Nanoscale Reversible Molecular Extraction from a Self-Assembled

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Langmuir 1998, 14, 7197-7202

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Nanoscale Reversible Molecular Extraction from a Self-Assembled Monolayer on Gold(111) by a Scanning Tunneling Microscope Wataru Mizutani,*,† Takao Ishida,‡ and Hiroshi Tokumoto† Joint Research Center for Atom Technology (JRCAT)sNational Institute for Advanced Interdisciplinary Research (NAIR), 1-1-4 Higashi, Tsukuba, 305-8562 Japan, and JRCATsAngstrom Technology Partnership (ATP), 1-1-4 Higashi, Tsukuba, 305-0046 Japan Received April 16, 1998. In Final Form: October 1, 1998 Alkanethiol self-assembled monolayers (SAMs) on Au(111) deposited in a vacuum were studied on the nanometer scale using a scanning tunneling microscope (STM). After about 17 h from the gas dose of 4200-6000 langmuirs nonanethiol, two-dimensional crystallized domains were observed. The areas covered with the molecules and the bare gold surface were identified by topography, current-voltage characteristics, and the threshold voltage required to modify the surface. By applying 2.6-3.0 V to the sample, we could extract molecules and create holes with diameters of 2-5 nm in the SAM film. Applying 14 voltage pulses of 2.6 V to a 10 nm diameter circle on the sample locally removed the SAM film. We could then observe the dynamic formation process of the SAM film with molecular resolution using the STM, and within 5 min, the removed area was seen to be almost recovered with the molecular lattice except for a small number of incurable defects. Since the recovered area looked identical to the pristine film, we concluded that the molecules can be locally extracted without causing damage to the gold substrate under this condition.

1. Introduction Nanometer-scale fabrication is a requirement for future microelectronic devices, and also has applications in highdensity data storage. Enormous efforts have been made in device technology and nanotechnology, and scanning probe microscopes (SPMs) are playing an important role in these fields.1 Self-assembled monolayers (SAMs) are expected to be used as a high-resolution resist, since the film thickness is uniform and the molecules are highly ordered.2 Patterning SAM films is therefore crucial for their applications. For example, a very promising microcontact printing method was developed by Whitesides and coworkers, and they demonstrated patterns with line widths as small as 100 nm.3-6 The performance of the monolayer resist was also shown for metals3,5,6 and silicon oxides.7-10 We have been investigating different methods of nanoscale * To whom correspondence should be addressed. E-mail: water@ nair.go.jp. † JRCATsNAIR. Permanent address: Electrotechnical Laboratory, Tsukuba, Ibaraki, 305-8568 Japan. ‡ JRCATsATP. (1) (a) Binnig, G.; Rohrer, H.; Gerber, Ch.; Weibel, E. Phys. Rev. Lett. 1983, 50, 120. (b) Scanning Tunneling Microscopy; Stroscio, J. A., Kaiser, W. J., Eds.; Academic Press: San Diego, CA, 1993. (c) Wiesendanger, R. Scanning Probe Microscopy and SpectroscopysMethods and Applications; Cambridge University Press: Cambridge, 1994. (2) (a) Ulman, A. An Introduction to Ultrathin Organic Films from Langmuir-Blodgett to Self-Assembly; Academic Press: San Diego, CA, 1991. (b) Ulman, A. Chem. Rev. 1996, 96, 1533. (3) Kumar, A.; Biebuyck, H. A.; Whitesides, G. M. Langmuir 1994, 10, 1498. (4) Kim, Y. Xia E.; Zhao, X.-M.; Rogers, J. A.; Pretiss, M.; Whitesides, G. M. Science 1996, 273, 347. (5) Xia, Y.; Whitesides, G. M. Langmuir 1997, 13, 2059. (6) Xia, Y.; Venkateswaran, N.; Qin, D.; Tien, J.; Whitesides, G. M. Langmuir 1998, 14, 363. (7) Sugimura, H.; Nakagiri, N.; Ichinose, N. Appl. Phys. Lett. 1995, 66, 3686. (8) Sugimura, H.; Nakagiri, N. J. Am. Chem. Soc. 1997, 119, 9226. (9) Sugimura, H.; Nakagiri, N. J. Vac. Sci. Technol., B 1997, 15, 1394. (10) Komeda, T.; Namba, K.; Nishioka, Y. Appl. Phys. Lett. 1997, 70, 3398.

