Studies of self assembled monolayers on highly oriented pyrolytic graphite using scanning tunneling microscopy and computational simulation 1

INTRODUCTION CHAPTER INTRODUCTION 1.1 The Highly Oriented Pyrolytic Graphite (0 1) Surface The highly oriented pyrolytic graphite (HOPG) (0 1) surface has been a subject of continued interest for more than decades Since the observation of self-assembled monolayers (SAMs) at the liquid/graphite interface [1, 2], a large number of SAMs studies have been carried out The HOPG is a highly ordered form of pyrolytic graphite with an angular spread of the c axis of less than degree It can be synthesized by heat treatment of pyrolytic graphite under compressive stress at temperatures above 3000K [3] As a new form of graphite, the structure of HOPG is now well understood The flatness and conductivity of the HOPG make it one of the best substrates for probe microcopies, such as scanning tunneling microcopy (STM) 1.1.1 Atomic Arrangement of HOPG crystal Graphite is one of the stable forms of pure carbon in nature Other allotropes of carbon include diamond, amorphous carbon, fullerenes, etc The physical properties of carbon vary widely with the allotropic form The atomic arrangement of the HOPG crystal is shown in Fig 1.1 [4] The graphite crystal is built up by layers with the honeycomb arrangement of carbon atoms being strongly covalently bonded to one INTRODUCTION another The nearest-neighbour distance AA’ is 1.42Å The in-plane lattice constant a0 is 2.46Å The layers are spaced 3.35Å apart and are held together by van der Waals forces The most abundant form of graphite in nature is the hexagonal graphite in which the neighboring layers are shifted and result in an ABAB stacking sequence This stacking sequence gives rise to two non-equivalent carbon atom sites within the surface unit cell: carbon atoms in white are on top of carbon atoms of the second layer, whereas the carbon atoms in black are located above the center of the six-fold carbon rings of the second layer [4] Fig 1.1 Crystal structure of HOPG [4]: The graphite crystal is built up by layers with the honeycomb arrangement of carbon atoms being strongly covalently bonded to one another The neighboring layers are shifted and result in ABAB stacking sequence 1.1.2 Electronic Structure of Graphite STM studies of the graphite (0001) surface have revealed images showing a triangular lattice (Fig 1.2) The spacing between the neighbouring bright dots INTRODUCTION observed in the STM images is 2.46Å, suggesting that only every other surface carbon atom appears as a protrusion As shown in the graphite model in Fig 1.1, there are two types of carbon atoms on the top layer: the ‘white’ carbon atoms and the ‘black’ carbon atoms The ‘black’ carbon atoms exhibit a higher local electronic density of states near Fermi level and are therefore expected to appear as protrusions in STM images, whereas the ‘white’ carbon atoms appear as saddle points Fig 1.2 STM image of a freshly cleaved HOPG surface (Vbias=80mV, Iset=30pA) Only every other surface carbon atom appears as a protrusion, hence the unit cell is triangle 1.1.3 Interaction between HOPG Surface and Adsorbates Since HOPG consists of layers held together by van der Waals forces, the layers can be easily cleaved, providing atomically flat terraces of up to several micrometer INTRODUCTION grain size The cleavage of the graphite layer does not create dangling bonds and therefore a freshly cleaved surface is able to stay clean for a long time The interaction between the inert HOPG surface and adsorbates is considered very weak in general [5, 6, 7, 8] Only when the adsobates contain aromatic fragments, the - interaction will be present between the organic compounds and graphite surface [9, 10, 11] - interaction is a noncovalent interaction between aromatic moieties caused by intermolecular overlapping of p-orbitals in -conjugated systems The strength of the interaction rises as the number of -electrons increases It is usually slightly stronger than other noncovalent bondings including van der Waals forces, or dipole-dipole interactions [9] For example, it acts strongly on flat polycyclic aromatic hydrocarbons such as anthracene, triphenylene, and coronene because of great number of delocalized -electrons The - interaction is also orientation dependent [10] Therefore