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 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. 74 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: O C12H25 N O C12H25 N O O Br O N O C12H25 O DDPER O S S Br N O C12H25 S170 C12H25 N O O C12H25 N O H3CO OCH3 O O N C12H25 S169 O N O C12H25 S171 75 FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS O C12H25 N O H3CO H3CO OCH3 H3CO OCH3 OCH3 O O N C12H25 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. 76 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, Vbias=-666mV, Iset= 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. 77 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, Vbias=-666mV, Iset= 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 78 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 79 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). 80 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* 81 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* 82 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* Functional Br Groups S170* S169* S171* S172* OMe S OMe OMe OMe Height (Å) Width (Å) 1.66 4.23 7.10 7.21 8.16 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. 83 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 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). 84 FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS Fig 5.11 Top view and side view of DDPER molecule on the HOPG (0 1) surface: Initial states 85 FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS Fig 5.12 Top view and side view of DDPER molecule on HOPG (0 1) surface after Dynamics and Geometry Optimization using COMPASS forcefield 86 FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS Fig 5.13 Top view and side view of S170 on HOPG: Initial states 87 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 Experimental the adsorption energies Ead is given by the equation: Ead = E(surface) + E(adsorbate) - E(adsorbate/surface) (2.1) The value of the E(surface) was set to be kcal/mol since all atoms were frozen. 88 FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS Table 5.2 The adsorption energies of DDPER and S170 on HOPG Sample E(surface) E(adsorbate) E(adsorbate/surface) Ead Ead DDPER (kcal/mol) 320.48 230.15 90.33 S170 (kcal/mol) 545.63 456.21 89.42 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 89 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. 90 FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS References: [1]. Newman; Melvin Spencer; (ed) Steric effects in organic chemistry, 1956, New York : John Wiley. [2] Wang, H.N.; Wang, C.; Zeng, Q.D.; Xu, S.D.; Yin, S.X.; Xu, B.; Bai, C.L. Surf. Interface Anal. 2001, 32, 266. [3] Liu, Y.H.; Lei, S.B.; Yin, S.X.; Xu, S.L.; Zheng, Q.Y.; Zeng, Q.D.; Wang, C.; Wan,L.J.; Bai, C.L. J. Phys. Chem. B. 2002, 106, 12569. [4] Xu, S.L.; Zeng, Q.D.; Wu, P.; Qiao, Y.H.; Wang, C.; Bai, C.L. Appl. Phys. A 2003, 76, 209. [5] Mamdouh, W.; Uji-i, H.; Ladislaw, J.S.; Dulcey, A.E.; Percec, V.; De Schryver, F.C.; De Feyter, S. J. Am. Chem. Soc. 2006, 128, 317. 91 [...]... 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) 84 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 85 FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS Fig 5. 12 Top view and side view of DDPER molecule on HOPG (0... after Dynamics and Geometry Optimization using COMPASS forcefield 86 FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS Fig 5. 13 Top view and side view of S170 on HOPG: Initial states 87 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...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 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... 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... 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. .. the equation: Ead = 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 88 FORMATION OF SAMs CONRTOLLED BY STERIC EFFECTS Table 5. 2 The adsorption energies of DDPER and S170 on HOPG Sample E(surface) E(adsorbate) E(adsorbate/surface) Ead Ead DDPER (kcal/mol) 0 320.48 230. 15 90.33 S170 (kcal/mol) 0 54 5.63 456 .21 89.42... at room 89 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,... 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 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 . 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. interaction. 83 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. 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 78 FORMATION OF SAMs CONRTOLLED