Studies of self assembled monolayers on highly oriented pyrolytic graphite using scanning tunneling microscopy and computational simulation 5

FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS
CHAPTER 5
FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS

5.1 Motivation
The steric effect is an important subject in chemistry. It arises from the fact that
each atom within a molecule occupies a certain volume of space. When atoms are
brought too close, the overlapping of electron clouds between them requires more
energy due to repulsive forces, and this may affect the molecule’s preferred
conformation. There are several types of steric effects, including: steric hindrance or
steric resistance, steric shielding, steric attraction and chain crossing. Among them the
most commonly observed effect is the steric hindrance, which usually occurs when
the size of groups within a molecule prevents chemical reactions. Although steric
hindrance is sometimes a problem, it is very useful to control the reaction reactivity,
the chemical reaction route, and the chirality of the product [1].
Besides its role in synthetic chemistry, the steric effect also plays an important
role in the formation of SAMs. Other factors like stabilization effect from long alkyl
substituents [2, 3, 4], solvent effect [5] have been studied by other researchers
throughly. However, the steric effect taking place in the SAMs formation process has
not been explored. Through the examination of experiments in which molecules were
difficult to form SAMs on HOPG, it was realized that the steric effect must be
reconsidered as they affect the formation process greatly.


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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS
5.2 The selected molecules
A series of molecules with perylene center and dodecyl groups as stabilizing
substituents were synthesized. These molecules have different halogen or alkyl groups
attaching to their perylene centers. The sizes of the attached groups vary from single
atom (Br) to bulky alkyl group with more than twenty atoms so that the strength of

steric effect can be varied correspondingly.
The chemical structures of the DDPER and its four derivatives (S170, S169, S171,
and S172) are shown below:
NO O
N OO
Br
Br
C
12
H
25
C
12
H
25

NO O
N OO
C
12
H
25
C
12
H
25
S
S

DDPER S170

NO O
N
O
O
C
12
H
25
C
12
H
25
H
3
CO
OCH
3

NO O
N OO
C
12
H
25
C
12
H
25

S169 S171


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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS
NO O
N
O
O
C
12
H
25
C
12
H
25
H
3
CO
H
3
CO
H
3
CO
OCH
3
OCH
3

OCH
3

S172
(DDPER: N,N’-Didocecyl-1,7-dibromoperylene-3,4:9,10-tetracarboxylic acid bisimide)
5.3 The STM results of the Self-Assembled Monolayers
During experiments, each sample was treated in the same way to minimize the
disturbance from environment and instruments. The details of the experimental
procedures are described in Chapter 2. After numerous attempts, only the SAMs
formed by DDPER could be observed under STM. On the other hand, no SAMs could
be observed when sample S169, S170, S171, S172 were studied, indicating those
derivatives have low probability to form stable monolayers at the liquid/HOPG
interface.
In Fig 5.1 there are two major sections A and B within the area scanned
(60nm×60nm). The DDPER lamella has a 33° angle and 77° angle with horizontal
direction within section A and B, respectively, as indicated by the black arrow. The
resolution at the boundary of the two sections was not as good as the centers of
section A and B, possibly due to better mobility of the molecules at the boundary.


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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS

Fig 5.1 The large-area STM result of the Self Assembled Monolayers formed by DDPER from
saturated phenyloctane solution (60nm×60nm, V
bias
=-666mV, I
set
= 30pA). Monolayers in section
A and B have different orientations.

Fig 5.2 is the enlarged image of the DDPER monolayers structure within section
A. It is noticed that the submolecular structure and the substituents of the molecules
were not very well resolved. The center of the DDPER molecule - perylene appeared
as the brightest part, some of which had a central depression inside. The dodecyl
groups appeared in pale yellow colour and not very clear, because of lower density of
electrons comparing to the aromatic perylene. These alkyl chains orientate along the
diagonal direction of the unit cell.


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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS

Fig 5.2 The enlarged STM results of the Self-Assembled Monolayers formed by DDPER from
saturated phenyloctane solution (13nm×13nm, V
bias
=-666mV, I
set
= 30pA). a=3.100.06nm,
b=1.600.03nm; c=1022°

The image shows that the DDPER molecules are packed side by side in the bright
strips while they are separated by the dodecyl lamellae from the neighbouring
DDPER array. The dodecyl chains are interdigitated in the dark area. Section analysis
showed that the DDPER centers had an average relative height of 0.2 nm (Fig 5.3).

Fig 5.3 The height profile of the DDPER Self-Assembled Monolayers

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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS

In conclusion, the DDPER molecules form stable self-assembled structures with a
characteristic two-fold symmetric stripe structure. The unit cell has a dimension of
3.1nm×1.6nm, with the angle c equals to 102°. Based on the STM results, the
configuration of molecules DDPER at the liquid/HOPG interface is constructed (Fig
5.4). The perylene center is on the diagonal of the unit cell. Eight molecules are
aligned in two rows. The distance between rows equals to 3.1nm, and two
neighbouring DDPER molecules within same row is 1.6nm apart. The orientation of
axis of the perylene is 57° with respect to horizon. The dodecyl groups are placed in
parallel position to minimize steric repulsion.

Fig 5.4 The molecular model of the DDPER arrays

5.4 The Computational Simulation
5.4.1 Conformation of gas phase DDPER and its derivatives
Building of the computational model started with the molecular structures in gas

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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS
phase. DDPER and its derivatives were set to be flat at first. The dodecyl groups were
replaced by the methyl groups to minimize the complexity of the system during the
geometry optimization (Fig 5.5).



Fig 5.5 The top view and side view of the DDPER* model (* means the dodecyl group was
replaced by methyl group)

The geometry optimization of DDPER* using Compass forcefield resulted in a
more stable configuration, where the perylene center was twisted. The carbon atoms,
oxygen atoms and bromine atoms were no longer within the same plane (Fig 5.6).

