NANO LETTERS
Cross-Step Place-Exchange of Oligo(phenylene−ethynylene) Molecules
2005 Vol. 5, No. 11 2292-2297
Amanda M. Moore,† Brent A. Mantooth,†,‡ Zachary J. Donhauser,†,§ Francisco Maya,| David W. Price, Jr.,| Yuxing Yao,| James M. Tour,*,| and Paul S. Weiss*,† Departments of Chemistry and Physics, The PennsylVania State UniVersity, UniVersity Park, PennsylVania 16802-6300, and Department of Chemistry and Center for Nanoscale Science and Technology, Rice UniVersity, Houston, Texas 77005-1892 Received August 27, 2005; Revised Manuscript Received October 3, 2005
ABSTRACT We have observed nitro-functionalized oligo(phenylene−ethynylene) molecules exhibiting motion up and down Au{111} substrate monatomic step edges within host self-assembled monolayers of n-alkanethiols, independent of previously observed conductance switching. Single molecules have been imaged with scanning tunneling microscopy to place-exchange reversibly between the top and bottom of monatomic substrate step edges.
If future devices are to operate on a single molecule basis, their design and operation will require an understanding of the electronic properties, dynamics, and interactions of the molecules utilized. We have examined these interactions for isolated, conjugated molecules inserted into insulating host self-assembled monolayers (SAMs) using scanning tunneling microscopy (STM). Conductance switching of inserted conjugated molecules has been well characterized by our group and others.1-9 In this Letter, we show that inserted molecules can diffuse between accessible sites up and down substrate step edges, in addition to exhibiting conductance switching. Various mechanisms have been suggested for conductance switching,1,2,4,6 yet the motion discussed in this Letter occurs independently and is uncorrelated with switching events observable on the time scale of these STM images. Previously, we have analyzed conductance switching for single oligo(phenylene-ethynylene)s (OPE)s inserted into host alkanethiolate matrices using STM. We have found these molecules to switch conductance reversibly and stochastically between discrete states with a bimodal distribution indicating an “on” and “off” state for the inserted molecules. The molecules display persistence times in each state varying from fractions of seconds to tens of hours.10 The packing of the host matrix around the inserted molecule is deterministic in conductance state stability and its interactions with the * Corresponding authors. E-mail:
[email protected],
[email protected]. † The Pennsylvania State University. ‡ Current address: Geo-Centers, Research and Development Center, Manassas, VA 20110. § Current address: Department of Chemistry, Vassar College, Poughkeepsie, NY 12604. | Rice University. 10.1021/nl051717t CCC: $30.25 Published on Web 10/18/2005
© 2005 American Chemical Society
surface.1,2,6,11 Through changes in the degree of order in the matrix,1,2 as well as changes in the functionality of the matrices themselves,3 we have shown effects on the rate of switching exhibited by the inserted molecules. From these results, we have concluded that conductance switching is the result of a change in hybridization at the substrate-molecule interface.1,2,6 Motion that leads to Ostwald ripening and domain coalescence has been observed within SAMs.12-16 During SAM deposition, substrate vacancy islands form, which are attributed to the ejection of Au surface adatoms during the relaxation of the Au{111} herringbone reconstruction.13-15,17-20 As the SAM develops from a disordered to an ordered state, vacancy islands evolve from many small vacancy islands to a few large vacancy islands, consistent with Ostwald ripening. This process occurs through single Au vacancies diffusing from the edges of smaller vacancy islands to the edges of larger vacancy islands. The driving force for this migration is the reduction of the total step energy. Since the relative location of vacancy islands remains fixed, it is unlikely that coalescence (island diffusion) is involved in large vacancy formation.13-15 Furthermore, motion is far more rapid at step edges and domain boundaries than elsewhere on the surface due to decreased coordination.21 Our previous work has discussed coalescence of SAM components via diffusion using mixed monolayers formed from two types of alkanethiolate chains with similar length but different terminal functionality.12,16 These alkanethiolates form phase-segregated SAMs with domains of common terminal functionality. After solution deposition of the mixed SAMs, small domains coalesce into larger domains, display-
Figure 1. (a) Thiol and (b) disulfide forms of nitro-functionalized oligo(phenylene-ethynylene) molecules inserted and analyzed for switching and motion up and down substrate step edges. Insertion onto the Au{111} surface occurs at existing defect sites in the host SAM matrix.