patterning, e.g., SAM lines with a width of 5 nm on GaAs,11,12 and phase-separated binary SAM with domains less than 100 nm.13-18 For practical use, however, these patterns need to be trimmed further by other techniques, such as SPM lithography. The resolution attained with nanoscale fabrication techniques is quite dependent on the materials. In some cases, individual atoms and molecules were successfully manipulated using SPM. For example, Eigler and Schweizer demonstrated sliding individual atoms using a low-temperature scanning tunneling microscope (STM).19 Recently, Cuberes et al., and Jung et al. moved single molecules on Cu surfaces at room temperature by pushing them with an STM tip.20,21 On the other hand, the sizes of the modifications of SAMs with SPM lithography by some groups were larger than 10 nm.22-26 Kim and Bard observed alkanethiols on gold, and etched the film in air under the condition of large current and low bias voltage.22 Under their conditions, the tip touched the films and a substantial mechanical force was exerted, resulting in the etching. They also applied voltage pulses (11) Ohno, H.; Nagahara, L. A.; Gwo, S.; Mizutani, W.; Tokumoto, H. Jpn. J. Appl. Phys. 1996, 35, L512. (12) Ohno, H.; Nagahara, L. A.; Gwo, S.; Mizutani, W.; Tokumoto, H. Mol. Cryst. Liq. Cryst. 1997, 295, 189. (13) Stranick, S. J.; Parikh, A. N.; Tao, Y.-T.; Allara, D. L.; Weiss, P. S. J. Phys. Chem. 1994, 98, 7636. (14) Tamada, K.; Hara, M.; Sasabe, H.; Knoll, W. Langmuir 1997, 13, 1558. (15) Ishida, T.; Yamamoto, S.; Mizutani, W.; Motomatsu, M.; Tokumoto, H.; Hokari, H.; Azehara, H.; Fujihira, M. Langmuir 1997, 13, 3261. (16) Yamamoto, S.-I.; Ishida, T.; Mizutani, W.; Tokumoto, H.; Yamada, H. Jpn. J. Appl. Phys. 1997, 36, 3868. (17) Ishida, T.; Mizutani, W.; Tokumoto, H.; Hokari, H.; Azehara, H.; Fujihira, M. Appl. Surf. Sci. 1998, 130-132, 786. (18) Mizutani, W.; Ishida, T.; Yamamoto, S.-I.; Tokumoto, H.; Hokari, H.; Azehara, H.; Fujihira, M. Appl. Phys. A 1998, 66, S1257. (19) Eigler, D. M.; Schweizer, E. K. Nature 1990, 344, 524. (20) Cuberes, M. T.; Schlittler, R. R.; Gimzewski, J. K. Appl. Phys. Lett. 1996, 69, 3016. (21) Jung, T. A.; Schlittler, R. R.; Gimzewski, J. K.; Tang, H.; Joachim, C. Science 1996, 271, 181. (22) Kim, Y.-T.; Bard, A. J. Langmuir 1992, 8, 1096.

