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ACS Nano
ACS Nano. 2010 December 28; 4(12): 7630–7636.
Published online 2010 November 15. doi:  10.1021/nn102371z
PMCID: PMC3010874

Polarizabilities of Adsorbed and Assembled Molecules: Measuring the Conductance through Buried Contacts


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We have measured the polarizabilities of four families of molecules adsorbed to Au{111} surfaces, with structures ranging from fully saturated to fully conjugated, including single-molecule switches. Measured polarizabilities increase with increasing length and conjugation in the adsorbed molecules and are consistent with theoretical calculations. For single-molecule switches, the polarizability reflects the difference in substrate−molecule electronic coupling in the ON and OFF conductance states. Calculations suggest that the switch between the two conductance states is correlated with an oxidation state change in a nitro functional group in the switch molecules.

Keywords: contacts, microwave measurements, molecular devices, polarizability, scanning tunneling microscopy, self-assembly, single-molecule spectroscopy

Scientific understanding is increasingly derived from studies of single-molecule physical properties and interactions. As such measurements become more robust, single-molecule metrology tools are being dramatically enhanced by combining additional signals providing further chemical, physical, and electronic information.18 For instance, single-molecule fluorescent labeling can be performed with fluorophores sensitive to specific environmental conditions(9) or using optics with anisotropic point-spread functions that can be analyzed to localize position in a third dimension.(10) Scanning probe topographic measurements can be performed with a functionalized atomic force microscope (AFM) tip that simultaneously provides both topographic and chemical information based on changes in cantilever resonance.(11)

Here, we have used the microwave frequency alternating current scanning tunneling microscope (ACSTM)1,2,4,5,12 to image the topography and polarizability of single molecules simultaneously. Standard STM topography measurements are performed with a constant DC bias applied to the tip. Previously, we have reported that a microwave frequency generator can be used to modulate the DC bias in the STM, a capability that enables imaging on semiconducting and insulating surfaces by measuring tunneling both to and from the surface.

Polarizable molecules have a “soft” electron cloud that deforms in response to the high-frequency bias modulation, in turn modulating the tunneling current. Thus, the magnitude of the transmitted microwave frequency modulation correlates with the polarizability of the molecule in the tunneling junction. Since the microwave frequency modulation (GHz) is fast relative to the feedback loop (1 kHz), polarizability can be collected simultaneously with standard molecular topography images. Although polarizability is also known to contribute to topographic imaging,13,14 here we are able to deconvolve the two components. Using this technique, we have imaged a variety of families of self-assembled monolayers (SAMs), compared relative experimental and calculated polarizabilities for each molecule, and used these measurements to study single-molecule switches.

Measurements made on surfaces have fundamental differences from those performed in the gas phase, which are important in the context of molecular devices. Gas-phase molecular polarizabilities reflect the dispersion forces within and between molecules. On surfaces, the measured electronic response also includes substrate electrons to the extent that these are coupled into the molecules. Such coupling is integral to the electronic behavior of the molecule and is known to vary with both the orientation of the molecule and the substrate topography.8,1518 The measurements described here are uniquely able to analyze the relationship between polarizability and these other physical factors.

Results and Discussion

For comparison to experiment, molecular polarizabilities were calculated using density functional theory (DFT) with the B3LYP functional and a 6-31++G** basis set ((11).(19) These include calculations for molecules aligned normal to the surface and in tilted conformations and for both anionic and neutral states of the nitro-functionalized oligo(phenylene ethynylene) (OPE) molecules ((1,1, bottom). While we have shown that we do not need to oxidize nor reduce the molecules directly in order to cause switching (an applied electric field without current flow is sufficient),15,17 it is possible that the ground states of molecules in different tilt conformations have different oxidation states.

Table 1
Calculated Polarizabilities (α) of Adsorbed Molecules in Atomic Units (Bohr(3)) Using Density Functional Theory As Described in the Texta
Figure 1
(A) Structures of molecules used in this study. (B) Schematic of the AC scanning tunneling microscope tip−sample junction containing self-assembled molecules of a C12 host SAM with a single switch molecule inserted at a defect site in the SAM. ...

We probed the polarizabilities of the molecules shown in in11 by forming SAMs of octanethiolate (C8), dodecanethiolate (C12), 3-mercapto-N-nonylpropionamide (1ATC9), and unfunctionalized OPE molecules (4,4′-di(ethynylphenyl)-1-benzenethiol). We further related the polarizability to conductance switching by inserting single nitro-functionalized OPE switch molecules (4,4′-di(ethynylphenyl)-2′-nitro-1-benzenethiol) into host C12 SAMs. SAMs.11 shows a schematic of this insertion with a single-molecule switch bound in a defect site of a host C12 SAM on Au{111} within the ACSTM tunneling junction.

