Assignments of Inelastic Electron Tunneling Spectra of

alkanethiol self-assembly monolayers with a scanning tunneling microscope and .... We have also calculated the coupling energy (Ecoup) between the...
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Assignments of Inelastic Electron Tunneling Spectra of Semifluorinated Alkanethiol Molecular Junctions Li-Li Lin,†,‡ Bin Zou,§ Chuan-Kui Wang,† and Yi Luo*,‡,^ †

College of Physics and Electronics, Shandong Normal University, Jinan 250014, China Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, S-106 91, Stockholm, Sweden § College of Science, Minzu University of China, Beijing 100081, China ^ Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China ‡

ABSTRACT: The peculiar experimental inelastic electron tunneling spectra of a series of hexadecanethiol molecular junctions have finally been reproduced by first-principles simulations. It is found that the debated spectral profile around 0.38 eV indeed originated from the C H stretching vibration associated with at least two terminal methylene groups close to the sulfur atom. The intensity of this spectral peak becomes dominant, as observed in the experiments when the molecule is titled 40 relative to the normal of the electrode surface, which is due to the opening of a new tunneling pathway bypassing the end sulfur atom. The dependence of this strong vibrational feature on the titled angle of the molecule is predicted with the help of the concept of effective coupling energy. The degree of the fluorination on the inelastic electron tunneling spectrum of hexadecanethiol molecules has also been discussed in detail.

’ INTRODUCTION Inelastic electron tunneling spectroscopy (IETS) of alkanethiol molecular junctions has served as the model system for both experiment and theory.1 11 However, many theoretical calculations have failed to reproduce the high intensity of the C H stretching vibration mode (ν(C H)) measured in the experiments.2 7 The origin of the ν(C H) in the IET spectra has long been under debate. Earlier theoretical studies found that this vibration mode was from the vibration of the CH3 group.3,5 Beebe et al.1 conducted a series of experiments on different fluorinated hexadecanethiol molecules. They have observed that, by fluorinating the end methyl (CH3) group and methylene (CH2) groups close to it, the intensity of the ν(C H) in the IET spectra remains almost unchanged, which strongly suggested this mode to be associated with the CH2 groups close to the S Au bond rather than the CH3 group. Our previous calculations also support this conclusion.6,8,9 Recently, Okabayashi et al. measured the IETS of alkanethiol self-assembly monolayers with a scanning tunneling microscope and compared it with first-principles calculations.12 They found that the ν(C H) includes both symmetric and asymmetric modes and comes from both CH3 and CH2 groups. However, their theoretical simulations did not predict the exact peak amplitude of the ν(C H). The spectral intensity of the IETS is strongly associated with the electron transport pathway in the junction,13 and it is very sensitive to the molecular conformation inside.8,9,14 A good agreement between the theory and the experiment is essential for obtaining reliable structural information of the molecule and the interface. We will show in this study that, with a proper molecular conformation, theoretical simulations are capable of reproducing the experimental IET spectra of different semifluorinated hexadecanethiol molecular junctions and provide the accurate spectral assignments for different spectral features and the orientation of the molecules. r 2011 American Chemical Society

’ THEORETICAL BASIS To calculate the IET spectra, we have first optimized the molecules in the gas phase and then connected them to two gold electrodes (see Figure 1a). Here, 12 gold atoms with the arrangement of 2 3 4 3 in one layer and the Au Au bond of 2.88 Å are used in each electrode. The two gold surfaces are both parallel to the XOZ plane. The molecule backbone is on the XOY plane with the sulfur atom at the zero point of the coordinate system. Both the terminal carbon atom and the sulfur atom are located at the central hollow site of each gold electrode surface with the S Au bond being 2.85 Å. The distance between the terminal carbon atom and the electrode surface is 3.30 Å here. The axis along the terminal sulfur atom and carbon atom has an angle with the normal of the electrode surface, which is defined as β. When the axis is located at the first quadrant, the value of β will be defined as positive. If it is in the second quadrant, the angle will be negative. The angle α is defined as the angle between the H C H plane of the CH2 group closest to the sulfur atom and the normal of the gold surface. The optimization of the molecules, the electronic structure, and the frequency calculation of the extended molecules are all performed in the Gaussian 03 program16 using the B3LYP functional and LanL2DZ basis sets. The IET spectra of the extended molecules are calculated by our own QCME program,17 which is based on the harmonic approximation and Green’s function theory.8,18 This analytic method has been successfully applied to several systems and provided reliable information about the molecular conformation, the contact configuration, the intermolecule interaction, the environment, and the transport mechanism in the molecular junction.8 11,18 20 Received: June 28, 2011 Revised: September 12, 2011 Published: September 12, 2011 20301

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Figure 1. (a) Structure of the Au12 F0 Au12 molecular junction. (b) IET spectra of five molecules calculated in a simple model system where the coupling between the molecule and the electrode is set to a constant, 0.05 eV. (c) Total energy of Au12 F0 Au12 as a function of the tilt angle β. (d) IET spectra of Au12 F0 Au12 calculated at four different tilt angles (50, 20, 25, and 40). The Lorentzian line shape is adopted, and the broadening factor for the calculated spectrum is set to 10 cm 1.