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(3 V) and created pits with diameters of 5-10 nm on SAM surfaces. However, they were unable to obtain molecular resolution in their experiments. In 1994, it was discovered that high-impedance observation conditions enabled individual molecules in SAM films to be visualized reproducibly and stably.27-29 Prior to that, molecular resolution was rather limited,30 and only “depressions” on the SAM surface were observed with the STM.22,31,32 The molecular images are obtained under the highimpedance conditions with the STM, namely, the tunneling gap is large. When we apply voltage pulses to the SAM film under the above conditions, the produced field cannot be confined to a molecular scale but often results in the modification with the size larger than 10 nm. In addition, the film surface is generally covered with a water layer in air, which might also make the modified area large. Surface modification by the STM tip is generally sensitive to environmental conditions such as humidity and oxygen. Under ambient conditions, some uncharacterized electrochemical processes might occur due to the surface water layer. For example, Schoer and Crooks studied STM lithography of the SAM film on gold.26 They applied voltages of 2.3-3.0 V to the SAM in air and in N2 and found that the modification did not take place at a relative humidity less than 25%. Thus, they proposed that the modification is caused via the faradaic electrochemistry in the adsorbed water. To develop a single molecular manipulation technique for SAM films, we have to avoid such reactions and to ensure repeatable experimental conditions by performing experiments in ultrahigh vacuum (UHV). We could actually create holes with diameters less than 5 nm on the SAM film by applying voltage pulses close to the threshold in UHV without degrading the molecular resolution. Furthermore, we observed that the extracted molecules returned to the uncovered area and re-formed the film. For the re-formation of the SAM film, the molecules must be desorbed without causing damage to the gold substrate and the molecules themselves. This finding of reversible extraction conditions will be of practical importance, since we will be able to refill other molecules into the extracted area as demonstrated by Xu and Liu25 and fabricate heterogeneous structures. 2. Experimental Section Gold substrates were prepared by evaporating gold onto cleaved mica at an elevated temperature in a vacuum. The detailed preparation method is described elsewhere.33,34 The (23) Dressick, W. J.; Calvert, J. M. Jpn. J. Appl. Phys. 1993, 32, 5829. (24) Lercel, M. L.; Redinbo, G. F.; Craighead, H. G. Appl. Phys. Lett. 1994, 65, 974. (25) Xu, S.; Liu, G.-Y. Langmuir 1997, 13, 127. (26) (a) Schoer, J. K.; Zamborini, F. P.; Crooks, R. M. J. Phys. Chem. 1996, 100, 11086. (b) Schoer, J. K.; Crooks, R. M. Langmuir 1997, 13, 2323. (27) Scho¨nenberger, C.; Sondag-Huethorst, J. A. M.; Jorritsma, J.; Fokkink, L. G. J. Langmuir 1994, 10, 611. (28) Delamarche, E.; Michel, B.; Gerber, Ch.; Anselmetti, D.; Gu¨ntherodt, H.-J.; Wolf, H.; Ringsdorf, H. Langmuir 1994, 10, 2869. (29) Poirier, G. E.; Tarlov, M. T. Langmuir 1994, 10, 2853. (30) Widrig, C. A.; Alves, C. A.; Porter, M. D. J. Am. Chem. Soc. 1991, 113, 2805. (31) Ha¨ussling, L.; Michel, B.; Ringsdorf, H.; Rohrer, H. Angew. Chem., Int. Ed. Engl. 1991, 30, 569. (32) Molecular lattice images with practically no defects were obtained by force microscopy by Alves and co-workers, but we think that the probe should touch the surface over a large area and detect only the periodicity of the surface in this case. (a) Alves, C. A.; Smith, E. L.; Porter, M. D. J. Am. Chem. Soc. 1992, 114, 1222. (b) Alves, C. A.; Porter, M. D. Langmuir 1993, 9, 3507. (33) Nie, H.-Y.; Mizutani, W.; Tokumoto, H. Surf. Sci. 1994, 311, L649.