Devices based on electronic switches are central to modern information technology. As miniaturization of such devices continues, nanostructures and single molecules that exhibit conductance switching must be understood and controlled within their physical environment.(21) To accomplish this, we must have the capabilities to address single switch molecules in both their ON and OFF conductance states, to predict when each molecule will be active as a switch, and to control their switching. By applying ACSTM imaging to systems of isolated OPE switch molecules, we are able to locate and to predict which molecules are likely to be active either through switching or through increased motion.(22) We can switch the conductance states of single molecules while simultaneously mapping the microwave difference frequency (MDF) signal to confirm the location of each switch (even when it is not visible in conventional STM topography) and to determine differences in the molecule−substrate coupling due to bonding and structural changes.

A number of techniques have been used to study fully conjugated OPE molecules for use as molecular wires and molecular switches.7,1518,2131 When single OPE molecules are isolated within host alkanethiolate SAM matrices and imaged using STM, they exhibit bistable conductance switching, defined as ON when a molecule appears to protrude from the host matrix and OFF when the molecule is less protruding (or no longer visible within the host matrix). The apparent height of the molecule depends on (among other things) the thickness of the alkanethiolate SAM and the location of the molecule within the matrix.(18) The observed switching is due to a convolution of the physical height (change) of the molecule and the conductance of the molecule−substrate system.15,16 Previously, we showed that conductance switching was regulated by the packing of and interactions with the host matrix,15,16,29,30 that the OPE molecules exhibited motion within the host matrix,15,18 and that the switching and motion events occurred on time scales faster than those of STM imaging.(22) Several hypotheses for the observed conductance switching were tested by modifying the molecular design of the OPE moieties.(17) The only mechanism consistent with our and others’ results is a change occurring at the substrate−molecule interface, which we posit to be a change in hybridization between the substrate and the molecule occurring mainly via molecular tilt.15,16,25,29,30 Theoretical data likewise suggest that changes in the Au molecule bonding and the Au−Au arrangements strongly modify molecular conductance.3235 Here, molecular polarizability provides insight into the dynamics of the buried interface.

Molecular polarizabilities were measured locally and imaged using ACSTM in which two microwave frequency AC signals (in the range of 0.5−20 GHz), offset by a difference frequency (5 kHz), were combined with the DC bias voltage. The current used for the STM imaging feedback loop is dominated by the DC bias, with small contributions from the rectified AC signals. Applying two AC frequencies into our nonlinear tunneling junction enables us to measure the heterodyned AC signal at the difference frequency. We recorded the signals due to the applied microwave frequencies through the current preamplifier (bandwidth ~30 kHz).1,36 To obtain microwave spectra and images, we used a lock-in amplifier referenced at the difference frequency to analyze the tunneling current, which carried the heterodyned microwave frequency information. The magnitude of the MDF signal is dependent on both the polarizability of the molecules and the STM tip-sample junction; therefore, the polarizability MDF images are, at present, relative measurements. We are able to compare the polarizabilities of molecules by measuring multicomponent monolayers and for switches by measuring the same molecules in the ON and OFF states. Thus, we are able to probe the electronic connection between the switch molecules and substrate (i.e., the contacts3740) by measuring polarizability (vide supra).

22 shows three different monolayers imaged using ACSTM and the corresponding schematic of each monolayer. These include fully saturated (no multiple bonds), partially saturated, and fully conjugated molecules, all of which form ordered monolayers. It also includes the simultaneously obtained polarizability maps. To compare the polarizabilities of different length alkanethiolate SAMs (shown schematically in in2),2), we formed a C12 monolayer and vapor-annealed it with octanethiol, thereby forming domains of C12 and C8.(41) The topographic ((2)2) and MDF polarizability ((2)2) images for a C12/C8-separated monolayer were recorded, and a small contrast was observed between the C12 and C8 molecules in the MDF signal. This small contrast was expected from the microwave spectra recorded over the different length alkanethiolate chains since the calculated C8 polarizability is ~76% that of C12.

Figure 2
(A) Schematic, (B) topographic image, and (C) simultaneously recorded microwave difference frequency (MDF) image of an artificially separated self-assembled monolayer (SAM) containing dodecanethiolate (C12) and octanethiolate (C8) (see text). The topographically ...