’ RESULTS AND DISCUSSION Figure 1b shows the calculated IET spectra of the hexadecanethiol molecule and four semifluorinated hexadecanethiol molecules in a simple model system where the coupling between the molecule and the electrode is assumed to be a constant (0.05 eV). Here, F0 represents the hexaecanethiol molecule (CH3(CH2)15SH). F1, F2, F3, and F10 represent CF3(CH2)15SH, CF3CF2(CH2)14SH, CF3(CF2)2(CH2)13SH, and CF3(CF2)9(CH2)6SH, respectively. The IET spectra of all the five molecules are very similar with the dominant peak from the CH2 scissoring mode (δ(CH2)). The peak at about 0.38 eV is too weak to identify. For the molecule F0 junction, we have calculated the total energy of the extended molecule (Au12 F0 Au12) as a function of the titled angle β, and the result is shown in Figure 1c. For all the cases, the terminal carbon atom is fixed to be 3.30 Å away from the electrode surface. It can be seen that the molecular junction has the lowest energy when the angle β is at 25. The calculated IET spectra of Au12 F0 Au12 with four different titled angles are illustrated in Figure 1d. When β changes from 50 to 10, one could not see any visible peaks around 0.38 eV. It is found that, when the angle becomes 40, a dominant spectral feature at 0.38 eV appears. It is noticed that this vibration mode starts to show its presence from the angle of 25. It is found that the total energy at the β of 40 is 4.61 kcal/mol higher than that at 25, which should occur under real experimental conditions. One thing that can be concluded is that the inclusion of a specific interaction between the molecule and the electrode has significant effects on spectral profiles of the IET spectra and a proper geometric arrangement can drastically enhance the intensity of the C H stretching vibration mode.

Figure 2. IET spectra of F0 at top (a) and bridge (b) sites of the electrode. The configurations of the F0 bonded at the top and bridge sites are shown in the insets, respectively. The Lorentzian line shape is adopted, and the broadening factor for the calculated spectrum is set to 10 cm 1.

Is the tilt angle the only factor that determines the intensity of the C H stretching vibration mode? The answer is “NO”. Two different contact positions in our model have also been investigated, as shown in the insets of Figure 2. For each configuration, the distance between the sulfur atom and the electrode surface is determined by the energy 20302

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Figure 3. (a) IET spectra of the semifluorinated hexadecanethiol molecular junction measured by Beebe et al.1 (b) Calculated IET spectra of F0, F1, F2, F3, and F10 molecular junctions with the angle β of 40. The Lorentzian line shape is adopted, and the broadening factor for the calculated spectra is set to 10 cm 1. (c) The five active vibration modes in the IET spectrum of Au12 F2 Au12 as examples.

calculation, which is 2.72 and 3.12 Å for the top and the bridge sites, respectively. When the tilt angle is 40, the calculated IET spectra of F0 at the top and bridge sites are shown in Figure 2, respectively. With the same molecular structure, but different bonding positions, the IET spectra of Au12 F0 Au12 change significantly. In both spectra, the C H stretching mode becomes weak compared with the spectra of F0 at the hollow site (Figure 1d). Our calculation indicates that the hollow site is the most probable bonding site when the F0 molecule assembled on the gold surface. On the basis of the results of the F0 junction, we have adopted the same orientation (tilted angle of 40) and the bonding site (hollow site) for the other four semifluorinated molecular junctions under investigation. It should be noted that the contact distance between the end CH3 and the electrode varies in different junctions owing to the different terminal fluorination. When F1, F2, F3, and F10 are located at their equilibrium position (with the contact distance being 4.7, 4.9, 4.9, and 5.1 Å, respectively), the calculated IET spectra are in good agreement with their experimental counterparts,1 as nicely demonstrated in Figure 3a,b. According to our calculations, the peaks assigned as ν(C C) and w(CH2) in the experimental spectra

