Studies of self assembled monolayers on highly oriented pyrolytic graphite using scanning tunneling microscopy and computational simulation 4

the SAMs formed by binary systems at the liquid/HOPG interface, in which two species of binary system are always significantly different in structure or chemical properties, for example:

CHAPTER 4 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG

For further investigation of the mechanism of SAMs formation, a binary system was studied using STM and computational method There are few reports regarding

the SAMs formed by binary systems at the liquid/HOPG interface, in which two species of binary system are always significantly different in structure or chemical properties, for example: unsaturated acid and saturated acid [13], acids with very different sizes [14], ion pairs [15], etc Matzger et al found the metastable phase formed by ester was ultimately replaced by the more stable phase formed by anhydride [16-18] No experiments on similar structures were performed before

Two saturated fatty acids - heneicosanoic acid (CH3(CH2)19COOH) and lignoceric acid (CH3(CH2)22COOH) were chosen for STM studies They have similar structure and chemical properties, with a slight difference of three CH2 units on the main chain Our aim is to find out how small change in structure can affect the final form of monolayers There could be two possible SAMs structures formed by such a binary system: phase-separated SAMs and phase-mixed SAMs The experimental results provide us a better understanding of the mechanism regarding SAMs formation at the liquid/HOPG interface At the same time the high resolution STM image would enable us to verify the existence of interaction between the adsorbate and graphite surface

4.2 STM Results and Computational Simulations

4.2.1 Solution Preparation

Three solutions of fatty acids in phenyloctane were prepared Their weight ratios are listed in Table 4.1:

Table 4.1: Weight ratios of heneicosanoic acid  lignoceric acid in phenyloctane solution

The solution A and C containing only pure acids were used as reference The solution

B comprised both acids molecules, with weight ratio at 2:1 (Heneicosanoic acid : lignoceric acid) The solutions were supersaturated, with a weight to volume value at around 30mg/mL The solutions contained a substantial amount of white precipitate at room temperature It would become transparent when they were heated up to around 60-70°C The solutions were heated to 70-80°C before a droplet of the hot transparent solution was deposited onto the freshly cleaved graphite surface Once the droplet was

in contact with the graphite surface at room temperature, the transparent droplet soon became gel-like, indicating precipitation of the acid molecules from the phenyloctane solution Under the optical microscope, the crystal-like structures could be observed (Fig 4.1)

Although the sample surface is covered by the organic solutions and crystalline layers, STM can study the monolayers formed on graphite At the same time, the non-conductive phenyloctane solution provides an insulation to prevent current leakage

Fig 4.1 Modified HOPG surfaces under optical microscope The crystalline and gel-like fatty

acids layer could be observed

4.2.2 STM images of Heneicosanoic acid: CH 3 (CH 2 ) 19 COOH

Fig 4.2 shows the STM image of a monolayer of CH3(CH2)19COOH adsorbed at the liquid/HOPG interface from the phenyloctane solution At room temperature (25°C) highly ordered lamellae of the flat-lying molecules were observed The area enclosed by the black box represents the STM image of a single CH3(CH2)19COOH molecule, which is in its most thermal stable zigzag configuration

Fig 4.2 STM image of a monolayer of heneicosanoic acid on HOPG surfaces (8nm×8nm, Vbias = 666mV, and I set = 50pA)

Within the box there are ten bright ellipse spots, which are due to the aliphatic hydrogens One bright spot corresponds to one CH2-CH2 unit, while the -COOH group is invisible under STM In previous studies the orientation of alkyl group on the HOPG surfaces [2, 3, 9, 14, 19] was thoroughly discussed, whereas no direct observation was made to demonstrate the orientation of molecules with respect to the graphite lattice In our experiment, the high resolution STM images of the monolayers formed by heneicosanoic acid (CH3(CH2)19COOH) were used to find out the spatial relationship between the adsorbates and the underlying graphite surface lattice After recording the STM image of heneicosanoic acid monolayers, the bias voltage was changed from 600mV to 80mV immediately At low bias voltage the STM is able to

reveal the lattice structure of the underlying graphite surface lattice The image of heneicosanoic acid monolayers and image of HOPG were put in same picture In Fig 4.3 the upper quarter is the STM image of the graphite (0 0 1) surface The bright spots represent the sp2 carbon atoms in the graphite lattice The lower three quarters

is the STM image of the C20H41COOH monolayers One bright ellipse corresponds to one -CH2CH2- unit The molecular models of a fragment of the graphite surface lattice and CH3(CH2)19COOH were built and fit into this STM image The orientation of the flat-lying CH3(CH2)19COOH on the HOPG surface was measured The bond distance

of the C-C single bond of the CH3(CH2)19COOH is 1.54Å, which is larger than the C-C partial double bond (1.42Å) of graphite

Fig 4.3 The molecular modeling of the heneicosanoic acid on graphite (8nm×8nm)