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Figure 1. (a) Derivative image of STM topography of the gold surface half covered with a SAM film. (b) Molecular lattice of the SAM film. Several point defects are seen. We used a bias voltage of 0.8 V and set the current at around 20 pA. gold substrate was taken out of the evaporation chamber, quickly mounted on a sample holder in air, and then loaded into a homebuilt UHV-STM. After evacuating the chamber down to 10-8 Torr, we introduced nonanethiol (CH3(CH2)8SH, Aldrich, purified by distillation under reduced pressure) gas through a valve.35 Nonanethiol is a liquid at room temperature; thus we need to heat the vial and the transfer line (a stainless tube extending to near the substrate). Before opening the valve, we evacuated the line by another vacuum pumping system. Our dosing conditions were (1.4-2.0) × 10-5 Torr for 5 min (4200-6000 langmuirs, 1 langmuir ) 10-6 Torr‚s). In this experiment, we activated the gauge in the vacuum chamber during deposition. Since the gas is introduced near the sample surface through a tube, and the reactivity of the thiol to gold is superior to that of the hydrocarbon fragments, the SAM formation should not be degraded, although atomic sulfur may be incorporated in the film and can be seen as defects whose density is not large, as shown in Figure 1. We controlled the pressure by a manual valve and roughly estimated the dosage, since the precise value is not necessary in this work. The order of magnitude of our evaluated value is comparable with the reported values, such as 40 000 langmuirs36 and 117 800 langmuirs.37 These authors observed the striped phase at the initial stage (5-20 langmuirs). It seems that a certain amount of molecular pressure may be needed to reorganize the initial phase into a more densely packed phase. The substrate temperature was 27-28 °C, a little higher than room temperature because of the hot filament of the vacuum gauge. We used a mechanically ground Pt tip. (We selected a noble metal whose reactivity to thiol is not high.) For molecular resolution STM imaging of the SAM films described in this paper, we used a bias voltage of 0.8 V and set the current around 20 pA. In this high-impedance observation mode, the STM tip is expected to be positioned a few tenths of a nanometer away from the film without touching the molecules. For the STM modification, we moved the Pt tip closer to the surface by 0.5-0.8 nm relative to the observation mode position prior to the application of the voltage pulse. After the approach, the tip position was fixed, and a voltage pulse of 2.6-3.0 V was applied to the sample.38 A pulse duration of 70-200 ms was used depending on the tip condition, and the current rose to a value larger than 140 nA. Application of voltages larger than about 3.5 V often caused drastic changes in morphology. Without (34) Mizutani, W.; Ohi, A.; Motomatsu, M.; Tokumoto, H. Jpn. J. Appl. Phys. 1995, 34, L1151. (35) We did not observe the Au(111) reconstruction in UHV in this experiment. We could observe the reconstruction in air for several hours after the gold was taken out of the evaporation chamber.33,34 The disappearance of the reconstruction suggests the existence of weak adsorbates in UHV, which should be easily replaced by thiols. (36) Himmel, H.-J.; Wo¨ll, Ch.; Gerlach, R.; Polanski, G.; Rubahn, H.-G. Langmuir 1997, 13, 602. (37) Kondoh, H.; Kodama, C.; Nozoye, H. J. Phys. Chem. 1998, B102, 2310. (38) Since the affected area can be reduced, this prior approach was often adopted for the atomic scale modification. (a) Lyo, I.-W.; Avouris, Ph. Science 1991, 253, 173. (b) Hosoki, S.; Hosaka, S.; Hasegawa, T. Appl. Surf. Sci. 1992, 60/61, 643.

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Figure 2. (a) Derivative image of the domain boundary of the SAM. On the left-hand side (A), the molecular lattice is seen. From the STM measurement, the domain A is 0.12 nm higher than the right-hand side (B). (b) Current (I)-voltage (sample bias) characteristics on the areas A and B. the prior approach, we could not modify the surface with a 100 ms pulse of 3 V. The choice of the voltage and the duration is a tradeoff between the reproducibility and the sizes of the holes.

