neighbour distance AA’ is 1.42Å The in-plane lattice constant a0

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

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 (Vbias =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

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

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

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 SiO2 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

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

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

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’,

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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