HOPG has been considered as one of the best substrates to study SAMs as its conductivity, flatness, and inertness provide us a suitable environment for STM experiments Last but not least, the structure of the HOPG is well understood and relatively simple and any possible interactions between adsorbates and substrates will not involve fairly intricate processes 1.2 Self-Assembled Monolayers (SAMs) The concept of the self-assembled monolayers (SAMs) is primarily introduced by Zisman in 1946 [12, 13] The traditional SAMs is an organized layer of INTRODUCTION amphiphilic molecules in which one end of the molecule is designed to have a favorable and specific interaction with the solid surface of the substrate A stable monolayer film can be formed when the designed molecules are deposited onto the substrate surface from either vapor or liquid phase A typical example is that the formation of thiolate monolayers on the gold (111) surface (Fig 1.3) Fig 1.3 Schematic of an n-dodecanethiolate monolayer self-assembled on an atomically flat gold substrate [14] The assembly is held together by the bonds between the sulfur headgroups and the gold surface as well as van der Waals interactions between neighboring hydrocarbon chains 1.2.1 Chemisorbed SAMs Much research has been focused on the SAMs because of their potential applications in materials design, nano-devices development, and biological process Works of thiols adsorbed on gold surfaces by Nuzzo and Allara [13, 15] in the early 1980s and trichlorosilanes on silicon oxide by Maoz and Sagiv [13, 16] introduced the two most popular SAMs systems Alkanethiol molecules consist of saturated hydrocarbon chains terminated by a thiol group, which can chemisorb onto gold and INTRODUCTION other metal surfaces [17] The chemisorption process usually involves the breaking of the S-H bond and formation of the S-Metal bond Organosilane molecules can assemble onto silicon dioxide substrates through the reaction with the surface hydroxyl groups [14] to form a monolayer of siloxane at the interface (Fig 1.4) Fig 1.4 Schematic of an organosilane self-assembled on a SiO2 substrate [14] The silane groups condense with surface hydroxyl groups to form a thin layer of polysiloxane The formation of thiolate SAMs and silane SAMs is primarily determined by the covalent bond strength between the adsorbates and substrates, the weak interactions which include hydrogen bonding, electrostatic forces and van der Waals forces not have a significant effect on the process [18] One proposed sequence of the formation of such SAMs is shown in the Fig 1.5 [13] The adsorbates are randomly distributed on the surface at low surface coverage, where the molecule either stands or lies on the surface with its head covalently bonded to the substrate As the surface coverage INTRODUCTION increases, the adsorbed molecules will form a close-packed matrix with uniform molecular orientation Fig 1.5 Schematic of the formation of the traditional SAMs [13] The adsorbates randomly distribute on the surface at low surface coverage, where the molecule either stands or lies on the surface with its head covalently bonded to the substrate As the surface coverage increases, the adsorbed molecules will form a close-packed matrix with uniform molecular orientation 1.2.2 SAMs at the Liquid/HOPG Interface: Current Research Status and Our Objective SAMs at the Liquid/HOPG interface have attracted more and more research attentions in the last two decades with the development of the STM technology Through the years a large number of SAMs formed by organic molecules at the Liquid/HOPG interface have been studied [1,2,19-28] Opposite to the traditional SAMs, the organic molecules deposited at the Liquid/HOPG Interface not form INTRODUCTION covalent bonds with the substrate Instead, the physisorbed molecules interact with the HOPG surface through weak interactions, including van der Waals forces and - interactions In addition to the adsorbates/substrates interactions, the intermolecular interactions also play important roles during the formation of the ordered two dimensional structures Hence the formation of the SAMs at the Liquid/HOPG interface is a rather complicated process in which factors from the intermolecular interactions, adsorbate-substrate interactions, solvent effect, and others must be considered Some