3. Results A. Characterization of Monolayer Film. About 17 h after dosing nonanethiol, we imaged the sample using STM and observed clear domains on the Au terraces (Figure 1a). The domains exhibited a highly ordered twodimensional hexagonal crystal structure with a lattice spacing of 0.5 nm (Figure 1b). At this later stage of the adsorption, we did not observe the striped phases39 where the molecules adsorb with their axes parallel to the surface. At the edge of the domain, the height of the film measures 0.12-0.14 nm.40 We measured current-voltage (I-V) characteristics on the area showing a molecular lattice (A in Figure 2) and on the other area (B). The I-V curves measured on area B are more linear and similar to data obtained on a bare gold substrate. We could not make a hole in area B by applying a voltage pulse of less than 3 V to the tip, suggesting that we observed the gold substrate on area B, since we reported that pulses larger than 3.5 V were required to produce holes on bare gold in UHV.41 It is, however, possible that some invisible molecules in the disordered phase or liquid phase are present on area B as well.37 In contrast, we could make a hole in area A by applying a voltage pulse of 3 V. Therefore, we conclude that area A was covered with a monolayer of the alkanethiol. There exist a small number of stable single molecular defects in the SAM film as shown in Figure 1b. In this paper, we focus on the artificial formation of such small defects. As shown in Figure 1a, the density of the depressions is smaller than that of SAMs made by dipping the substrate in a molecular solution. The origin of those depressions has been studied extensively,27,42,43,44 but is still controversial.45 Since molecules are often observed (39) Poirier, G. E.; Pylant, E. D. Science 1996, 272, 1145. (40) From the length of the molecule and the tilt angle (30° from surface normal), we estimated the actual film thickness to be about 1 nm. The thickness of 0.13 nm measured by the STM does not agree with the film thickness in this case, because the electronic state of the film is different from that of the substrate.22 For comparison, we note that Poirier and Pylant measured the film thickness of mercaptohexanol on Au as 0.08 nm,39 while the estimated thickness is about 0.7 nm. (41) Ohi, A.; Mizutani, W.; Tokumoto, H. J. Vac. Sci. Technol. 1995, B13, 1252. (42) Poirier, G. E.; Tarlov, M. T. J. Phys. Chem. 1995, 99, 10966. (43) Poirier, G. E. Langmuir 1997, 13, 2019. (44) Dishner, M. H.; Hemminger, J. C.; Feher, F. J. Langmuir 1997, 13, 2318. (45) Patten, P. G. Van; Noll, J. D.; Myrick, M. L. J. Phys. Chem. 1997, B101, 7874.

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Figure 3. (a) Nanoscale hole formation on SAM films by voltage pulses using the STM. (b) Magnified image of a created hole. Around the holes, the molecular lattice is often disordered.

in these depressions,27,42 the depression structure is not directly related to the molecular extraction and will not be discussed in this paper. B. Modification. Figure 3 shows an example of the modification. We applied 14 voltage pulses of 2.7 V onto a 50 nm diameter circle and created 11 holes with depths between 0.1 and 0.12 nm and one protrusion as shown in Figure 3a. Here we achieved a success rate of 85%, but the reproducibility of the modification was strongly dependent on the tip condition; good tips were usually degraded after hours of operation, and often recovered by the application of large voltage pulses. Figure 3b shows one of the smallest structures created by a 100 ms pulse of 2.6 V. Newly created holes seem to be active, and some of them caught materials which are imaged as protrusions instead of depressions. We can speculate on various reasons for the activity of the newly created holes. For example, an electric dipole layer due to the S-Au bonds is formed.46 The field gradient generated from the exposed dipole at the hole may attract charged materials. The measured depth of the created holes is almost identical to the measured height of the film (0.12-0.14 nm), showing that the voltage application did not etch the gold substrate.47 Some of the I-V characteristics measured at the created holes are similar to those measured on the bare gold surfaces (B in Figure 2b). We thus conclude that the molecules were removed from the surface by the voltage pulse, leaving the holes behind. It should be noted that, at some holes, we observed I-V curves similar to the ones measured on the SAM film. We will discuss the differences among the created holes later. Even with the same tip and under the same conditions, the diameters of the depressions were still distributed between 2 and 5 nm. This variation of the size may result from uncontrollable tip change after each modification. C. Recovery of the Film. It was difficult to create holes separated by less than 5 nm; they usually merged. Applying 14 voltage pulses of 2.6 V to a small area, e.g., onto a 10 nm diameter circle, resulted in the removal of the SAM film in the area, as shown on the right-hand side of Figure 4a. We could not observe the periodic structure (atomic lattice or reconstruction) in the uncovered area just after the removal of the film. Figure 4 shows a series of STM images recorded every 25 s. The experiment was carried out under a pressure of 10-8 Torr, and we did not supply extra molecules to refill the area during this experiment. (46) Scho¨nenberger, C.; Jorritsma, J.; Sontag-Huethorst, J. A. M.; Fokkink, L. G. J. J. Phys. Chem. 1995, 99, 3259. (47) With STM, the depth of the hole with a lateral size comparable to the tip radius is measured smaller, when the tip apex cannot reach the bottom while the side of the tip senses the edge of the hole. This geometric artifact may be one of the reasons for the smaller measured depth than the measured film thickness.

