Review Paper Manipulation of Organic Molecules in Ambient

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e-Journal of Surface Science and Nanotechnology 12 April 2014 e-J. Surf. Sci. Nanotech. Vol. 12 (2014) 157-164 Review Paper

Manipulation of Organic Molecules in Ambient Condition and Liquid Studied by Scanning Tunneling Microscopy

Tomohide Takami∗ Department of Physics, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea, and VRI Inc. 4-13-13 Jingumae, Shibuya, Tokyo 150-0001, Japan (Received 10 January 2014; Accepted 24 February 2014; Published 12 April 2014)

This review describes how the manipulation of single molecules on solid state surface is available in air or at the liquid/solid interface, observed with scanning tunneling microscope (STM). First, the inﬂuences of the STM tip on the observation and manipulation of molecules are discussed. Then how the STM tip induced the ordering and how the molecular structures on the surface can be manipulated are shown. Second, the manipulation of single molecules with STM tip is demonstrated. Last, the STM observations of the manipulation of molecules by changing the ambient conditions such as solvent, photon irradiation, and electrochemical potential, are shown. [DOI: 10.1380/ejssnt.2014.157] Keywords: Atom/molecule manipulation; Scanning tunneling microscopy; Graphite; Phthalocyanine; Porphyrin, Self- assembled monolayer

I. INTRODUCTION

Since Eigler and Schweizer at IBM Almaden demonstrated how single atoms can be manipulated with the tip of a scanning tunneling microscope (STM) [1] and Jung et al. at IBM Zurich demonstrated how single molecules can be manipulated [2], various kinds of atoms and molecules were manipulated with the STM tip [3]. The scanning tunneling microscope [4] is an instrument not only used to see individual atoms by imaging but also used to touch and take the atoms or to hear their vibration by means of manipulation, and it can be considered as the eyes, hands and ears of the researcher,connecting our macro-world to the nano-world [5]. In case of ultrahigh vacuum (UHV) and low temper- atures (< 77 K), STM observation is stable and diffusion of molecules is constrained and no obstacles such FIG. 1: Schematic diagram of molecular adsorption and mo- as adsorbents exist so that the manipulation of a single tion on surface. The blue line shows the energy potential (E) in vertical direction (z), with the potential well corresponding atom/molecule is with facility [6]. In case of ambient con- to the adsorption energy of E . Red line shows it in the lateral dition, however, we have to consider not only the interac- a direction (x), with the diffusion barrier of Edif . tion between the single atom/molecule and the substrate but also the effect of drift, diffusion, and adsorbates [7]. The author has made progress in the manipulations of from the substrate to allow manipulation with the STM the large molecules thanks to collaborators who are ex- tip. Moresco and Gourdon demonstrated how the DtBP pert in large-molecule synthesists. Phthalocyanine on sil- group works as a leg [10]. icon surface [8] is not suitable system for the study of The other famous example of the use of molecular de- single molecular manipulation due to the strong interac- sign for the single-molecular manipulation is “nanocar” tion between the molecule and dangling bonds of the sub- synthesized by Jim Tour’s group. The nanocar was strate. Though changing the substrate to a noble metal first driven with the STM tip in UHV by Kevin Kelly’s can reduce the interaction, the manipulation at room tem- group [11]. Recently, a motor has been added to the perature is not available due to the “skating” (diffusion) nanocar and it now can be driven by photons – no need of the molecules on the substrate. In order to overcome to push with the STM tip [12]. The other example is the diffusion problem, the author consulted with Ken-ichi “Molecular Landers”, or “Molecular Moulds”, synthesized Sugiura and in 1992 we had the idea to attach four 3,5- by Andre Gourdon [13]. The DtBP groups are utilized for di-tert-butylphenyl (DtBP) groups on the large molecule the legs, and the molecular landers have been manipulated as legs [9]. The DtBP group has been widely used for the with the STM tips [14]. legs of molecules, maintaining the active part high enough On the other hand, in liquid, electrochemical STM is a powerful method since it is possible to use potential to control the surface structure [15]. However, the STM tip ∗Corresponding author: [email protected],takami@institute. used for electrochemical STM is covered with insulator for jp; Present address: RcMcD, Graduate School of Science, Hi- the reduction of leakage current and the covered insulator roshima University, [email protected] can be an obstacle for the manipulation. This is a prac-

