Studies of self assembled monolayers on highly oriented pyrolytic graphite using scanning tunneling microscopy and computational simulation 6

6.2.2 Chiral SAMs High resolution STM images of the HHB monolayers reveal the arrangement of molecules within the monolayers.. Although the atomic resolution was not achieved, the shape

CHAPTER 6 SURFACE-ADSORPTION INDUCED CHIRAL SELF-ASSEMBLED

MONOLAYERS OF HEXAALKYL HEXAPHENYLBENZENE (HHB) ON

HIGHLY ORIENTED PYROLYTIC GRAPHITE (HOPG)

6.1 Motivation

Since the separation of the sodium ammonium salt of racemic tartaric acid in enantiomorphous crystals by Pasteur 150 years ago [1], the concept of chirality has become an important research subject in chemistry Chiral structures can be formed not only from pure chiral molecules but also by the asymmetric assembly of the molecules In the two-dimensional realm, potential applications such as enatio-selective heterogeneous catalysts [2, 3], nanometer scale patterning, development of molecular electronic devices, and chemical sensors have drawn much interest in the study of chiral structures on surfaces [2-25] Depositing chiral molecules on the surface is a typical way of generating a chiral surface [3-5], such as (R,R)-tartaric acid have been successfully used as surface modifiers in enantioselective heterogeneous catalysis [3, 4] At the supramolecular level, chiral structures may be formed by asymmetric assembly For example, racemic mixtures of certain chiral molecules spontaneously separate on the surface to form chiral domains [6-9] Hydrogen bonded chains [4, 11] have been reported to show chiral structures on the surface Studies of surface-adsorption induced chirality revealed that the interaction between the substrate and adsorbate plays a key role in inducing structural

changes and the symmetry breaking which results in chirality [9, 12, 17, 21-25]

The development of the scanning probe techniques especially scanning tunneling microscopy (STM) and atomic force microscopy (AFM) made it possible to locally probe monolayers at atomic resolution Spontaneous breaking of chiral symmetry by achiral molecules in a Langmuir-Blodgett (LB) film was determined by Viswanathan

et al with AFM [9] Separation of achiral molecules into lattices with chiral packing [9] and separation of chiral phases of chiral organic molecules in LB films have been observed by AFM [26] Chiral liquid crystals have also been investigated with STM and found to form domains that exhibit two-dimensional chirality [27] Supramolecular clusters of 1-nitronaphthalene on gold have been observed to aggregate in 2D domains that are mirror images of each other [28]

In this chapter we present an STM study at the liquid-solid interface of hexaalkyl hexaphenylbenzenes (HHB) physisorbed onto a graphite surface

Chemical Structure of HHB

This is an example of the formation of an asymmetric structure on the surface, which involves the supramolecular assembly through van der Waals’ forces The molecule

used in this experiment is hexaalkyl hexaphenylbenzene (HHB) - a precursor of the polycyclic aromatic hydrocarbons (PAHs) with peripheral substituents PAHs can self-assemble into columnar mesophases [29] which are well suited materials for the study of one-dimensional transport processes such as electrical conductivity [30] and photoconductivity [31] along the columnar axis Research toward electronics on the scale of individual molecules can be performed by investigating highly ordered monomolecular adsorbate layers of HHBs Using the STM, single molecules in these two-dimensional patterns can be visualized with submolecular resolution At the same time, information on their electronic properties can be obtained

6.2 STM Results

6.2.1 STM Images of HHB

Fig 6.1 STM image of a monolayer of HHB on HOPG surfaces (100nm100nm, V bias =100mV,

I set =150pA)

Fig 6.1 displays the STM current image of a monolayer of HHB physisorbed at the interface between organic solution and the basal plane of HOPG It shows the monolayer is right beside the step on the HOPG (bright part at the right-top corner) The conductivity of the graphite is better than the organic monolayers therefore the step becomes the brightest part in the STM current image Each bright dot within the SAMs corresponds to one physisorbed HHB molecule The angle AOB=89±1, which is almost a right angle Section analysis of OA and OB (Fig 6.2) shows that the neighbouring molecules are apart by distance of 3.910.08nm along direction OA and 2.970.06nm along direction OB respectively In another words, the unit cell of the HHB monolayers is a rectangle with two sides at 3.910.08nm and 2.970.06nm respectively

Fig 6.2 Section analysis of HHB monolayer A: Section analysis of OA in Fig 6.2 The distance

containing 21 neighbouring molecules is 78.1nm B: Section analysis of OB in Fig 6.2 The distance containing 21 neighbouring molecules is 59.4nm

6.2.2 Chiral SAMs

High resolution STM images of the HHB monolayers reveal the arrangement of molecules within the monolayers In Fig 6.3 the aromatic part of the HHB molecule – the benzene rings appeared as brightest part in the STM image The aliphatic dodecyl groups appeared as dark part and could barely be observed Although the atomic resolution was not achieved, the shape of the bright part was able to help us to determine the configuration of the HHB molecules on HOPG surfaces The bright part exhibited three ‘legs’, two pointing upwards and one pointing downwards These

three ‘legs’ were assigned to the three carbazole groups The molecular models of HHB with benzene rings highlighted fit into the STM image very well