ing motion working (enthalpically) toward a local minimum. The observed coalescence of different molecular species through the monolayer mainly occurs at defects, steps, and other areas where surface coverage is lowered because motion in a tightly packed monolayer is only available through collective hindered motions.12,16 Of relevance to the discussion below are place-exchange mechanisms at step edges, such as one proposed by Kellogg and Feibelman.22 Using field-ion microscopy, they determined the activation barrier for diffusion of Pt adatoms on a Pt substrate. Diffusing adatoms have two possible mechanisms to reach the lower terrace: over the top of a surface atom or replacement of a surface atom in a concerted motion. Adatoms traveling over the top of the surface atoms would have a relatively high barrier for migration due to decreased coordination with substrate atoms. For the concerteddisplacement process, a Schwoebel barrier was calculated. This barrier is the difference of the barrier for motion of the adatom down a step minus the barrier for motion of the substrate atom being displaced.23,24 Since the activation barrier for self-diffusion of the adatom was low, Kellogg and Feibelman concluded that the adatom-substrate atom exchange process with a small Schwoebel barrier was the only feasible mechanism because hopping over a surface atom would have a significantly higher activation barrier.22 Here, nitro-functionalized OPEs were analyzed using a custom-built STM operating under ambient conditions.25 Both thiol and disulfide versions of this OPE molecule were used for insertion (Figure 1), as conjugated molecules including the OPEs have been of interest due to their electronic properties and function.1-7,26-31 Methods for sample preparation and insertion have been discussed previously.1,2,6,32 Briefly, to insert the OPE molecules, solutions of 0.1 µM of an OPE were prepared in anhydrous tetrahydrofuran in a nitrogen environment. Au{111} substrates with preassembled SAMs (24 h deposition) were placed in the tetrahydrofuran solution for ∼3 min allowing the conjugated molecules to adsorb to the Au surface at the SAM defect sites.32,33 The matrix thickness influences the apparent heights of the inserted molecules when imaged by STM; thus short alkanetholate monolayers were used to resolve the lower apparent heights of inserted molecules in the lower conductance state. We have used octanethiolate and decanethiolate Nano Lett., Vol. 5, No. 11, 2005
SAMs in the work presented here; dodecanethiolate SAMs were used in earlier studies.1,2 To analyze the behavior of the inserted molecules, a timelapse series of STM images were acquired over sample areas ranging from (200 Å × 200 Å) to (2000 Å × 2000 Å). During data acquisition, thermal fluctuations and piezoelectric translator creep can cause the field of view to drift, so an active tracking algorithm was applied to keep the molecules of interest within the field of view during acquisition.34 With STM, imaged heights are convolutions of both the physical and electronic structures of the molecules.35 Thus, changes in either or both will result in a change in the apparent height; therefore, we use the apparent height to monitor the state of a molecule. The apparent height of an inserted molecule is defined as the difference between the imaged height of the inserted molecule and the imaged height of the SAM. To generate sufficient statistics for the hundreds of molecules analyzed over hundreds of frames, automated analyses are required. In our previously reported method,34 variations in the calculated apparent height occurred due to scan size (i.e., how many image pixels represent the molecule of interest) and variations of the substrate (i.e., Au vacancy islands and Au step edges within the extracted frame). Thus, the local environment of the molecule influenced the apparent height using this algorithm. To circumvent this problem, we have developed a new background subtraction routine to obtain more accurate and reproducible apparent heights for inserted molecules, thereby reducing the influence of the measurement of the local environment. Bumm et al. have shown that the measured apparent height differences for mixed monolayers of decanethiolate and dodecanethiolated observed by STM differ from that of the actual physical length of the molecules composing the SAM due to the imaging mechanism of STM.33,36 It was also shown that a substrate vacancy defect appears as a ∼2.4 Å depression equal to that of the Au substrate step height.18,20,36,37 Correspondingly, molecules adsorbed in identical conformations and environments at the top vs the bottom of a substrate step will exhibit an apparent height difference equivalent to a substrate atomic step height. We note below that adsorbed molecules displaying this height difference of ∼2.4 Å correspond to motion up and down monatomic steps. The noted variations in the measured height of the background dodecanethiolate SAM used in the