ISSN 1348-0391 ⃝c 2014 The Surface Science Society of Japan (http://www.sssj.org/ejssnt) 157 Volume 12 (2014) Takami Fig. 3

FIG. 2: Schematics showing how the electric ﬁeld from the STM tip puts a perturbation to the structure of observing molecule. tical reason why manipulation with the electrochemical STM is diﬃcult. There are a number of review papers on the manipula- FIG. 3: Initial stage STM image of 2,9,16,23-tetra- tion of single molecules with STM [5, 6, 16–19]. However, tert-butylphthalocyanine at the graphite-octylbenzene inter- most of the manipulation studies have been conducted face. The drift during the observation was compensated in UHV or low temperature. In this review paper, we and the compensation sequence is schematically described show our work on the manipulation of organic molecules in http://www.ttakami.com/drift html/DriftTakamiFig1.jpg and DriftTakamiFig2.jpg. The HOPG surface vectors a and at the interface between liquid and solid state substrate 1 a2 were determined from the step line in the upper right of and would like to answer a question “To what extent can the image. The directions of the molecular alignments in each we manipulate single molecules in the air or in liquid?”. domain were indicated at the right side of the image. The matrices give the structure of each domain. From Ref. [31]. Copyright 2010 Surface Science Society of Japan. II. THEORY ON STM MANIPULATION

When a molecule is adsorbed on the surface with the that STM tip surface is clean. We can also control the environment by adding diﬀerent liquid such as polar solvent, adsorption energy Ea and trapped in the well of diﬀu- as discussed in Chapter V. sion barrier Edif , and vibrating laterally in the well with the period τ0 (typically in the order of picoseconds), as shown in Fig. 1, the mean dwelling time of molecule on the surface, τ, is estimated from the following equation III. EFFECT OF STM TIP ON OBSERVING (1) [20]. MOLECULES

τ = τ0 exp (Edif /kT ) , (1) Scanning tunneling microscopy is a powerful tool for the determination of atomic structures such as the Si(111)7×7 where k is Boltzmann constant and T is ca. 300 K (room structure [22, 23]. However, the electric field from temperature) in this study. The binding energies of for the STM tip can perturb the structure of an adsorbed physisorbed molecules are typically 0.25 eV or less [20]. molecule, as shown in Fig. 2. It is possible to argue that We have to consider this interaction between the molecule structure determined by STM might differ from other and substrate during the manipulation. Hla categorized methods such as X-ray diffraction. Considering the in- the STM manipulation as lateral manipulation and verti- fluence of the strong electric field from STM tip, in the cal manipulation [5]. In liquid, however, we can add two order of 1 V/nm (109 V/m), deformation of the molecule more categories in the STM manipulation; insertion and under an STM tip is unavoidable. Soe et al. [24] demon- extraction of the molecules in the solution, since the liquid strated with their STM study that the D4h flat structure solution can be the source or drain of the molecules. of copper phthalocyanine is distorted into C4v structure In the air, we cannot forget to treat the effect of menis- due to the adsorption on Au(111) surface [25]. Girard cus between the tip and surface due to the existence of et al. [26] calculated the local electric field in the tip- water. The existence of water caused the oxidation of ma- sample gap, and field induced diffusion processes of a ph- terials in some case, which can be utilized for the nano- ysisorbed atom were discussed. Moresco et al. [27, 28] ob- fabrication of graphene oxides on graphene surface [21]. served Cu-tetrakis-di-tert-butylphenylporphyrin and the In liquid, on the other hand, the environment between observed molecules had two-fold symmetry whereas the the STM tip and sample is more well-defined than that original molecular structure has four-fold symmetry. The in the air because the liquid can be chosen in such a way author concluded that the perturbation to the observing