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Figure 4. Time-lapse observation of recovery of the uncovered area by the voltage pulses. The images were recorded every 25 s. (It took nearly 20 s to scan one image.) The observed area moved slightly from one frame to the other. The arrows indicate the same spot as a guide for the eye.

In Figure 4b, we moved the scanning area to the center of the denuded area, and a faint image of small domains showing a molecular lattice with a periodicity of 0.5 nm appeared. Such faint images were reported by Stranick et al.,48 and will be discussed later. In Figure 4c, the removed area was occupied by more stabilized domains, whose positions still fluctuated as shown in parts d-g of (48) Stranick, S. J.; Kamna, M. M.; Weiss, P. S. Science 1994, 266, 99.

Figure 4. The domains grew larger and the gaps between the domains became smaller as more molecules adsorbed back onto the surface. The molecular readsorption continued further as we continued scanning the tip. Due to the thermal drift, the observed area moved slightly from one frame to the other. The arrows in the figures indicate the same spot. In general, the molecular lattice grew constantly, but the defects seemed to grow as seen from Figure 4f to Figure 4g, and from Figure 4j to Figure 4k. In the domains, the molecules are expected to be

Reversible Molecular Extraction

arranged on the (x3×x3)R30° adsorption site on Au(111). Because there are six equivalent choices (phase) of the adsorption site on Au(111), the individual domains may have different phases in the beginning. When the domains with different phases meet, a phase boundary will be formed if both domains are sufficiently large. In the case of small domains such as the ones we observed in the re-formation process, we speculate that they can adjust the phase by removing one of the domains by thermally activated motion and the molecules should adsorb again with the same phase as the remaining domain. Within 5 min, the denuded area of 10 nm square was almost recovered with the molecular lattice, and the recovery process proceeded further till most of the defects shrank and disappeared. (Some defects remained, e.g., the one indicated by the arrow and the three holes in the upper-right are in Figure 4l. Note that the positions of these defects also fluctuated.) In this series of experiments, we did not observe the striped phase where the molecules adsorb with their axes parallel to the surface during the re-formation process. Poirier and Pylant observed the formation of the molecular layer in situ using a UHV-STM.39 They discovered that the reconstruction of the Au(111) substrate plays an important role in the initial adsorption, involving the reorganization of the substrate which forms the depressions, and the characteristic molecular adsorption phase such as the striped phase. It is, however, worthwhile to compare the self-assembly process without such reconstruction. Actually, our observation of the SAM reformation process on the uncovered substrate exhibited a simple formation of a two-dimensional molecular crystal which should reflect intermolecular interaction and the interactions between the molecules and the substrate. 4. Discussion In UHV, the modification of the gold surfaces required voltage pulses larger than 3.5 V to the STM tip,41 while the modification was possible with a voltage pulse of 3 V in air.34 The difference may be due to the existence of a surface water layer which may alter the tunneling condition or mediate some chemical reactions. The field strength should be weaker if such a layer contributed to the electric conduction, because the surface would be shielded by the layer. The lower threshold voltage observed for the modification of gold surfaces in air suggests that the contribution from other effects should be significant. Such effects may be considered to account for the contradiction between our results and the observation by Crooks and co-workers.26 Since the molecules used in their experiments are almost twice as long as ours, the field strength may not attain the threshold value for the molecules to be extracted in the dry condition. In high humidity, it is possible that some adsorbates might mediate the modification and reduce the threshold voltage. Several models are proposed for the mechanism of the surface modification in UHV by voltage pulses using the STM. For a gold tip and a gold surface, Mamin et al. explained the phenomena by field evaporation.49 Avouris et al. concluded that an electronic excited state should contribute to the STM-induced hydrogen desorption from Si(100) surfaces.50 We found that negative voltages of -3 V to the sample did not extract molecules from SAMs, although negative voltage pulses to the sample sometimes (49) Mamin, H. J.; Guethner, P. H.; Rugar, D. Phys. Rev. Lett. 1990, 65, 2418. (50) Avouris, Ph.; Walkup, R. E.; Rossi, A. R.; Shen, T.-C.; Abeln, G. C.; Tucker, J. R.; Lyding, J. W. Chem. Phys. Lett. 1996, 257, 148.