previous OPE studies lead to difficulty in differentiating molecules in the “off” conductance state at the top of substrate step edges from molecules in the “on” state at the bottom of step edges. This does not contradict the observation of conductance switching but rather gives an indication that two unrelated mechanisms can affect the measurement of molecules under study. To treat the measured matrix imaged background height properly, we now extract two areas from each image as shown in Figure 2, one to calculate an independent background (the height of the SAM) and the other to characterize the molecule. The white boxes in parts a and b of Figure 2 highlight the area extracted to calculate the raw imaged height of the inserted molecule; Figure 2c displays the first 2293
Figure 2. Tracking motion and conductance switching events from an octanethiolate SAM with inserted nitro-functionalized thiol-terminated OPE molecules with background correction. Panels show frames 1 (a) and 138 (b) of a sequence of STM images, respectively. The white boxes highlight the extracted region for one inserted molecule while the red boxes correspond to the extracted area used for calculating the background for the inserted molecule. Imaging conditions: Vsample ) 1.0 V, Itunnel ) 2.0 pA, 1000 Å × 1000 Å imaged area, frame acquisition ) 6.23 min/frame, delay between frames ) 1 min. (c) Extracted frames 1-50 from the molecule highlighted in (a) and (b). (d) Schematic illustrating the apparent height calculation at a step edge. The blue dashed line illustrates the path of the scanned probe tip; the position of the red dashed line on the upper terrace corresponds to the calculated height of the decanethiolate SAM used as the background level to calculate the apparent height. For an inserted OPE switch molecule located near a substrate step edge, the background is standardized by acquiring the imaged height of the SAM on the upper terrace. Note that the inserted switch molecule will protrude from the SAM even if it is located on the lower terrace of a substrate step, where it will appear to be ∼2.4 Å shorter than when it is located on the upper terrace of a substrate step with the same background. The tip trajectory is drawn closer to the OPE molecule than the host SAM, consistent with our previous measurements.33,36
50 of these extracted frames. The median of the top five pixel values for each extracted frame of the inserted molecule determines the raw imaged height of the inserted molecule. The red boxes in panels a and b of Figure 2 show the area extracted for the background; these small regions of the SAM contain no vacancies or step edge sites. The mean value of this extracted area is used as the background. The difference between the raw extracted height of the molecule and the background yields the apparent height (Figure 2d), thereby alleviating background variations in the apparent height due to the local environment of the inserted molecule. Using this improved apparent height calculation, we can easily differentiate between conductance switching and place-exchange up and down substrate step edges. We find that molecules at step edges and substrate defects often change apparent height by ∼2.4 Å, equal to that of the Au substrate monatomic step height, and we therefore attribute this to motion up and/or down the step edge. This is in addition to conductance switching, which is typically a larger apparent height change. The new background measurements yield apparent OPE heights that vary with the thickness of the SAM matrix; for example, an octanethiolate matrix yields apparent OPE heights greater than a dodecanethiolate matrix due to the difference in matrix thickness (see Supporting Information for further detail).36 For some inserted OPE molecules, we observe three apparent heights, as shown in Figure 3, while for others we find bimodal distributions.1,2 The three apparent heights for inserted molecules are highlighted by the colors red, green, and blue in Figure 3. In the data presented here, the thickness of the SAM was chosen (decanethiolate and octanethiolate) to enable differentiation of these height differences as a function of location on the substrate. Although the apparent height of the inserted molecules varied with the SAM matrix, 2294