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Fig. 4 adsorbed benzene and carbon monoxide molecules on rhodium (111). Lippel et al. [34] reported high-resolution images of phthalocyanine on copper (100) surface. Hall- mark et al. [35] observed the rotation of naphthalene on platinum (111) surface at room temperature. Griessl et al. succeeded in playing “nanosoccer”, as shown in Fig. 4 [36]. They manipulate single Buckminster fullerene molecules with a Pt/Ir STM tip at the interface between the solvent of heptanoic acid and the template monolayer of trimellitic acid on graphite. They mentioned phenyloctane or dodecane did not work as the solvent in this study [36], which might be due to the property of heptanoic acid forming the monolayer network. Gimzewski and co-workers manipulated molecular abacus of fullerenes at copper steps in UHV [37]. Although functioning only slowly as a calculator for demonstration purposes, the work shows that complex molecules can be manipulated with STM. Shigekawa et al. manipulated molecular abacus of rotaxane necklace with the STM tip FIG. 4: Playing “nanosoccer” with fullerene. (a) STM topo- in air [38], as shown in Fig. 5. Each bead of the abacus graph of the starting situation with a single C60 guest molecule is a single molecule of a glucose complex of cyclodextrin. inside the trimesic acid host network. (b) Manipulation step: The cyclodextrin molecule is shaped like a truncated hol- after half the molecule was scanned, the tunneling current was low cone. Each molecular bead slides along a “wire” made switched from imaging to manipulation conditions; after the from polyethylene glycol. molecule was transferred to the adjacent cavity the imaging conditions were restored. (c) Final result of the lateral manip- Scudiero and Hipps [39] manipulated physisorbed self- ulation with the whole molecule imaged in the target cavity. assembled nickel octaethylporphyrin (NiOEP) monolayer (d) Illustration of the trimesic acid network and the manipula- on graphite. They fabricated the pattern of molecule- tion process; the horizontal line indicates the lines which were free regions created by removal of NiOEP molecules from scanned with an increased reference current. From Ref. [36]. the surface when the STM is operated at the tunneling Reprinted with permission. Copyright 2004 American Chem- resistance of about 120 MΩ or less. They showed that ical Society. the removed molecules were not collecting at the bound- aries of the scanned regions. Once the molecular film was damaged, the size of the uncovered area kept on growing molecule from the STM tip should be considered for the with subsequent scans. They also observed that the tri- structure analysis with STM. This kind of deformation clinic and tetragonal monolayer structures formed under induced by STM tip should be considered during the ma- the same experimental conditions. nipulation of single molecules. These works were conducted with the STM tip, and Also, scanning the STM tip in liquid can induce the more sophisticated method of manipulation is necessary ordering of the surface structure, which was pointed out in order to meet practical needs. To be useful, a much from the early days of STM studies of liquid crystal, called faster method of manipulation is needed. Molecular ma- anchoring the molecule [29]. However, the initial stage nipulation without using an STM tip is shown in the next imaging with molecular resolution is usually difficult due chapter. to the initial large mechanical drift of the position between the tip and sample. The initial mechanical drift can be avoided in the following sequence. (1) Observe substrate V. MANIPULATION OF MOLECULES WITH and scan until the drift stopped. (2) Retract the STM ENVIRONMENTAL CONDITIONS tip slightly from the sample in the order of several ten nanometers. (3) Drop the solution on the substrate. (4) Tip manipulation can also be used to perform chemi- Close the STM to the sample until tunneling, and observe. cal reactions with single molecules. Lafferentz et al. [40] In this way, we obtained the virgin scan STM image with measured the conductance of single polymer chains with molecular resolution as shown in Fig. 3 [30, 31]. The Y STM. In their work, polyfluorene chains were synthesized scan direction is from lower to upper in the image. The on Au(111) surfaces and the individual manipulation of large periodic Moire pattern was observed at the initial these chains by the STM tip allowed the length-dependent stage, as shown in the lower domain in the image. measurement of chain conductivity [40]. The STM tip can also be used to initiate and control the growth of single- chain molecular wires. Okawa et al. [41] reported the IV. MANIPULATION OF SINGLE MOLECULE controlled synthesis of polydiacetylene chains on graphite WITH STM TIP surfaces. They demonstrated that this technique allows construction of molecular electronics made single-chain Initial studies of the observation of organic molecules polymer devices realize. were conducted by Shirley Chiang and co-workers [32]. On the other hand, molecular manipulation with ex- The first observation of organic molecule with STM was ternal variables, such as illumination or electrochemical reported by Ohtani et al. [33] on the surface of co- potential, is possible at the nanoscale and the process can http://www.sssj.org/ejssnt (J-Stage: http://www.jstage.jst.go.jp/browse/ejssnt/) 159 Volume 12 (2014) Takami Fig. 5