The angle between the fatty acid’s orientation and the fragment of graphite surface’s orientation is 118 (±3) It is apparent that when the angle between the acid and graphite surface fragment is 0, 60 or 120, they are actually identical In another words, the orientation of heneicosanoic acid is parallel to the orientation of the HOPG lattice as illustrated in Fig 4.4

Fig 4.4 Diagram of CH3 (CH 2 ) 19 COOH on HOPG

Furthermore, the large-area scanning result shows that the acid molecule has only three possible orientations: OA, OB and OC which are separated by 60 That is consistent with the results of alcohols SAMs which were observed by Rabe and coworkers [2]

4.2.3 STM images of Lignoceric Acid CH 3 (CH 2 ) 22 COOH

Fig 4.5 shows the STM image of a monolayer of CH3(CH2)22COOH adsorbed on

graphite from the phenyloctane solution At room temperature, highly ordered lamellae of flat-lying molecules were observed The area enclosed by the black box represents the STM image of a single CH3(CH2)22COOH molecule Despite the poor quality of the image, twelve bright spots where each bright spot corresponds to one -CH2CH2-unit were still discernible within the box

Fig 4.5 STM image of a monolayers of lignoceric acid on HOPG surface (8nm×8nm, Vbias = 666mV, and I set = 50pA)

4.2.4 STM images of 2:1 Binary Acids Solution

It has been shown in section 4.2.2 and 4.2.3 that CH3(CH2)19COOH and

CH3(CH2)22COOH can be differentiated by STM based on the number of bright spots observed within the unit cell The SAMs formed by several binary mixtures with different weight ratios have been studied Only the binary mixture with weight ratio 2:1 showed sufficiently high resolution for further investigation The monolayer

formed by binary mixture of CH3(CH2)19COOH and CH3(CH2)22COOH with weight ratio of 2:1 is shown in Fig 4.6.

Fig 4.6 STM image of a monolayer formed of heneicosanoic and lignoceric acid with a ratio of

2:1 on HOPG (120×120nm, with V bias = 750mV, and I set = 50pA)

There are two different regions within the Fig 4.6, notably separated by the step-like structure in the middle of the image Such lamella structures are quite commonly observed in monolayers High resolution STM studies are necessary to identify the molecular structures of the SAMs The high resolution STM images of the monolayers at different locations of the same piece of sample are shown in Fig 4.7

Fig 4.7 High resolution STM image of the binary monolayers (Vbias =750mV, I set =50pA) A: There are twelve bright spots within unit cell The molecules can be easily identified as lignoceric acid

heneicosanoic acid (CH 3 (CH 2 ) 19 COOH)

Single molecule or unit cell in the high resolution images is enclosed by black box In picture A there are twelve bright spots within the unit cell The molecules can easily been identified as lignoceric acid (CH3(CH2)22COOH) based on previous results of section 4.2.3 It was also observed that within the scanned area in A, all

molecules are very densely packed with uniform lengths and orientation There are no irregular parts within the SAMs to break continuity Therefore it is believed the SAMs within the scanned area are formed by single species - lignoceric acid In picture B the repeating unit which has ten bright spots is identified as heneicosanoic acid (CH3(CH2)19COOH).

Hence, the high resolution STM images of SAMs have shown that the binary species, although mixed in the solution, will form phase-separated monolayers spontaneously instead of the phase-mixed monolayers

4.2.5 Dynamics of SAMs formed by Binary Acids

Considerable dynamics of SAMs were observed during STM studies In Figure 4.8 (A) it was found the lamellae of fatty acids monolayers were not straight but zigzagged, as labeled by the black line on the left The image was captured at t=0s, with tip positioned at x=12.5nm, y=78.6nm At t=245s STM image was captured again with tip positioned at the same place The result was shown in Fig 4.8 (B) The acids molecules packed in such a way that the lamellae became straight, as indicated

by the black line

Fig 4.8 STM images of monolayers at same location (20×20nm, with Vbias = 666mV, and I set = 50pA) (A): zigzag lamellae observed at t = 0s; (B): straight lamellae observed at t = 245s

4.3 Computational Simulations

Computational simulations were carried out for structural modeling and adsorption energies calculations for binary acids that physisorbed on the HOPG surfaces In addition to the STM results, computational simulations can provide supplemental information about the configuration of two species within the

monolayers formed by the binary acids solution

Fig 4.9 Top view of Model A and B with graphite lattice being set to invisible

Two models A and B are shown in Fig 4.9 Model A consisted of two levels of graphite (0 0 1) sheet with each containing 12×30 cells and an array of acids All the carbon atoms from graphite were constrained to represent the bulk property of the graphite crystal Four lignoceric acid molecules were aligned on the left side in a lamella, and four heneicosanoic acids were aligned on the right side in a lamella The acids molecules chose the ‘head to head and tail to tail’ configuration Two lamellae were positioned such that the distance between two closest carbons is ~3.6Å, same as observed in STM results The two nearest oxygen atoms from different acids were 2.5Å apart, which was within the range of hydrogen bonding Model A represented the configuration of phase-separated SAMs Model B represented the configuration of

phase-mixed SAMs In Model B, there are two lignoceric acid molecules and two heneicosanoic acid molecules in each lamella They are placed alternatively in each lamella to represent phase-mixing