we observed the difference in apparent height between the middle and highest value apparent heights always to be 2.4 Å corresponding to the substrate Au{111} monatomic step height. From these observations, we assign the three apparent heights as follows: apparent heights highlighted in red correspond to molecules in the “off” conductance state, apparent heights highlighted in green correspond to molecules in the “on” conductance state on the lower terrace below a substrate step or in a substrate vacancy, and apparent heights highlighted in blue correspond to the molecule in the “on” conductance state on the terrace above a substrate step or above a substrate vacancy defect. Reasons for these assignments are discussed below. We cannot differentiate the location of the “off” conductance state as at the top or bottom of a terrace or vacancy site separately because the apparent height of the “off” state at the bottom of a vacancy site is buried by the host SAM matrix. The only molecules that exhibit all three apparent heights are those located near step edges or substrate vacancy islands. Molecules at other locations within terraces, such as domain boundaries, exhibit only two apparent heights. Figure 3a displays the first 50 frames extracted for a nitrofunctionalized OPE thiol-terminated molecule inserted at a step edge in an octanethiolate host matrix. Using the color scheme described above, this single molecule exhibits all three apparent heights as indicated by the colored boxed areas. Figure 3b is the corresponding apparent height versus frame number for the molecule extracted in Figure 3a. The color intensity gradient in Figure 3b corresponds to the Gaussian fit to the apparent height distribution histogram (Figure 3c) for the cumulative data of all the inserted molecules from this particular data set. We observed a trimodal distribution containing peaks centered at apparent heights of 0.5, 2.5, and 4.9 Å. The height difference between Nano Lett., Vol. 5, No. 11, 2005
Figure 3. (a) Frames 1-50 for an inserted nitro-functionalized thiol-terminated OPE molecule in an octanethiolate host matrix. The molecule was at the edge of a substrate vacancy island. The boxed areas (red, green, and blue) correspond to the apparent heights in parts b and c. (b) Apparent height per frame for the extracted molecule in part a. Two phenomena are displayed for this molecule. The transition between the red boxed area and the blue boxed area is the molecule switching conductance states. The height difference of the green box and blue box is that of a Au{111} step height (2.4 Å), indicating that the molecule was mobile in to and out of the substrate vacancy islands. The motion at substrate step edges is reversible between the top and bottom of the step (frames 32-41). (c) Histogram of occurrences versus apparent height for all molecules in this data set. The number of occurrences at each apparent height varied by data set. Additional histograms for different samples are available in the Supporting Information.
the middle and highest peaks is 2.4 Å, again corresponding to a Au step. From this we posit that two of the peaks correspond to different conductance states and that the third peak corresponds to the inserted molecules in one of the conductance states, but on a different terrace. We infer that the lowest apparent height (red, ∼0.5 Å) corresponds to the “off” conductance state when the molecule is located at the top of a Au step. We assign the middle apparent height (green, ∼2.5 Å) as that of the “on” conductance state when the molecule resides at the bottom of a monatomic Au step. The highest apparent height (blue, ∼4.9 Å) corresponds to the “on” conductance state at the top of a Au step, i.e., on the upper terrace. We do not image the “off” state for the molecule when it is located in a Au vacancy island or at the bottom of a substrate step because the apparent height of the molecule is below that of the host SAM. Following our hypothesis, the “off” state on the lower terrace of the substrate step edge would in principle be imaged at an apparent height of -1.9 Å with respect to the SAM at the top of the step edge and is thus masked by the matrix in our measurements. The molecule displayed in Figure 3a exhibits all three apparent heights, demonstrating that both conductance switching and motion up and down the step edge are possible for a single inserted molecule. However, switching and motion up and down a substrate step appear to be independent events on the time scale of our images. In Figure 3a, the red box around frames 9-13 indicates the “off” conductance state at the top of the step edge. Frames 8 and 14, which precede and follow the red boxed area, respectively, are boxed in green, indicating the middle apparent height which is the “on” state at the bottom of the step edge. Nano Lett., Vol. 5, No. 11, 2005
This identifies the molecule as exhibiting both motion and switching between frames. However, each time motion up and down the substrate step occurs, conductance switching does not necessarily occur simultaneously. A green box around frames 33-40 again indicates the “on” state at the bottom of the substrate step edge. The frames preceding and following this green boxed area are boxed in blue indicating the molecule in the “on” conductance state at the top of the substrate step edge. This identifies the molecule as exhibiting motion up and down the substrate step without a simultaneous switching event. Therefore, it is possible for a switching event to occur simultaneously with motion up or down a substrate step within the imaging time scale, yet we have shown that motion up or down a substrate step and switching