FIG. 5: Manipulation of cyclodextrin beads in rotaxane with STM tip in air. Left figures: (a) Structure of the “molecular necklace”, and three modes (b, c, and d) of the shuttle manipulation by STM. Middle figures: a typical STM image of the molecular necklace (upper) and its schematic structure (lower). Right figure: STM images of the simple-shuttling (a-c). From Ref. [38]. Reprinted with permission. Copyright 2000 American Chemical Society. be observed with STM. Kumar et al. manipulated the dimensional arrays of phthalocyanine derivative molecules cis-trans azobenzene molecular switch with ultraviolet controlled by the choice of solvent. A pseudosquare lat- light [42]. Figure 6 shows that the isolated azobenzene- tice array was formed using 1-bromo-4-n-octylbenzene, functionalized molecules in the matrix of dodecanethi- whereas a pseudohexagonal two-dimensional ordered ar- ols rendered stability, allowing the control over reversible ray was formed using 1-bromo-8-phenyl-octane. In the photoswitching. Such rigid assembly can potentially be parent solvent, octylbenzene, only one-dimensional order- utilized in stabilizing single molecules for other switching ing is observed with occasional regions of dimer row for- studies in which the matrix plays a key or interfering role. mation. Solubility and solvent-metal complexation mech- The assembly of practical molecular devices may become anisms were ruled out as major contributors to the struc- possible with increased stability in ambient conditions and tural reorganization. improved understanding of photoswitches. The author et al. also succeeded in manipulating Ye et al. manipulated a molecular shuttle with electro- double-decker phthalocyanine complexes with the STM chemical potential [43]. Using electrochemical STM, they tip [45]. They have controlled and manipulated phthalo- observed electrochemically controlled station changes of cyanine and the double-decker molecules with STM. Par- individual bistable rotaxane molecules in situ, as shown tial substitution of the double-decker monolayers with in Fig. 7. Motions of the cyclobis(paraquat-p-phenylene) octakis(octyloxy)-phthalocyanine was accomplished by rings were correlated with redox states of the tetrathiafu- nanografting, and the substituted domains formed bi- lalene station relative to the 1,5-dioxynaphthalene station layer stacks epitaxially on graphite. Figure 9 demon- and showed partial reversibility. The trajectories of the strates nanografting of double-decker phthalocyanine rings suggest that once a bistable rotaxane molecule is ad- molecules in matrices of single layer octakis(octyloxy)- sorbed on a surface, the motion of the cyclobis(paraquat- phthalocyanine. Rectangular scans with a STM tip at p-phenylene) ring relative to the dumbbell is affected by low bias voltage resulted in the removal of the adsorbed its local environment and the flexibility of the molecule. double-decker molecular layer and substituted bilayer- Bistable rotaxane molecules with rigid dumbbells should stacked octakis(octyloxy)-phthalocyanine from phenyloc- enable consistent and fully reversible motions, as well tane solution. These results demonstrate compositional as direct visualization of the rings and the shafts of control through scanning probe lithography at the liquid- the molecules. The molecular design and synthesis of solid interface at room temperature. Moreover, single- such systems are underway. Consistent and complete re- molecular decomposition of heteroleptic double-decker versibility of switching in these bistable molecules will molecules of a lutetium complex sandwiched with naph- be required for efficient actuation of nanoelectromechani- thalocyanine and octaethylporphyrin with voltage pulses cal devices and for reliable nanoelectronic device applica- applied by the STM tip was demonstrated: the top oc- tions. taethylporphyrin ligand was removed, and the bottom The author et al. manipulated surface structure naphthalocyanine ligand remained on the surface. A do- with polar solvents [44]. Figure 8 demonstrates two- main of the decomposed molecules was formed in the