N

Fig 6.3 Left: High resolution image of HHB monolayers: Bright hexagons represent the benzene

and I set = 150pA)

The STM results showed that within that scanned area HHB molecule had only one configuration: two carbazole groups on top and one carbazole group at the left bottom, which we called it left-HHB (L-HHB) Its mirror image configuration with two carbazole groups on top and one carbazole group at the right bottom (R-HHB) was not observed within this scanned area Therefore the monolayers were formed by L-HHB and could be considered as chiral monolayers Another STM images captured

in other region was shown in Fig 6.4 The resolution of this image is lower comparing

to Fig 6.3, especially for molecules at the boundary, because they had higher mobility than the molecules at the center of the monolayers In each molecule, top half was brighter than rest part of molecule so it stood for two carbazole groups The

brightness of bottom half is uneven, with right part being more intensive This suggested the molecule HHB’s configuration was mirror image of L-HHB, that is, R-HHB The monolayer formed by R-HHB was also a chiral monolayer Measurements of R-HHB monolayers and L-HHB showed that both unit cells were rectangles with two sides at 3.900.80nm and 2.950.60nm

N

Fig 6.4 Left: High resolution image of HHB monolayers: Bright hexagons represent the benzene

and I set = 150pA)

6.3.3 Symmetry Transformation of SAMs

We regularly observed these two sets of domains with a reproducible small angle relationship between the sets of 14.01.0 (Fig 6.5)

Fig 6.5 Top: STM image of two types of SAMs arrangement and their boundary Bottom: The

surface plot of the STM image (current profile) The height of each pinnacle is proportional to the magnitude of current (V bias = 100mV, and I set = 150pA)

In the high-resolution image in Figure 6.5 the phenyl groups of molecule HBB appear as regions of highest intensity, consistent with the occupied frontier orbitals being localized on these sites The contrast in STM images of organic molecules has often been successfully compared to the frontier orbitals, either the HOMO or LUMO, according to the polarity of the applied potential In the STM images of HBB, the aliphatic groups are harder to identify than the aromatic groups The differences between the left part and the right part of Figure 6.6 cannot be a consequence of

instrumental technique since they are from the same image After using spectrum 2D function to remove the noise, the differences between the left part and the right part are apparent as shown in Fig 6.6: (i) the alignment of the individual molecules within the rows and (ii) different ‘internal’ structure of the molecules Further studies of the SAMs showed that the unit cell on the right hand side is rectangular with two sides at a=4.000.08nm and b=2.950.06nm On the contrary, the unit cell on the left hand side is rhombic with two sides at c=4.100.08nm, d=3.020.06nm respectively and angle =761 It was observed that at the center bottom of the Fig 6.5 (highlighted

by black circle) the object did not match well with the neighbouring HHB molecules

A surface plot of that region revealed that the tunneling current within the black circle was higher than over the remaining part of the monolayers It is however difficult to determine the nature of the object directly from the STM image

Fig 6.6 STM image of two types of SAMs arrangement and their boundary Data was treated with

Spectrum 2D function (V bias = 100mV, and I set = 150pA)

6.3 Discussion

6.3.1 STM Images of HHB

A large area scan of the HHB monolayers showed the monolayers started at the steps of the HOPG surfaces (Fig 6.1) The molecules near the step are not as bright as the molecules at the center of SAMs, but this is an artifact due to the hysteresis effect

of the STM when the tip moves across the steps These bright dot arrays show that the HHB molecules are localized firmly on the HOPG surfaces On the contrary, in Fig 6.7 the molecules at the boundary are not as clear as the molecules at the center of the SAMs because of their higher mobility That suggests the steps assist the stabilization

of the molecules on the surface, which makes them the favorite physisorption sites on the HOPG surfaces

Fig 6.7 STM images of SAMs formed by HHB without presence of steps (Vbias =100mV,

I set =50pA)

Furthermore, the SAMs formed not by the side of the steps are usually small in lateral size (Fig 6.7) because the molecules at the SAMs’ boundary can easily move

away from the monolayers The presence of rectangular unit cell of the monolayers indicated that the structure and symmetry of the monolayers are mainly determined by the interaction between the adsorbates rather than the substrate/adsorbates interactions, since the arrangement of the unit cell do not follow the orientation of the graphite surface lattice

6.3.2 Chiral SAMs

In general, HHB is not planar, and its point group is being assigned as Ci This group consists of only element E and hence does not contain an improper-rotation axis Therefore the molecule HHB is chiral It was found that HHB was quite flat in STM image, especially the aromatic moieties, allowing us to simplify HHB molecular structure The illustration of the physisorption process was shown in Fig 6.9, where the HHB molecule is represented by a chiral center with three different attachments A,

