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

PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG CHAPTER PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 4.1 Motivation n-Alkanes, alcohols and alkyl acids can readily form self-assembled monolayers (SAMs) on highly ordered pyrolytic graphite (HOPG) surface. Since the observation of organic SAMs on HOPG by McGonigal et al. [1], this subject had been extensively studied. Rabe et al. examined the two dimensional molecular patterns formed by long chain alkanes, alcohols, fatty acids and dialkylbenzene on HOPG by STM together with Molecular Dynamics (MD) simulation, in which they found that the substrate could effect the orientation of the adsorbates [2, 3]. Determination of chirality of molecules on HOPG surfaces using STM was achieved by Flynn and coworkers [4]. Hydrogen bonding in SAMs was studied by Bai et al. using STM and DFT calculations [5]. The temperature effect of the alkanes monolayers on HOPG was also investigated by Rabe et al. [6] and Kern et al. [7]. In addition, the alkane monolayers were used as buffer layers to support nanometer-sized domains of other organic molecules on the HOPG surface [8-12]. However, a detailed understanding on the formation mechanism of SAMs is still to be gained, necessary for the development of the technologies to build up two dimensional molecular nanostructures, which may in turn benefit the development of molecular electronics. For further investigation of the mechanism of SAMs formation, a binary system was studied using STM and computational method. There are few reports regarding 52 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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: 53 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG Table 4.1: Weight ratios of heneicosanoic acid  lignoceric acid in phenyloctane solution Ratio A Ratio B Ratio C Heneicosanoic Acid 100 67 Lignoceric Acid 33 100 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. 54 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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: CH3(CH2)19COOH 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. 55 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG Fig 4.2 STM image of a monolayer of heneicosanoic acid on HOPG surfaces (8nm×8nm, Vbias = 666mV, and Iset = 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 56 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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 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) 57 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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(CH2)19COOH 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 CH3(CH2)22COOH Fig 4.5 shows the STM image of a monolayer of CH3(CH2)22COOH adsorbed on 58 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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 Iset = 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 59 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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 Vbias = 750mV, and Iset = 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. 60 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG Fig 4.7 High resolution STM image of the binary monolayers (Vbias=750mV, Iset=50pA). A: There are twelve bright spots within unit cell. The molecules can be easily identified as lignoceric acid (CH3(CH2)22COOH); B: the repeating unit which has ten bright spots is identified as heneicosanoic acid (CH3(CH2)19COOH). 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 61 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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. 62 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG Fig 4.8 STM images of monolayers at same location (20×20nm, with Vbias = 666mV, and Iset = 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 63 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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 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 64 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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: Ead = 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. 65 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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]. 66 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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 67 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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 68 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG conformation S - the final state. Proposed potential energy diagram for physisorption process is shown in Fig 4.11. When the temperature of the sample is raised high enough, the adsorbates at the final states can overcome the energy barrier E’– this is the melting of the monolayers which have been observed by Bruch et al. [21]. Fig 4.11 Proposed schematic potential energy diagram for the proposed physisorption of binary acids on HOPG surface 4.4.3 Dynamics of SAMs formed by Binary Acids In Fig 4.8 (A), the atomic resolution was not achieved. It can still be observed that the edges of the lamellae are parallel to each other although they are zigzag. This observation suggested that the monolayers contained not binary mixture but one type of acid only so the lamellae would exhibit same width. The scan of Fig 4.8 (A) started about one hour after first drop of sample solution was applied onto freshly cleaved HOPG surface. It implies that the formation of the 69 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG fatty acids SAMs on HOPG is not an instant process. The zigzag conformation of lamellae is rarely observed in our STM studies. On the contrary the conformation shown in Fig 4.8 (B) is much more common. Therefore the SAMs structure in Fig 4.8 (A) is considered as a meta-stable conformation, while the SAMs structure in Fig 4.8 (B) is the thermodynamically favored state. That means it is the most stable conformation of SAMs on HOPG at room temperature. 4.4 Conclusions The STM and computational calculations were used to study the physisorption of binary acids (heneicosanoic acid and lignoceric acid) mixture on HOPG surfaces at room temperature. On the basis of STM results, the heneicosanoic acid and lignoceric formed phase-separated SAMs spontaneously. Furthermore, the high resolution STM image revealed that the orientation of long alkyl group was parallel to the orientation of the graphite surface lattice, providing an experimental evidence for the existence of adsorbate-substrate interaction. Two models were built to simulate the two possible configurations of acids within SAMs: phase-mixed and phase-separated. Forcite program package of Materials Studio was applied to both systems. The calculation results agree with the experimental results that the phase-separated SAMs are more stable than the phase-mixed SAMs. Through the binary system we studied, the mechanism of the SAMs formation 70 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG has been proposed. More data collection and insightful discussion are presented in Chapter 7. 71 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG Reference [1] McGonigal, G.C.; Bernhardt, R.H.; Thomson, D.J. Appl. Phys. Lett. 1990, 57, 28. [2] Rabe, J.P.; Buchholz, S. Science 1991, 253, 424 [3] Hentschke, R.; Schürmann, B.L.; Rabe, J.P. J. Chem. Phys. 1992, 96, 6213. [4] Fang, H.B.; Giancarlo, L.C.; Flynn, G.W. J. Phys. Chem. B, 1998, 102, 7311. [5] Yin, S.X.; Wang, C.; Xu, Q.M.; Lei, S.B.; Wan, L.J.; Bai, C.L. Chem Phy Lett 2001, 348, 321. 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Soc. 2003, 125, 1655. 73 [...]... configuration of two species within the 63 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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... conformation of lamellae is rarely observed in our STM studies On the contrary the conformation shown in Fig 4. 8 (B) is much more common Therefore the SAMs structure in Fig 4. 8 (A) is considered as a meta-stable conformation, while the SAMs structure in Fig 4. 8 (B) is the thermodynamically favored state That means it is the most stable conformation of SAMs on HOPG at room temperature 4. 4 Conclusions... 666mV, and Iset = 50pA) (A): zigzag lamellae observed at t = 0s; (B): straight lamellae observed at t = 245 s 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... 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... zigzag This observation suggested that the monolayers contained not binary mixture but one type of acid only so the lamellae would exhibit same width The scan of Fig 4. 8 (A) started about one hour after first drop of sample solution was applied onto freshly cleaved HOPG surface It implies that the formation of the 69 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG fatty acids SAMs on HOPG is not an instant... model A and B are -1 245 .9kcal/mol and -1228.7kcal/mol respectively 65 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG 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... (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... 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. .. 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... [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 . 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. 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. STM results, computational simulations can provide supplemental information about the configuration of two species within the 63 PHYSISORPTION OF BINARY FATTY ACIDS ON HOPG monolayers formed