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FIG. 6: Azo-molecular switch. Upper left: schematics showing photo-induced changes in apparent height of the azobenzene- functionalized molecules in STM images due to isomerization of the azobenzene moiety between trans and cis are defined as on (apparent height ) 2.1 (0.3 A)˚ and off (apparent height ) 0.7 (0.2 A)˚ states, respectively. Right images: azobenzene- functionalized molecules switch off and switch on upon irradiation with ultraviolet (∼365 nm) and visible (∼450 nm) light, respectively. Images are recorded after irradiating (A) 0 min, (B) 10 min, (C) 35 min, (D) 60 min, and (E) 160 min with ultraviolet light and visible light irradiation for (F) 30 min. A–E show switching off of single molecules with continued UV illumination. The squares in E and F show switching on of molecules with visible illumination. The arrow in E shows switching on of a molecule with UV illumination. Lower left: fraction of azobenzene-functionalized molecules in the on state decreases as a function of time of ultraviolet irradiation (12 mW/cm2). The decay constant (τ) under these conditions is 54 minutes. From Ref. [42]. Reprinted with permission. Copyright 2008 American Chemical Society.

(lower middle), a double-decker molecule was extracted from the layer and another double-decker molecule ﬁlled in a vacancy. In this way, room temperature manipulation of single molecules with the STM tip at the liquid-solid interface is available. Recently, Mao et al. [46] measured the lateral critical force for the manipulation of single phthalocyanine molecule on Pb(111) surface in UHV with the STM combined with non-contact atomic force microscope. The observed average value of 25 pN is typically two times larger than the molecule–substrate interaction. At the liquid–solid interface, the critical force should be increased while the desorption of manipulated molecules from the interface is suppressed by the solvent.

FIG. 7: Rotaxane shuttle controlled by electrochemical potential. (A) The tetracationic cyclobis(paraquat-p-phenylene) VI. CONCLUSION AND FUTURE DIRECTIONS ring (CBPQT4+, blue) is known to move along the thread between two recognition sites (tetrathiafulvalene, TTF, green and 1,5-dioxynaphthalene, DNP, red stations) depending on This review paper has demonstrated that the manipu- the redox state of the TTF unit. (B) The protrusions are as- lation of molecules in air or in liquid is available in several signed as CBPQT4+ rings. (C) In its reduced state at +0.12 V, cases. 1-phenyloctane is one of the best solvents for this the CBPQT4+ ring prefers to encircle the TTF station. (D) purpose because it prevents molecules in liquid from the Upon oxidation (+0.12 to +0.53 V) of the TTF station into adsorption on STM tip. Stability of STM tip is also im- a radical cation, electrostatic repulsion propels the ring to portant in order to realize the certain manipulation with- the DNP station (blue arrow). (E) Upon reduction (+0.53 out destroying the manipulated structure. to +0.12 V) of the TTF station to neutrality, the metastable Finally, the author would like to demonstrate the per- state of the bistable rotaxane relaxes back to its thermody- spective for the future study on nanoscale patterning with namically favorable state, wherein the CBPQT4+ ring occu- pies the TTF station (red arrow). From Ref. [43]. Reprinted self-assembly observed with the STM. with permission. Copyright 2010 American Chemical Society. Fabrication of Penrose patterning with local five-fold symmetry [46, 47] using five-fold symmetrical molecules such as ferrocene [48] would be interesting for the control of surface nanoscale properties. In case of metals and double-decker molecular domains, and the boundary of alloys, the fabrication of five-fold symmetric structure is the decomposed molecular domain re-formed to be rectan- available, such as quasi-crystal [49] and multiply-twinned gular via self-curing. Figure 10 demonstrated a molecular particle [50]. Though the STM images of the quasi-crystal “sliding block puzzle” with the cascades of double-decker alloys with five-fold symmetric structure have been re- molecules. After the first image was recorded (lower left), ported [51–53] and there are several attempts to fabricate two double-decker molecules slid to the adjacent vacan- Penrose tiling with five-fold symmetric molecules [54–56], cies. Moreover, after the second image was recorded nobody has succeeded in fabricating two-dimensional Pen- http://www.sssj.org/ejssnt (J-Stage: http://www.jstage.jst.go.jp/browse/ejssnt/) 161 Volume 12 (2014) Takami