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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS

Fig 5.6 The side view of the DDPER* after geometry optimization

Gas phase S169*, S170*, S171*, and S172* were constructed using the same
method. The conformations of the DDPER derivatives after geometry optimization
were attached in Fig 5.7-5.10.

Fig 5.7 Side view of geometry optimized S170*

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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS

Fig 5.8 Side view of geometry optimized S169*


Fig 5.9 Side view of geometry optimized S171*


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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS

Fig 5.10 Side view of geometry optimized S172*

With increasing size of the attached groups on perylene center, the height and
width of the molecule also increases (Table 5.1).

Table 5.1 The attached alkyl groups and the corresponding molecule size
Molecules DDPER* S170* S169* S171* S172*
Functional
Groups
Br
S

OMe

OMe
OMe
OMe
Height
(Å)
1.66 4.23 7.10 7.21 8.16
Width
(Å)
7.35 12.2 15.5 17.3 17.3
Due to the steric hindrance caused by different attached groups, the surface
contact between the adsorbates and substrate will be different. As for DDPER which
is relatively planar, its surface contact with the graphite lattice will be larger than that
of its derivatives (S170, S169, S171, S172). Therefore DDPER experiences larger
attractive van der Waals’ forces than others with closer surface interaction.


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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS
5.4.2 DDPER/HOPG vs S170/HOPG
Computational simulation was applied to compare the adsorption energies of
DDPER and S170 on graphite surfaces. To find out the gas phase structure of the

sample, the dodecyl groups, which might be twisted during geometry optimization,
were replaced by methyl group. The simplification helped to obtain the conformation
change of the perylene center. Furthermore the dodecyl groups must be flat and
straight when the adsorbates were attached on the HOPG surfaces. Hence the dodecyl
groups would be put back when the cluster were constructed.
To build the clusters, one DDPER or S170 with dodecyl groups was placed on the
center of the HOPG (0 0 1) surface (15×15 cells). The graphite lattices were
constrained to represent the bulk property of the graphite crystal. Both clusters were
positioned 2.5 nm (distance between the oxygen atom and the graphite surface) above
the substrate. These clusters underwent geometry optimization to reach a more stable
configuration so that the studies of the adsorption energies can be carried out
subsequently. The distance between the oxygen and surface increased to 3.3nm and
3.5nm for Cluster A (DDPER/HOPG) and Cluster B (S170/HOPG) respectively after
geometry optimization. The results showed that S170 center was farther from the
surface than DDPER. The initial and resulting structures were shown in the Fig
5.11-14. The detailed computational results were attached at the end of thesis
(Appendix 5.1).



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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS


Fig 5.11 Top view and side view of DDPER molecule on the HOPG (0 0 1) surface: Initial states


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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS

Fig 5.12 Top view and side view of DDPER molecule on HOPG (0 0 1) surface after Dynamics
and Geometry Optimization using COMPASS forcefield


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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS


Fig 5.13 Top view and side view of S170 on HOPG: Initial states


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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS


Fig 5.14 Top view and side view of S170 on HOPG after Dynamics and Geometry Optimization
using COMPASS forcefield

As defined in Chapter 2 Experimental the adsorption energies E
ad
is given by the
equation:
E
ad
= E(surface) + E(adsorbate) - E(adsorbate/surface) (2.1)
The value of the E(surface) was set to be 0 kcal/mol since all atoms were frozen.


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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS
Table 5.2 The adsorption energies of DDPER and S170 on HOPG
Sample DDPER (kcal/mol) S170 (kcal/mol)
E(surface) 0 0
E(adsorbate) 320.48 545.63
E(adsorbate/surface) 230.15 456.21
E
ad
90.33 89.42
E
ad
0.91
The computational results showed that adsorption energy of DDPER on HOPG is
larger than adsorption energy of S170 by 0.91kcal/mol.

5.5 Discussion
Unlike the previous studies on SAMs formed by fatty acids, it was difficult to
observe the STM images of the DDPER on HOPG although the solution was
supersaturated. The low resolution and difficulties in observing the SAMs could be
due to the mobility of the adsorbates on the substrates, which means the weaker
interaction between DDPER and HOPG comparing to fatty acids. In addition, the
poorer packing of DDPER comparing to fatty acids caused weaker intermolecular
interactions, and therefore the instability of the DDPER monolayer matrix.
The bulky side groups significantly increased the size of the molecules and
hindrance effect. This led to the poor molecule/surface contact. At the same time the
bulky side groups also increased the inter-molecular repulsions. Therefore the steric
effect of the bulky side groups reduces the possibility of forming SAMs on HOPG
The computational simulation further supports the above proposed explanations:
the adsorption energy of DDPER on graphite is 0.91kcal/mol more than the
adsorption energy of S170. This value is similar to the thermal energy at room

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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS
temperature (0.60kcal/mol). Thus, it is believed that there must be additional
stabilization effect from the neighbouring adsorbates within the monolayer matrix
since DDPER within well packed monolayer experience stronger attractive van der
Waals forces.

5.5 Conclusions:
It was shown experimentally that the DDPER forms SAMs on a graphite surface,
but not for its derivatives: S169, S170, S171, and S172. It is suggested the difficulties
for these derivatives to form monolayers are attributed to poor adsorbates/surface
contact and intermolecular steric repulsion, both caused by the hindrance effect due to
presence of bulky attached groups. The computational results also show that the
DDPER is slightly more stable on graphite than S170.
The size of the side groups can affect the formation of the monolayers at the
liquid/HOPG interface. By varying the size of the attached side groups, we may be
able to control the stability of the monolayers.








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FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS

91

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