can occur independently. It is important to note that the conductance states and position are determined by several scans across a molecule even within one image, thereby reducing the possibility that current fluctuations or instabilities lead to erroneous assignments. To show that molecular motion is responsible for the trimodal distributions observed, we have imaged a highresolution area of our SAM with the inserted nitro-functionalized OPE disulfide molecule. The disulfide molecules require more open space for insertion and thus favor step edges and substrate vacancy islands over domain boundaries, relative to thiols. Monolayer coverages are lower at step edges than elsewhere on the surface; domain boundaries favor single molecule insertion.21,33 Nonetheless, we find occasional insertion of the disulfides into SAM matrix domain boundaries, but to a substantially lesser extent than for thiols. Figure 4a is an imaged area (500 Å × 500 Å) from a time-lapse series of 140 frames. The switch boxed 2295
Figure 4. (a) Topographic STM image of the nitro-functionalized OPE disulfide molecule inserted into an octanethiolate matrix. Imaging conditions: Vsample ) -1.0 V, Itunnel ) 2.0 pA, 500 Å × 500 Å imaged area, frame acquisition ) 80 s/frame, delay between frames ) 20 s. The magenta box highlights a switch located at a domain boundary. The cyan box highlights a switch on the upper terrace (white arrow) and a switch on the lower terrace (yellow arrow) of a substrate vacancy island. (b) Extracted frames of the “on” and “off” states of a switch at a domain boundary. At this location, far away from any substrate steps, switches exhibit only two apparent heights. (c) Extracted frames of the two possible conductance states when a switch is located on the upper terrace of the substrate step at the edge (white arrows) switching from “off” to “on” (left frame to right frame), and when a switch is located on the lower terrace of the Au step (yellow arrows) switching from “on” to “off” (left frame to right frame). Note that the switch on the upper terrace of the substrate step protrudes to a greater extent in the “on” state than the switch located at the bottom of the substrate terrace in the “on” state. A switch located on the upper terrace of the substrate step edge in the “off” state protrudes only slightly from the SAM, whereas, within the vacancy site, the switch in the “off” state is not imaged by STM.
in magenta is located at a SAM domain boundary with no substrate defects nor steps nearby. Note that in this case we do not resolve whether the two nitro-functionalized OPE molecules remain together on the surface after disulfide cleavage. Throughout imaging, this switch (or pair of switch molecules, as noted above) exhibits only two apparent heights, as shown in Figure 4b. The limitation of only two states is attributed to the lack of substrate steps proximate to the molecule; therefore the molecule or molecules can exhibit only the two apparent heights (switch molecules in the same bundle switch together). This demonstrates a mechanism for conductance switching independent of motion up or down substrate steps, indicating that motion up and down the substrate step is not the cause of conductance switching. The second extracted area, boxed in cyan in Figure 4a, encompasses the area around a Au vacancy island. This vacancy island allows the switch, through place-exchange up and down the substrate step, to occupy locations across the Au step within or outside of the vacancy island. The possible locations for molecules descending a step edge are shown in the extracted frames in Figure 4c. Each frame 2296
displays two extracted molecules: one (white arrows) just outside and thus on the upper terrace, a monatomic substrate layer above the Au vacancy island, the other (yellow arrows) within the vacancy island. The left extracted frame displays the “off” conductance state for the switch at the top of the substrate step edge with the “on” conductance state for the switch within the vacancy island. The frame on the right displays the opposite conductance state for each switch at the same location. Note that the switch on the upper terrace of the substrate step protrudes to a greater extent in the “on” state than the switch located at the bottom of the substrate terrace in the “on” state. These correspond to our two observed “on” apparent heights. A switch located on the upper terrace of the substrate step edge in the “off” state protrudes only slightly from the SAM (less than 1 Å), whereas within the vacancy site the switch in the “off” state is not imaged by STM, leading to a calculated apparent height of 0 Å. As discussed above, this is due to the conductance being lower than that of the host matrix. Since the calculated apparent heights for the “off” state are not significantly different on the upper and lower terrace, both locations contribute to the third observed apparent height we label as the “off” state. The apparent heights of the