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caused deposition from the tip, especially shortly after the modification experiments. These results are consistent with the report by Kim and Bard22 and strongly indicate the field evaporation mechanism. However, longer pulses (∼500 ms) of voltages below the threshold sometimes caused modification, suggesting that some excitation is induced by the large current. Therefore, we conclude that the modification is made through the combination of injected electrons and strong fields, as proposed by Wang et al.51 This mechanism can explain the reduction of the threshold voltage observed in the experiments performed in air, because some adsorbates may enhance the current flow by reducing the tunneling barrier. We observed that a small number of holes did not heal over and remained in the film as shown in Figure 4. Generally, all extracted molecules may not return to the denuded area; some of them may be captured at other sites or some may simply diffuse away. If the molecules are extracted without changing the gold substrate and the created holes remain uncovered simply due to the shortage of molecular supply, the I-V characteristics will be similar to those of bare gold (B in Figure 2b). We actually obtained such I-V curves at some holes, but we also recorded I-V characteristics similar to the ones observed on the SAM films (similar to A in Figure 2b). In a different experiment, we created two adjacent holes separated by 10 nm and observed them continuously for 1 h. One of the holes shrank, while the other remained unchanged. In this case, because the molecular supply should have been similar, there should have been some structural difference between the holes caused during the extraction process. There is a possibility of, for example, cleavage of the S-C bond in the molecule due to the electron transfer through the molecules by the voltage pulse.52 If the S-C bond is cleaved and only the upper part of the molecule is extracted by the voltage pulse, the remaining sulfur could block the thiol adsorption on the site, although the appearance of the created holes would look similar. The binding energy of the S-C bond is about 74 kcal/mol,53 while the Au-S binding energy is estimated to be 45 kcal/mol.54 Since the estimated energy difference is within a order of magnitude, we think that the probability of the S-C cleavage is not negligible and that a higher energy will produce more S-C cleavage. We observed that the holes made with a pulse voltage around 3 V were more stable than those with 2.6 V pulses, but the diameters of the created holes tended to be larger as pulses of larger voltage were applied. For creating smaller holes, we have to use pulses of smaller voltages, and the defects created by the pulse close to the threshold voltage are apt to recover. For the molecular scale patterning, stabilization of the modified area is of great importance. Thus the blocking mechanism may be crucial for realizing the single molecular manipulation. We speculate that some of the natural single molecular defects shown in Figure 1b might be occupied by some adsorbates. Now we discuss where the molecules extracted with this method go; they can stay either around the area or on the tip. The molecules may diffuse on the denuded area, but they could not be visualized by the STM because of their quick motion. Such an invisible gas phase was (51) Wang, C.; Li, X.; Shang, G.; Qiu, X.; Bai, C. J. Vac. Sci. Technol. 1997, B15, 1378. (52) Lamp, B. D.; Hobara, D.; Porter, M. D.; Niki, K.; Cotton, T. M. Langmuir 1997, 13, 736. (53) Zhong, C.-J.; Porter, M. D. J. Am. Chem. Soc. 1994, 116, 11616. (54) Nuzzo, R. G.; Zegarski, B. R.; Dubois, L. H. J. Am. Chem. Soc. 1987, 109, 733.