factors which affect the formation of the SAMs at the Liquid/HOPG interface have been scrutinized The alkyl chains of adsorbates were found to be able to enhance adsorbates’ desorption barrier, and the stability of the monolayers is strengthened as increasing the alkyl chain length [28-31] The choice of the solution can affect greatly the SAMs patterns, although the exact pattern is hard to be predicted [32] The odd-even effect in the SAMs has also been discussed in details [33-42] Temperature is another important factor that affects the SAMs patterns, as the physisorbed molecules are sensitive to the thermal energies [43] Last but not least, the molecular structure and its functional groups are also crucial during the formation of the SAMs [44, 45] In contrast, very few systematic works towards understanding the mechanism of SAMs formation at the Liquid/HOPG interface has been carried out We devised some simple experiments to provide additional knowledge regarding the SAMs formation mechanism at the liquid/HOPG interface In the first experiment a solution consisting INTRODUCTION of two fatty acids deposited on the HOPG surface was studied (Chapter 4) A series of solutions of perylene derivatives on the HOPG were studied and their results were compared in the subsequent experiment (Chapter 5) The formation of chiral SAMs is shown in Chapter However, for the insightful understanding of the SAMs formation mechanism, theoretical studies employing the Materials Studio programme were also performed to complement the experimental data The calculated results mainly comprised energies of the clusters with different molecular configurations on HOPG 1.3 Proposed Mechanism: 2D crystal Despite decades of study focused on the ordered structures of the SAMs, the principle guiding the formation of these two-dimensional structures is still to be established Previously Steven De Feyter and Frans C De Schryver discussed the usefulness of the STM in studying the physisorbed organic monolayers and types of the SAMs on the HOPG surface [46, 47] Similar works were performed by Wan and coworkers [48] An important phenomenon - odd-even effects in organic SAMs have also been reviewed by Tao and Bernasek [33] On the other hand, Matzger et al [44] classified the ordered two-dimensional monolayers structures according to their symmetry groups, as an important step to link the formation of SAMs on HOPG to the crystallization process systematically In the context of our proposed mechanism, SAMs are considered as two dimensional crystals A crystal is composed of regularly repeating ‘structural motifs’, INTRODUCTION which may be atoms, molecules, or groups of atoms, molecules, or ions [49] Traditionally the repeating ‘structural motifs’ are reproduced in three spatial directions (X, Y, Z) However, in SAMs they are restricted on HOPG surfaces Repeating of ‘structural motifs’ on a plane results in two-dimensional crystals (2D crystals) With the help of 2D crystal model, the derivation of the equations relating the process of SAMs formation was carried out All the factors which affect the SAMs formation process will be referred and further discussed later (refer to Chapter 7) 1.4 Outlook for the Future Work SAMs technology has great potential in many fields: such as biology and nano-electronics Patterning surface with features on the low end of nano-scale can efficiently be achieved with SAMs By understanding the theory behind the formation of SAMs on HOPG, it is possible for us to design SAMs to meet specific application requirements The adsorbates could be synthesized using retrosynthetic methods developed by Nobel Laureate E.J Corey [50-51] Combining these two methods, SAMs with specific patterns and functions can be grown In other words, we may be capable of producing molecular circuit and nano-devices Furthermore, the SAMs which can be formed on HOPG have potential to modify the graphene sheets - one of the hottest ‘future’ materials which might play significant roles in industry and technology [53, 54] 10 INTRODUCTION References [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] Fitzer E.; Kochling, K.