should be he CH2 twisting vibration mode (t(CH2)) and the CH2 scissoring vibration mode (δ(CH2)), respectively. The relative intensity of the vibration modes with lower frequencies varies irregularly in our calculation, which shows an obvious intensity increase of the S C stretching mode of F2. However, the ν(C H) dominates the IET spectra in all the five spectra. It seems like that the titled angle of the molecule and the binding sites are the two key factors behind the disagreement between the earlier theoretical3 6 and the experimental spectra. The five active vibration modes in the IET spectrum of Au12 F2 Au12 are given in Figure 3c. We have also found that the C F vibration is not active, which has exactly the same reason as suggested by Beebe et al. Now, we can clearly see that the C H stretching mode, ν(C H), comes from the contribution of CH2 groups close to the sulfur atom rather than the CH3 group, which is in agreement with the conclusion of Beebe et al. By careful inspection, it can be seen that the C H stretching mode is mainly associated with the two CH2 groups close to the sulfur atom. When the CH2 group closest to the sulfur atom is fluorinated, labeled as F1*, the peak of ν(C H) drops its intensity in comparison with that without fluorination, as clearly 20303

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Figure 4. Calculated IET spectra of (a) the Au12 F0 Au12, (b) the Au12 F1* Au12, and (c) the Au12 F2* Au12 molecular junctions. The tilt angle for all the three systems studied here is 40. The Lorentzian line shape is adopted, and the broadening factor for the calculated spectra is set to 10 cm 1.

illustrated in Figure 4a,b. If the two CH2 groups close to the sulfur atom are both fluorinated, marked as F2* in Figure 4c, the ν(C H) becomes very weak. The configurations of F0, F1*, and F2* molecules are displayed in the insets of Figure 4a c, respectively. Our calculations indicate that the IET spectrum is sensitive to the fluorine substitution of the atoms close to the sulfur atom, but insensitive to the substitution of the atoms far away from the sulfur atom. This supports the hypothesis about the existence of the proximity effect, as suggested by Beebe et al. In a recent study, Okabayashi et al.7 deuterated the CH2 group closest to the sulfur atom and observed a considerable intensity decrease for the ν(C H) mode. Unfortunately, they did not investigate the situation, like F2*, when the second closest CH2 group is also simultaneously deuterated. On the basis of their limited experimental results, Okabayashi et al. concluded that the IETS amplitude should not significantly depend on which part of the molecule is deuterated. Such a conclusion is thus questionable in light of our results presented in this study. From vibration frequency analysis, one can notice that there are many vibration modes in the energy region of 0.37 0.39 eV. Figure 5a gives a typical example taken from the high-energy peak around 0.38 eV of Au12 F0 Au12. Remarkably, among so many modes, only one shows a large intensity. Here, we select only four representative vibration modes in Figure 5b to discuss some general behaviors. The first vibration mode corresponds to the symmetric stretching vibration of the CH3 group. It is inactive in the spectrum due to the weak coupling between the end CH3 group and the electrode. The second vibration mode mainly comes from the symmetric stretching vibration of the CH2 group closest to the sulfur atom. At the titled angle β of 40, this CH2 group gets very close to the electrode and can result in a new tunneling path bypassing the end sulfur atom. The electron tunneling path bypassing the end group has also been reported by other groups.21,22 In this tunneling path, the CH2 stretching

Figure 5. (a) Contributions from all vibration modes to the high-energy peak of the Au12 F0 Au12 molecular junction around 0.38 eV with the tilt angle being 40. (b) Four typical vibration modes. The red arrows represent the new tunneling path bypassing the end sulfur atom.

vibration mode plays the pivotal role for the electron transport. The third vibration mode is a coupled mode of CH2 groups in the central of the molecule. Its stretching motion is almost perpendicular to the tunneling path of the transport electron and is thus inactive. The fourth mode is dominated by the asymmetric vibration of the CH2 groups, which should be inactive according to the propensity rule of the IETS.15 Taking Au12 F0 Au12 with the end groups both located at the hollow site as an example, we have further investigated how the tilt angle influences the electron tunneling path. Figure 6a shows the relationship between the intensity of the ν(C H) vibration mode and the δ(CH2) vibration mode at different tilt angles. The relative intensity of the ν(C H) vibration mode remains very weak until the angle β changes to 25. With the tilt angle β of 5, the intensity of the ν(C H) vibration mode becomes the lowest. We have also calculated the coupling energy (Ecoup) between the carbon atom (representing the CH2 group) and the electrode at different tilt angles, and the results are shown in Figure 6b. An obvious angle dependence of the coupling energy can be observed. It is known that the coupling energy should decay exponentially with the distance between the atom and the electrode surface, which is somewhat reflected by the change of the angle. For instance, at the tilt angle of 35, the distance between the carbon atom and the electrode surface is the longest, which leads to the weakest coupling energy. However, we do not find the direct connection between the coupling energy and the relative intensity of the ν(C H) vibration mode. We now define the projection of the CH2 stretching vibration along the normal of the electrode surface as a function of cos α, 20304