imaged conductance and position states correspond to the trimodal or bimodal distributions, dependent on the molecules’ locations on the substrate. Figures 3 and 4 show the dependence of apparent height both on conductance switching and on location relative to substrate steps. Although STM cannot directly probe the molecule-substrate interactions responsible for the observed motion, possible mechanisms for this motion can be related to previously discussed mechanisms for adsorbate motion. As Stranick et al. observed,21 in Au diffusion, covalently bound molecules can remain attached to substrate atoms and move as a complex. If this mechanism describes the step motion observed here, a single uncoordinated vacancy would exchange sites with the inserted molecule attached to its substrate atom, allowing it to move reversibly between the top and bottom of the step edge as in the place-exchange mechanism for metals proposed by Kellogg and Feibelman.22 The inserted rigid aromatic molecules would more likely exhibit such motion than SAM (matrix) counterparts, because they are not held in place by the same strength of van der Waals interactions that exist between the saturated alkanethiolate molecules. Decreased stability and thus increased mobility are expected at substrate step edges due to the limited coordination of atoms located at these step edges. However, it would be less energetically favorable for the vacancy to have mobility through the SAM matrix because of the alkanethiolate intermolecular interactions that would need to be disrupted for such motion to occur. While it is known that attaching thiolates weakens the bonds of the toplayer Au atoms to the substrate,21,38 the relative strengths of these interactions for alkanethiolates vs conjugated thiolates are not known. Having two OPE molecules in close proximity could lower the place-exchange barrier for the Kellogg-Feibelman mechanism.22 We expect that with OPE disulfide insertion, Nano Lett., Vol. 5, No. 11, 2005
there is more than one inserted molecule in proximity. However, adjacent molecules are difficult to resolve due to their proximity, especially at Au steps because of the STM imaging mechanism.35 As noted above, the insertion of the nitro-functionalized OPE disulfides requires more space than their nitro-functionalized OPE thiol analogues. We believe that a single uncoordinated vacancy could exchange sites with the inserted OPE molecule attached to one or more substrate atoms, allowing it to move reversibly between the top and bottom of the step edge. We do observe qualitatively more place-exchange activity up and down steps for insertion performed with the nitro-functionalized OPE disulfides. This could be due to interactions between these molecules enhancing this motion, but we cannot rule out the preselection of larger void species required to insert the disulfides that would also lead to more motion. We have demonstrated motion of inserted molecules up and down substrate step edges. Previously observed stochastic conductance switching is not dependent on the presence of substrate vacancy islands nor on place-exchange up and down substrate step edges. Our results show that motion up and down step edges is possible even for well-ordered SAM matrices. It should be noted that while motion up and down substrate steps was observed, minimal lateral diffusion within terraces at insertion sites such as domain boundaries was observed. Several mechanisms may play roles in interactions on the molecular level that govern these types of motion, and we posit that these interactions will be increasingly important as attempts are made to pattern and to control the function of single molecules. Acknowledgment. The authors thank Dr. Penelope Lewis and Arrelaine Dameron for insightful discussions. The authors gratefully acknowledge support from the Army Research Office, Defense Advanced Research Projects Agency, Air Force Office for Scientific Research, National Institutes for Standards and Technology, National Science Foundation, the Office of Naval Research, and the Semiconductor Research Corporation. Brent Mantooth thanks the American Chemical Society Division of Analytical Chemistry for a fellowship sponsored by GlaxoSmithKline. Supporting Information Available: Additional histograms for molecules inserted into a decanethiolate SAM and into an octanethiolate SAM. This material is available free of change via the Internet at http://pubs.acs.org. References (1) Donhauser, Z. J.; Mantooth, B. A.; Kelly, K. F.; Bumm, L. A.; Monnell, J. D.; Stapleton, J. J.; Price, D. W.; Rawlett, A. M.; Allara, D. L.; Tour, J. M.; Weiss, P. S. Science 2001, 292, 2303-2307. (2) Donhauser, Z. J.; Mantooth, B. A.; Pearl, T. P.; Kelly, K. F.; Nanayakkara, S. U.; Weiss, P. S. Jpn. J. Appl. Phys. 2002, 41, 48714877. (3) Lewis, P. A.; Inman, C. E.; Yao, Y. X.; Tour, J. M.; Hutchison, J. E.; Weiss, P. S. J. Am. Chem. Soc. 2004, 126, 12214-12215.
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