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Determination of the Configuration of a Single Molecule Junction by Inelastic Electron Tunneling Spectroscopy Li-Li Lin,†,‡ Xiu-Neng Song,‡ Jian-Cai Leng,† Zong-Liang Li,† Yi Luo,‡ and Chuan-Kui Wang*,† College of Physics and Electronics, Shandong Normal UniVersity, Jinan 250014, P. R. China, and Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNoVa, S-10691 Stockholm, Sweden ReceiVed: February 16, 2010
First-principles calculations for inelastic electron tunneling spectroscopy (IETS) of a single 1,3-propanedithiol molecule covalently bound to gold electrodes are presented. Inelastic electron tunneling spectra of the single molecule junction with different contact geometries and molecular orientations at the interface are simulated. It is demonstrated that the delicate variation in the configuration of the single molecule junction caused by separating the two electrodes can result in significant changes in the inelastic electron tunneling spectral profile of the junction. The two most probable configurations of the molecular junction formed in the experiment (Nano Lett. 2008, 8, 1673) are theoretically identified, and the experimental IET spectra are correctly assigned. Although significant advances have been made in molecular electronics in recent years, there still exist several unsolved issues, such as how to identify configurations of molecular junctions, how to repeatedly build a single molecular junction, and how to understand the electronic tunneling mechanism through the junctions, just to name a few. Recently, one of the most exciting developments in this field is the application of inelastic electron tunneling spectroscopy (IETS) to molecular junctions, from which a chemical signature of the molecular junctions has been obtained.1-22 Some experimental works have measured the vibrational spectra of single molecules using scanning tunneling microscopy (STM),1 an electron-migrated junction,9 a mechanically controlled break junction,10 and a cross-wire tunneling junction11 where the molecules are not directly connected to the electrodes in the junction. Moreover, some studies have been carried out on bulk junctions where an ensemble average of a large number of molecules is considered. As a consequence, these studies are difficult in probing delicate changes in molecular configurations of single molecular junctions. Very recently, using an STM-break junction technique at cryogenic temperatures, Hihath et al. have performed IETS on a single molecular junction in which the molecule is covalently bound between the two electrodes.7 The separation of the two electrodes can be controlled with subangstrom precision. The molecular junction contact geometries and the molecular conformations can thus be adjusted systematically. The possibility of performing IETS can give detailed information on details of the configuration. Taking the 1,3-propanedithiol molecular junction as the studied system, they have proven that the systematical and precise measurements allow for a better comprehension of the relationship among the molecular configuration, the contact geometry, and the electron-phonon spectrum. With available experimental IET spectra for molecular junctions, theories are needed to make accurate assignments, * To whom correspondence should be addressed. E-mail: ckwang@ sdnu.edu.cn. † Shandong Normal University. ‡ Royal Institute of Technology.
to interpret the features of the spectra, and to deduce structures of the molecular junctions. With these, the good comprehension of the relationship between the molecular junction configuration and the electron-phonon spectrum can be obtained. Inelastic electron transport in molecular junctions has been studied by several groups using either model calculations or first-principles simulations.12-22 These studies have concluded that the IETS can be used not only to understand the influence of nuclear motion of molecule on electronic transport behavior but also as a powerful tool for determining the geometrical structure of molecular junctions. In this article, we present our theoretical study on IETS of a single 1,3-propanedithiol molecule covalently bonded to two gold electrodes. Based on the excellent agreement between our calculated and experimental spectra, the most probable molecular junction configurations formed in the experiment are determined. The strategy for this study is outlined as follows. The molecular geometric structure is first optimized, then three contact geometries are considered, and the most probable contact geometry is selected. In succession, the orientation of the molecule relative to the electrode is investigated. The calculated IETS results are then directly compared with the corresponding experimental results.7 In this work, all the optimization and the energy calculations are performed at density functional theory (DFT) level with B3LYP functional23 and LanL2DZ basis set24 as implemented in the Gaussion 03 program.25 The IET spectrum is calculated using our QCME code that implements a generalized quantum chemical model for the elastic and inelastic transport in molecular junctions based on the Green’s function formalism.26 Details of the method can be found elsewhere.21,27 Since we only focus on the spectral intensity rather than the specific spectral line width, a uniform broadening factor, 1.24 meV or 10 cm-1, is adopted for all spectral features, which is only for the purpose of discussion. The molecular junctions with three different contact geometries are shown in Figure 1. In the first case, the outermost Au atom in a linear gold chain (Ch) is bonded to the sulfur atom. In the second case, the sulfur is located above the middle of a triangular gold trimer (Tr), representing a bond over the hollow
10.1021/jp101428d 2010 American Chemical Society Published on Web 03/02/2010
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Figure 1. Structures of molecular junctions with three contact geometries, in which Ch (a), Tr (b), and Tet (c) represent the chain, triangular, and tetrahedral structure of gold atoms, respectively.