When we imaged monolayers formed at room temperature from 1ATC9 molecules containing buried amide functionalities that are able to form hydrogen bonds, we observed two apparent height domains in the images, which we interpret as being due to different polar tilt angles of the 1ATC9 molecules (shown schematically in in2).2). This observation is consistent with surface infrared spectroscopy data that measured the possible tilt angles (between normal and tilted 18° from normal) to the surface to enable hydrogen bonding of the amide functionality.(42) When we imaged these monolayers, the apparent topographically less protruding (tilted) domains ((2)2) had a stronger MDF polarizability signal ((2)2) than the more protruding (normal to the surface) domains. Since the 1ATC9 molecules within the tilt domains are identical, and since their calculated gas-phase polarizabilities change very little when normal to the surface or tilted, we posit that the difference in the polarizabilities between the tilt domains is due to differences in the bonding at the molecule−surface interface.(44)

The monolayer packing of unfunctionalized OPE molecules has been described previously and is shown schematically in in22 with the phenyl rings on neighboring molecules aligned perpendicular to one another.(43) From our polarizability calculations, we expect the unfunctionalized OPE molecules to have polarizabilities ~3−4 times that of C12, and when we measured these monolayers ((2),2), we found the experimental (relative) polarizabilities ((2)2) to be ~3 times that of C12.

We are unable to assemble complete, ordered monolayers of the nitro-functionalized OPE switch molecules due to their typical disorder and their limited stability in air.(44) However, using the insertion scheme detailed above, we are able to measure the polarizabilities and to follow the dynamics of these OPE-based single switch molecules. Time-lapse series of STM images recorded over fixed areas (500−1000 Å)(2) enabled us to record and to extract switching behavior and polarizabilities for each molecule in each frame (~5 min/frame) over several (8−18) hours. The first frame from one series of images is shown in in3,3, topography and MDF magnitude, respectively. Each inserted OPE molecule has been numerically labeled to correspond to the extracted frames in in3,3, which display the most dynamic 25 frames for each inserted molecule.

Figure 3
Simultaneously acquired (A) topographic and (B) MDF images of a dodecanethiolate SAM with inserted nitro-functionalized OPE molecular switches. A series of 200 images was acquired (5 min/frame, 30 s between frames). (C) Areas of 120 Å × ...

Since we are able to use MDF imaging to measure the polarizabilities of the nitro-functionalized OPE molecules, even at times when the molecules did not appear in the topographic images, we have used this as a means to locate switches in the OFF state and have attempted to switch molecules deterministically using the electric field applied by the STM tip.(15) Our ability to switch these molecules was indicated (predicted) by instabilities in the MDF signal prior to applying the switching field. We and others have shown that substrate atom motion is important in switching.22,45 Also note that we could deterministically switch OPE molecules from the ON to the OFF conductance state using the electric field applied by the STM tip without desorbing the switches, as shown in in4.4. Controlled switching required different bias voltage magnitudes and tunneling gaps for different molecules, presumably due to the varied chemical environment created by defects in the surrounding monolayer matrix.15,16,29,30 A more reliable method for controlled switching and stabilized conductance states has been demonstrated using the applied electric field and the stabilizing effects of hydrogen-bonding interactions between the active molecules and a specifically designed matrix;29,30 however, for the purposes of this work, we have shown examples using only electric field.

Figure 4
Controlled switching from the ON to the OFF (A−D) and from the OFF to the ON (E−H) conductance states for nitro-functionalized OPE molecules inserted into C12 SAMs. (A,B) Simultaneously acquired topographic and MDF images in which two ...

44 shows a molecule switched from the ON to the OFF conductance states (boxed in in4),4), of topography and MDF magnitude, respectively.(46) The same area was imaged after switching ((4,4, topography and MDF image, respectively); the molecule’s signature no longer appeared in the topographic image (it “disappears” into the matrix), but MDF imaging confirmed that the nitro-functionalized OPE switch was still present after the molecule was switched OFF. The ratios of the MDF signal for the ON and OFF nitro-functionalized OPE molecules to C12 were 6.8 ± 3.6 and 2.5 ± 1.0, respectively. The ON state had a similar ratio to that calculated for the anionic nitro-functionalized OPE molecules oriented normal to the surface, while the OFF state ratio is most similar to the calculations for the neutral nitro-functionalized OPE molecule having a tilted geometry ((2).2). This large ratio between ON and OFF states indicates that the contribution to the measured polarizabilities of the molecules in the ON state due to the substrate electrons is substantial and at least equal to the contribution from the molecules’ electrons.

Table 2
Comparison of Calculated and Experimental Polarizabilities for Nitro-Functionalized OPE Moleculesa

Previously, we were typically limited to studying only molecules that appeared at some point in the ON conductance state during imaging, due to the difficulty in locating molecules continually in the OFF state in large topographic images.15,16 With this method, we have the additional capability of locating, imaging, and measuring molecules that are in the OFF conductance state and do not appear in topography.