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reported by Stranick et al. using a low-temperature STM.48 They imaged the benzene molecules on a Cu surface adsorbing in two to four rows at the step edges. At the third and fourth rows, the molecular image is faint, similar to what we observed in Figure 4b, because the molecules stayed there for only a fraction of the time, while for the rest of the time, they were moving as two-dimensional gas molecules on the terrace. Thus, we consider that the invisible molecules may exist around the area during the recovery process. Just after the extraction, however, the presence of invisible molecules on the surface is unlikely. We applied voltage pulses and scanned the area once to confirm the modification. Then we set the tip position at about 100 nm above the film surface, waited for 1 min, and approached again. The uncovered area observed after these procedures did not recover as much as the surface continuously scanned for 1 min. As the surface was continuously scanned, the re-formation proceeded. Thus, we concluded that most of the extracted molecules were transferred to the tip and that during the re-formation process, the molecules were supplied from the tip. The surface diffusion of the molecules is substantially enhanced by the presence of the STM tip. This is known as field-assisted diffusion observed on Cs atoms and explained by the induced dipole moment.55 Surface diffusion of Sb dimers was studied using the STM by Mo,56 and the displacement y of each dimer was measured. Then, the diffusion coefficient D was estimated using the formula 〈y2〉 ) 2Dt, where t is the time in which the displacement occurred. In our experiments, the molecules cannot be identified; therefore, the square displacement 〈y2〉 cannot be measured directly. We can roughly estimate the (55) Stroscio, J. A.; Eigler, D. M. Science 1991, 254, 1319. (56) Mo, Y. W. Phys. Rev. Lett. 1993, 71, 2923.

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molecular displacement from the images shown in Figure 4, if we assume that the molecules that refill the hole and form the lattice exist in the hole (supplied from the tip) in the previous image (e.g., the hole near the bottom in Figure 4e). Since the displacement estimated from the hole size is y ∼ 2-3 nm, we obtain D ∼ 0.1 nm2/s (t ) 25 s was used). Since molecules need not diffuse directly, this estimation gives a lower limit of the diffusion coefficient. In a previous work on the domain formation of binary SAM, we estimated D ∼ 1 nm2/s at 100 °C.15 5. Conclusion In summary, we formed SAM films of nonanethiol on Au(111) surfaces in UHV and locally removed the molecules from the film by applying voltage pulses using the STM in the absence of the humidity-mediated reaction. The threshold voltage for the hole creation is around 2.6 V, which is smaller than the threshold for modifying bare gold surfaces in UHV. Although we were unable to manipulate single molecules, we were able to fabricate holes with a minimum diameter of 2 nm, i.e., in terms of molecular number, less than 10 molecules could be removed from the film. By choosing a pulse voltage near the threshold value, we could remove the film without causing damage to the gold substrate. We then observed the re-formation process of the SAM film with molecular resolution using the STM. The recovery occurred in a time scale of several minutes. For realizing the nanoscale patterning by extracting single molecules from the film, we need to suppress the recovery process by, for example, supplying other molecules in the created holes. Acknowledgment. This work was supported by the New Energy and Industrial Technology Development Organization (NEDO) of Japan. LA9804379