Forcite program of Materials Studio was used to optimize the clusters and to obtain the adsorption energies of the adsorbate in various configurations The adsorbate molecules were allowed to be optimized while the carbon atoms from graphite lattice were frozen so as to simulate a bulk-like environment The adsorption energies, Ead for the different configurations were calculated by subtracting the energies of the clusters comprising of the adsorbate molecules and the substrates from the total energies of the free substrate clusters and the gas-phase adsorbate as shown

in equation 2.1:

E ad = E(surface) + E(adsorbate) - E(adsorbate/surface) (2.1) The larger the value of Ead indicates the more stable the cluster is In Models A and B, E(surface) is the energy of the graphite surface; E(adsorbate) is the sum of energy of the gas phase acid molecules, including four lignoceric acids and four heneicosanoic acids; E(adsorbate/surface) is the energy of the whole cluster Apparently, Models A and B have the same E(surface) and E(adsorbate) since they have the same HOPG surface lattice and the same number of adsorbates The E(adsorbate/surface) will be changed accordingly because of the different configuration of acids within the SAMs, The details of calculation results are attached in Appendix 4.1 The final structure energies E(adsorbate/surface) for model A and B are -1245.9kcal/mol and -1228.7kcal/mol respectively

Table 4.2 Comparison of Energies of Model A and Model B after Optimization

The main results are listed in Table 4.2, the contribution from valence energy terms, electrostatic terms and hydrogen bond are almost identical for both Models A and B The largest difference in energy is contributed from the van der Waals, with a difference of 17.2kcal/mol Therefore Model A is more stable than Model B by 17.2kcal/mol and is the thermodynamically favored configuration

4.4 Discussion

4.4.1 Alkyl Group on HOPG

It was observed directly under STM that long alkyl groups were oriented parallel

to the graphite lattice The result is consistent with the conclusions from other groups [2, 3, 9], although those were derived indirectly based on their observations In some previous studies, the relationship between alkyl group and substrate was poorly treated For example, the sp3 C-C bonds of alkyl groups were set to exactly match the sp2 C-C bonds of graphite lattice [14, 22] There has been question about whether the alkane adsorption is driven by the registry between the carbon lattices of adsorbate and substrate or by a 2-D crystallization of the adsorbate on a flat substrate, independent of the substrate lattice [2]

Based on the experimental results, it is suggested that when the alkyl group is parallel to the graphite lattice, the molecule will be more stable Our proposed model

of the first physisorbed molecule beside the step of HOPG surface is shown in Fig 4.10, as the adsorption always starts at the surface defect [20]

Fig 4.10 Proposed adsorption site and orientation of first adsorbed alkyl group on HOPG surface

(top view): The dark lines on the left hand side and middle of the picture are step and adsorbate respectively The honeycomb structure represents the underlying graphite lattice

The latter adsorbates will follow the orientation of the first few with the growth

of SAMs Therefore the driving force of the SAMs formation is not hundred percent

of adsorbate/substrate interaction or crystallization of adsorbate, but a complicated crystallization process with effects from the lattice structure of the substrate.

4.4.2 Phase-separated SAMs vs phase-mixed SAMs

Two possible SAMs formations (phase-separated and phase-mixed) were proposed for the binary system of interest Only phase-separated monolayers were

observed by STM In order to illuminate the experimental results, two clusters consisting of same molecules with different configuration (Model A - phase-separated SAMs and Model B - phase-mixed SAMs) were constructed for computational simulation The results showed that the phase-mixed SAMs were less stable than the phase-separated SAMs by a magnitude of 17.2kcal/mol on the basis of the cluster It is noticeable in the Model A the packing of the adsorbates is more dense than the packing of adsorbates in B Adsorbates within densely packed monolayers experience stronger attractive van der Waals’ forces as they come closer This explanation is in agreement of the fact that the difference in energies of two models is mainly from the factor van der Waals interaction as shown in Table 4.2

Our computational simulation does not reveal the physisorption route and steps of the monolayers formation, instead, it can only provide the energies of the final state of the constructed clusters Hence, the possible SAMs formation routes must be derived based on the experimental results The physisorption of acids onto the HOPG surfaces

is not selective since both heneicosanoic acid and lignoceric acid have very similar molecular structures and chemical properties Pure sample studies also prove that both acids can readily form monolayers on HOPG In this case, when the first layer of adsorbates is formed, it must contain mixture of two species, which may be aligned in lamellae or distributed randomly on the surface This is named as intermediate state S* and can be represented by Model B The van der Waals interactions between the adsorbates and substrates are weak in general therefore the energy barriers E can be overcome easily at room temperature with thermal energies to reach a more stable