44 shows a molecule that was switched from the OFF conductance state to the ON state. In the initial topographic and MDF image ((4,4, topography and MDF image, respectively), the signature for the boxed molecule appeared in the MDF image and only as a slight protrusion in the topographic image. After several voltage pulses, the molecule switched to the ON conductance state ((4,4, topography and MDF image, respectively). This process is reversible. Note that the process also destabilized the STM tip somewhat, leading to noisier images.15,16

Conclusions and Prospects

Using the ACSTM to obtain MDF images, we are able to measure single-molecule polarizabilities and to correlate them with calculated values. This enables us to relate the conductance state with the electronic coupling between the molecules and their contacts. As frustrated rotations partly determine this coupling, and electric fields can be used to actuate the switches, at higher applied microwave amplitudes, it may also be possible to determine the slew rates of the switches, which are expected to be in this range.6,7,21,22

The ability to measure conjugation and surface contact provides unique insights into the electronic interactions between single molecules and their immediate environment. The measurements described simultaneously and independently characterize surface topography and the substrate coupling at the buried interface. This is important because the behavior of conductive molecules depends strongly on their local coupling with macroscale electrodes, a fact that has hindered development in the field of molecular electronics.

Dielectric response measurements should also be possible at higher amplitude, enabling direct experimental evaluation of the relationship between individual dopant atom placement and nanoscale material properties in semiconductors.

Finally, we anticipate that these measurements may also enable chemical identification of local structural features in a macromolecule based on polarizability. Such a capability could represent a direct method for label-free, real-space structure determination from a single molecule.

Experimental and Theoretical Methods


The chemicals octanethiol, dodecanethiol, tetrahydrofuran (Sigma-Aldrich, St. Louis, MO), and 200-proof ethanol (Pharmco, Brookfield, CT) were used as received. Syntheses of compounds 4,4′-di(ethynylphenyl)-1-benzenethiol (OPE), (4,4′-di(ethynylphenyl)-2′-nitro-1-benzenethiol) (nitro-OPE), and 3-mercapto-N-nonylpropionamide (1ATC9) have been described previously.47,48

Sample Preparation

The SAM matrices were formed on Au{111} on mica substrates (Agilent Technologies), which were annealed with a hydrogen flame immediately prior to film preparation. Matrices studied for polarizability were deposited from 1 mM ethanolic solutions of the matrix molecule for 24−48 h. Monolayers used for subsequent insertion were deposited from 1 mM solutions of dodecanethiol in ethanol for 5 min. This short adsorption time forms a less ordered matrix and enables more switching of the inserted molecules.(15) The samples were rinsed with neat ethanol and blown dry with nitrogen. Insertion of OPE was performed under a nitrogen environment by placing the preformed SAMs into 0.1 mM solutions of 4,4′-di(ethynylphenyl)-1-benzenethiol in tetrahydrofuran for 1 min. The samples were rinsed with ethanol after insertion and dried with nitrogen prior to imaging.

STM Measurements

All STM measurements were performed in a custom Besocke-style STM under ambient conditions. The STM is equipped with two microwave frequency generators (Hewlett-Packard, 8263B), which are used to add a sinusoidal bias modulation at microwave frequencies from 0.5 to 20 GHz.25 The applied frequencies are offset by a small difference frequency (typically 5 kHz), mixed (Hewlett-Packard, 87302C), and split through a directional coupler (Hewlett-Packard, 87300C). One output of the directional coupler is combined with the DC bias voltage using a bias tee (Hewlett-Packard, 11612A) and used to apply a bias to the STM tip. The other output first passes through a detector diode (Narda, 4503A), then to a low-pass filter (Frequency Devices, ASC-50), which amplifies the difference signal before passing it to the lock-in amplifier (Stanford Research Systems, SR850) as a reference. Microwave difference signals applied to the sample through the STM tip first passed through the current preamplifier (Axon CV-4, bandwidth 30 kHz) and were detected at the lock-in amplifier.


Polarizability values were calculated using density functional theory (DFT) with the B3LYP functional and a 6-31++G** basis set.(19) These include calculations for molecules aligned normal to the surface and in tilted conformations and for both anionic and neutral states of the nitro-functionalized OPE molecules. Calculations are performed for molecules in the gas phase, with no explicit contribution from substrate atoms.


We gratefully acknowledge support from DoE (DE-FG02-07ER15877), NSF (NSF-CHE-1041943), AFOSR, NIH (NRSA postdoctoral fellowship, S.A.C.), and the Kavli Foundation (P.S.W.). The authors thank D. L. Allara, L. A. Bumm, P. Han, K. F. Kelly, and M. J. Shuster for helpful discussions.

Funding Statement

National Institutes of Health, United States


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