B and C, which are not within the same plane

Fig 6.8 Illustration of physisorption of HHB molecule onto HOPG surfaces

The physisorption process can be considered as an addition reaction between the HHB and graphite surface, although no covalent bonds were formed The resulting products or the physisorbed molecules were shown in 1 and 2 when graphite attacked HHB through route 1 (L-HHB) and 2 (R-HHB), respectively As discussed in chapter

4 and chapter 5, the configurations of the adsorbates on the surface must be in such way to maximize the intermolecular interaction between them Similar to the system

in Chapter 4, the resulting monolayers are the thermodynamically stable products of the physisorption process In both L-HHB monolayers and R-HHB monolayers, the molecules have to orientate in the same direction as the adsorbates physisorbed at an early stage Therefore the phase-separated chiral monolayers will form on the achiral surfaces

The proposed addition reaction mechanism is similar to the second step of an SN1 reaction If the adsorbate has one side being blocked by bulky groups, the probability for graphite attacking from the blocked site will be much lower than from the unblocked site In other words, the more open face of the adsorbates has a stronger affinity towards the substrates Based on the discussion, we may be able to synthesize desired chiral monolayers simply by blocking one side of the adsorbates using bulky groups

6.3.3 Symmetry Transformation of SAMs

The shape of the unit cell of the HHB varied as shown in Fig 6.6 while the orientation of the HHB did not change with it The plane group of the unit cell

transformed from pg to p1 [32]

Detailed studies showed that the appearances of HBB under STM are different for molecules on the left hand side and right hand side of the boundary (in black, Fig 6.7) The observation strongly suggested the ‘internal’ structures of molecules were different within these two regions, although only near atomic resolution was achieved during STM studies

It was also noticed that at the boundary (Fig 6.6) there was a region with higher tunneling current This region could possibly be: a) overlap or mismatching of the adsorbates; b) surface defects; c) impurities It is quite difficult to identify the object directly from the STM results The sharp rise in current suggests it is more likely the surface defects as the graphite has larger conductivity

On the other hand, the unit cell of SAMs is a rectangle with two sides at a=4.000.08nm and b=2.950.06nm, while the graphite has an in-plane lattice constant of 2.46Å and a rhombic unit cell with angle equals to 60° The mismatch between the monolayers and substrate can possibly lead to transformation of SAMs unit cell Therefore the change of the symmetry group of SAMs unit cell was possibly caused by i) the presence of the unknown object; ii) incommensurate lattice constant between the graphite and SAMs The monolayers conformation was sensitive to the

6.4 Conclusion

An ordered monolayer formed from the hexaalkyl hexaphenylbenzene (HHB) on

an HOPG substrate is imaged by STM Analysis of the STM images shows that the molecules form chiral monolayers on the HOPG surfaces The chirality of the SAMs

is due to the different binding sites that the adsorbates can have upon physisorption onto HOPG The existence of phase separated chiral monolayers also indicated the physisorbed monolayers were the thermodynamically stable products of self-assembly process Formation of desired chiral surface is made possible using the self-assembled technique Meanwhile, we noticed that the monolayers unit cell was transformed within certain regions, possibly due to the presence of the surface defects or incommensurability between the SAMs and substrate

Reference

[1] Pasteur, L C.R Seances Acad Scie 1848, 26, 535

[2] Wan, K.T.; Davis, M.E Nature 1994, 370, 449

[3] Blaser, H.U Tetrahedron: Asym 1991, 2, 843

[4] Lorenzo, M O.; Baddeley, C J.; Muryn, C.; Raval, R Nature 2000, 404, 376

[5] Switzer, J A.; Kothari, H M.; Poizot, P.; Nakanishi, S.; Bohannan, E W Nature

2003, 425, 490

[6] Eckhardt, C J.; Peachey, N M.; Swanson, D R.; Takacs, J M.; Khan, M.A.;

Gong, X.; Kim, J.-H.; Uphaus, R A Nature 1993, 362, 614

[7] Stevens, F.; Dyer, D J.; Walba, D M Angew Chem., Int Ed Engl 1996, 35, 900 [8] Fang, H.; Giancarlo, L C.; Flynn, G W J Phys Chem B 1998, 102, 7311

[9] Viswanathan, R.; Zasadzinski, J A.; Schwartz, D K Nature 1994, 368, 440 [10] Weckesser, J.; De Vita, A.; Barth, J V.; Cai, J.; Kern, K Phys Rev Lett 2001, 87,

096101

[11] Lorenzo, M O.; Haq, S.; Bertrams, T.; Murray, P.; Raval, R.; Baddeley, C J J

Phys Chem B 1999, 103, 10661

[12] Charra, F.; Cousty, J Phys Rev Lett 1998, 80, 1682

[13] Cai, Y.; Bernasek, S L J Am Chem Soc 2003, 125, 1655

[14] Li, C J.; Zeng, Q D.; Wu, P.; Xu, S L.; Wang, C.; Qiao, Y H.; Wan, L J.; Bai, C

L J Phys Chem B 2002, 106, 13262

[15] Yablon, D G.; Guo, J S.; Knapp, D.; Fang, H B.; Flynn, G W J Phys Chem B

2001, 105, 4313