FIG. 8: Manipulation of interface structure of copper-tetra(t-butyl)phthalocyanine at the interface of octylbenezene solvent and graphite. (Upper) Scanning tunneling microscope images of the phthalocyanine molecules before adding extra solvents. Image scale: 50 nm×50 nm (left), 20 nm×20 nm (middle), and 1.8 nm×1.8 nm with molecular resolution (right). (Lower) the STM images after adding the 0.1 ml solvent of octylbenezene with no change (left), 1-bromo-4-n-octylbenzene changed into square lattice (middle), and 1-bromo-8-phenyl-octane changed into hexagonal lattice (right). The local density of state maps of each solvent for highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) obtained from the ab initio molecular orbital calculation are shown beside the corresponding STM images. The STM images are from Ref. [44]. Reprinted with permission. Copyright 2010 American Chemical Society.

FIG. 9: Sliding block puzzle (upper left) playing with double- decker molecules. (Upper middle) Schmatics of the double- decker molecules aligned on surface. (Upper right) Scanning FIG. 10: (Left) Schematics showing the preparation of tunneling microscope image of naphthalocyanine-lutetium- mixed layers of octakis(octyloxy)phthalocyanine and octaethylporphyrin double-decker molecules on graphite be- naphthalocyanine-lutetium-octaethylporphyrin double- fore the playing of nanoscale sliding block puzzle. Scan- decker on graphite by nanografting. (Right) Scanning ning tunneling microscope images of sliding blocks of tunneling microscope images of the mixed double-layered naphthalocyanine-lutetium-octaethylporphyrin double-decker octakis(octyloxy)phthalocyanine and naphthalocyanine- molecules: (lower left) before sliding, sliding molecules are lutetium-octaethylporphyrin double-decker molecules on indicated by arrows, (lower middle) after sliding but before graphite, prepared by STM tip manipulation (nanografting), extracting and ﬁlling the double-decker molecule, indicated as shown in the left schematics. From Ref. [45]. Reprinted by arrows, and (lower right) after extracting and ﬁlling. The with permission. Copyright 2010 American Chemical Society. STM images are from Ref. [45]. Reprinted with permission. Copyright 2010 American Chemical Society.

order [58]. Though one-dimensional Fibonacci superlat- rose tiling with molecules with the bottom-up method. tice has been fabricated and studied [59, 60], nobody has Various examples of Fibonacci patterning are available in ever succeeded in fabricating two-dimensional Fibonacci nature; phyllotaxis as a dynamical self-organizing process pattern with molecules, either. These are the near-future during the ontogeny [57] or the seed pattern of helianthus topics of nanoscale self-assembly, which provide the novel annuus (sunﬂower) with the predominance of Fibonacci application from organic surface science.

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Acknowledgments Jianzhuang Jiang Group at Shandong University, China (present: University of Science and Technology Beijing), The author would like to thank his collaborators and the STM work at Washington State University were on this work; the STM studies at Pennsylvania State conducted in Professor Kerry W. Hipps Group. The au- University were conducted in Professor Paul S. Weiss thor is also grateful to Professor Kerry W. Hipps for the Group (present: CNSI, UCLA), the double-decker corrections in this paper. This study is supported by Vi- molecules used in this study were synthesized at Professor sionarts Inc. (present: VRI Inc.).

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