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Figure 6. (a) Intensity of the ν(C H) vibration mode relative to the δ(CH2) vibration modes at different tilt angles. (b) Coupling energy of the C atom closest to the S atom with the electrode at different tilt angles (green rectangles) and distance between the C atom nearest to the S atom and the electrode surface at different tilt angles (red circles). (c) Values of cos α at different tilt angles. (d) Relationship between the relative intensity of the ν(C H) vibration mode and the effective coupling energy of the carbon atom nearest to the S atom with the electrode.

whose value is determined by the angle (α) between the H C H surface of the CH2 group and the normal of the electrode surface. The calculated values of cos α for different titled angles are illustrated in Figure 6c. With this definition, when β is 5, the value of cos α has the smallest value. In this case, the H C H surface of the CH2 group is nearly perpendicular to the normal of the electrode surface. According to the propensity rule of IETS, one can expect that the intensity of the ν(C H) mode should be very small at this configuration. This observation has led us to examine the relationship between the intensity of the ν(C H) and the newly defined effective coupling energy, Eeff coup = Ecoup  cos α. Expectedly, a nice linear dependence between them is observed, as shown in Figure 6d. In general, when β is negative, the new tunneling path through the CH2 group will gradually increase and compete with the original tunneling path through the S Au bond, whereas for positive β, the effective coupling energy is always very small and the new tunneling channel is suppressed. These results have clearly demonstrated that the intensity of the CH2 vibration mode depends on both the coupling energy between the carbon atom and the electrode and the projection of the vibration mode.

’ SUMMARY In conclusion, our first-principles simulations have successfully reproduced the experimental IET spectra of the fluorinated hexadecanethiol molecular junctions measured by Beebe et al. Our calculations not only confirm that the peak of ν(C H) in the IET spectra of the alkanethiol molecular junctions should correspond to the CH2 symmetric stretching vibration mode but also reveal that the high intensity of the peak is a result of opening of a new electron tunneling pathway trigged by the appropriate titled angle of the molecule. The hollow site is indicated as the most probable bonding site for the alkanethiol molecules in the experiment.1 The sensitivity of the IET spectral profile on the fluorination position has also been

demonstrated and analyzed. This study illustrates again the importance of the theoretical modeling for the interpretation of the experimental results of molecular junctions.

’ AUTHOR INFORMATION Corresponding Author

*E-mail: [email protected].

’ ACKNOWLEDGMENT This work is supported by the National Nature Science Foundation of Shandong Province under Grant No. ZR2010AZ002, the National Natural Science Foundation of China (Grant Nos, 10804064, 10974121, 10947131, and 20925311), the National Basic Research Program of China (2010CB923300), the G€oran Gustafsson Foundation for Research in Natural Sciences and Medicine, and the Swedish National Infrastructure for Computing (SNIC). L.-L.L. thanks the China Scholarship Council for the financial support. ’ REFERENCES (1) Beebe, J. M.; Moore, H. J.; Lee, T. R.; Kushmerick, J. G. Nano Lett. 2007, 7, 1364–1368. (2) Chen, Y. C.; Zwolak, M.; Di Ventra, M. Nano Lett. 2005, 5, 621–624. (3) Troisi, A.; Ratner, M. A. Phys. Rev. B 2005, 72, 033408. (4) Solomon, G. C.; Gagliardi, A.; Pecchia, A.; Frauenheim, T.; Di Carlo, A.; Reimers, J. R.; Hush, N. S. J. Chem. Phys. 2006, 124, 094704. (5) Paulsson, M.; Frederiksen, T.; Brandbyge, M. Nano Lett. 2006, 6, 258–262. (6) Wang, C. K.; Zou, B.; Song, X. N.; Li, Y. D.; Li, Z. L.; Lin, L. L. Front. Phys. China 2009, 4, 415–419. (7) Okabayashi, N.; Paulsson, M.; Ueba, H.; Konda, Y.; Komeda, T. Nano Lett. 2010, 10, 2950–1955. (8) Jiang, J.; Kula, M.; Lu, W.; Luo, Y. Nano Lett. 2005, 5, 1551–1555. 20305

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