-H.; Boehm H.P.; Marsh H Pure & Appl Chem 1995, 67, 473 [4] Thomas W Ebbesen, Carbon Nanotubes: Preparation and Properties, CRC Press, 1996, p10 [5] Tsai, W.H.; Cave, N.G.; Boerio, F.J.; Langmuir 1992, 8, 927 [6] Nicolau, D.V.; Watson, G.S.; Cahill, C.; Blach, J.; Myhra S Technical Proceedings of the 2004 NSTI Nanotechnology Conference and Trade Show, 2004, 1, p103 [7] Tao, F.; Cai, YG.; Bernasek S.L.; Langmuir 2005, 21, 1269 [8] Zheng, Z.J.; Zuo, D.L.; Li D.H.; J Vac Sci Technol B 1994, 12, 1832 [9] http://en.wikipedia.org/wiki/Stacking_(chemistry) [10] Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M.; Tanabe, K J Am Chem Soc., 2002, 124, 104 [11] Hunter, C.A.; Sanders, J.K.M J Am Chem Soc., 1990, 112, 5525 [12] Bigelow, W.C.; Pickett, D.L.; Zisman, W.A J Colloid Interface Sci 1946, 1, 513 [13] Schwartz, D.K Annu Rev Phys Chem 2001, 52,107 [14] Smith, R.K Lewis, P.A Weiss, P.S Prog Surf Sci 2004, 75, [15] Nuzzo, R.G.; Allara, D.L J.Am.Chem.Soc 1983, 105, 105 [16] Maoz, R.; Sagiv, J J.Colloid Interface Sci 1984, 100, 465 11 INTRODUCTION [17] Palmer, R.E; Guo, Q Phys Chem Chem Phys 2002, 4, 4275 [18] Ulman, A Chem Rev, 1996, 96, 1545 [19] Plass, K E.; Engle, K M.; Cychosz, K A.; Matzger, A J Nano Lett 2006, 6, 1178 [20] Venkatraman, B.; Breen, J.J.; Flynn, G.W J Phys Chem 1995, 99, 6609 [21] Gesquiere, A.; Jonkheijm, P.; Hoeben, F.J.M.; Schenning, A.P.H.J.; De Feyter, S.; De Schryver, F.C., Meijer, E.W Nano Lett 2004, 4, 1175 [22] Rohde, D.; Yan, C.J.; Yan, H.J.; Wan, L.J Angew Chem Int Ed 2006, 45 3996 [23] Schuurmans, N.; Uji-I, H.; Mamdouh, W.; De Schryver, F.C.; Feringa, B.L.; Jan van Esch; De Feyter, S J AM Chem Soc, 2004, 126, 13884 [24] Watson, M.D.; Jäckel, F.; Severin, N.; Rabe, J.P.; Müllen, K J Am Chem Soc 2004, 125, 1402 [25] Lei, S.B.; Yin, S.X.; Wang, C Wan, L.J.; Bai, C.L J Phys Chem B, 2004, 108, 224 [26] Qiu, X.H.; Wang, C.; Zeng, Q.D.; Xu, Bo.; Yin, S.X.; Wang, H.N.; Xu, S.D.; Bai, C.L J Am Chem, Soc 2000, 122, 5550 [27] Yablon, D.G.; Wintgens, D.; Flynn, G.W J Phys Chem B 2002, 106, 5470 [28] Tao F.; Bernasek, S.L J Am Chem Soc 2005, 127, 12750 [29] Lei, S.B.; Yin, S.X.; Wang, C.; Wan, L.J.; Bai, C.L Chem Mater 2002, 14, 2837 [30] 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 [31] Qiu, X.H.; Wang, C.; Yin, S.X.; Zeng, Q.D.; Xu, B.; Bai, C.L J Phys Chem B 12 INTRODUCTION 2000, 104, 3570 [32] 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 [33] Tao, F.; Bernasek, S.L.; Chem Rev 2007, 107, 1408 [34] Tao, F.; Bernasek, S L J Phys Chem B 2005, 109, 6233 [35] Fang, H.B.; Giancarlo, L C.; Flynn, G.W J Phys.Chem B 1998, 102, 7421 [36] Yablon, D.G.; Giancarlo, L C.; Flynn, G.W J Phys Chem B 2000, 104, 7627 [37] Kim, K.; Plass, K.E.; Matzger, A.J J Am Chem Soc 2005, 127, 4879 [38] De Feyter, S.; Grim, P.C.M.; van Esch, J.; Kellogg, R.M.; Feringa, B.L.; De Schryver, F.C J Phys Chem B 1998, 102, 8981 [39] Wei, Y.; Kannappan, K Flynn, G.W.; Zimmt, M.B J Am Chem Soc 2004, 126, 5318 [40] Taki, S.; Kai, S Jpn J Appl Phys., Part 2001, 40, 4187 [41] Wintgens, D.; Yablon, D.G.; Flynn, G.W J Phys Chem B 2003, 107,173 [42] Tao, F.; Bernasek, S.L Langmuir 2007, 23, 3513 [43] Rohde, D.; Yan, C.J.; Yan, H.J.; Wan, L.J Angew Chem Int Ed 2006, 45 3006 [44] Plass, K.E.; Kim, K.; J Matzger, A.J Acc Chem Res., 2007, 40, 287 [45] De Feyter, S.; De Schryver, F C.; Chem Soc Rev., 2003, 32, 139 [46] De Feyter, S.; Gesquiére, A.; Abdel-Mottaleb, M.M.; Grim, P C.M.; De Schryver, F C Acc Chem Res 2000, 33, 520 [47] De Feyter, S.; De Schryver, F.C J Phys Chem B 2005, 109, 4290 [48] Wan, L.J Acc Chem Res 2006, 39, 334 13 INTRODUCTION [49] Atkins, P.W Physical Chemistry, Oxford University Press, 1998, p 620 [50] Corey, E J.; Cheng, X.M The Logic of Chemical Synthesis, New York: Wiley 1995 [51] Corey, E J Chem Soc Rev 1988, 17, 111 [52]Corey, E J Angew Chem Int Ed 1991, 30, 455 [53] Geim, A.K Science 2009, 324, 1530 [54] Geim, A.K ScienceWatch 2008: August 2008 Author Commentaries 14 ... concept of the self- assembled monolayers (SAMs) is primarily introduced by Zisman in 19 46 [12 , 13 ] The traditional SAMs is an organized layer of INTRODUCTION amphiphilic molecules in which one... development, and biological process Works of thiols adsorbed on gold surfaces by Nuzzo and Allara [13 , 15 ] in the early 19 80s and trichlorosilanes on silicon oxide by Maoz and Sagiv [13 , 16 ] introduced... deposited onto the substrate surface from either vapor or liquid phase A typical example is that the formation of thiolate monolayers on the gold (11 1) surface (Fig 1. 3) Fig 1. 3 Schematic of an n-dodecanethiolate