TABLE 1: Some Selective Bond Lengths (Å) for the Three Molecular Junctions model
S(1)Au(12)
S(1)C(2)
C(2)C(5)
C(5)C(8)
C(8)S(11)
S(11)Au(15)
Ch Tr Tet
2.46 2.83 2.41
1.87 1.96 1.89
1.53 1.54 1.54
1.54 1.54 1.55
1.85 1.98 1.88
2.44 2.85 2.41
site of an Au(111) surface. The contact geometry is a tetrahedral Au cluster (Tet) for the third case. For all the three contact structures, the molecular geometry is optimized and the energy is calculated for different distances between the two electrodes varying with a step of 0.04 nm. The Au-Au bonding length is fixed to be 2.88 Å, and the molecule is relaxed completely except for the endmost S atoms that have been fixed in the Y and Z directions. The optimized geometries have a distance of 1.036 nm between the two electrodes for all the three bonding situations, and the calculated main bond lengths are listed in Table 1. The S-Au bond lengths at the two sides in the Tr model are 2.83 and 2.85 Å, respectively, consistent with the previous result.19 In the Tet model the S-Au bond lengths take the shortest value. Furthermore, the lengths of the molecule are respectively 0.55, 0.58, and 0.56 nm for the three contact models, from which one observes that the molecule in the Tr case is most stretched. The calculated IET spectra of molecular junctions with three different bonding configurations are shown in Figure 2. It can be seen that large differences exist among the three IET spectra. For the Ch configuration, the dominant spectral peak is at 186 meV due to the scissoring of CH2, and the ν(S-Au) mode cannot be resolved. However, one finds that the highest spectral peaks for the Tr and Tet configurations are respectively contributed by the modes ν(S-Au) at 20 and 25 meV. It is noted that there are large differences between the theoretical
Figure 2. Calculated IET spectra of molecular junctions with three contact geometries. The vibration modes are assigned for the spectral peaks.
and the experimental7 IET spectra in terms of both the spectral intensities and the locations. We have simulated IET spectra for a large numbers of configurations. Here we just present the results of the single molecule junction with a contact structure Tet because the simulated IETS are mostly relevant to the experimental ones. It is known that molecular vibrations with net dipole moment changes perpendicular to the interface of the tunneling junction have larger peak intensities than vibrations with net dipole moments parallel to the interface.8 The orientation of the molecule relative to the electrode has therefore significant effect on the IETS of molecular junctions,28,29 which could be a key parameter in adjusting the spectral profile of the junction. For convenience, the sulfur atom S(1) is fixed at zero point, and
IETS of a Single Molecule Junction
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Figure 3. Calculated IET spectra of the molecular junction with β of 10° (a) and 25° (b), together with the experimental result (c) (the lowest curve of Figure 3c in ref 7). The configuration of the molecular junction is in the inset. Vibration modes are assigned for the spectral peaks.
the S(1)-C(5) bond is set along the X axis first as shown in Figure 1c. The molecule is rotated around the Z axis in the XOY plane. The angle between the S(1)-C(5) bond and the X axis is defined as β and is set to be positive when the molecule is tilted toward the positive Y axis (see the inset in Figure 3). The molecule is rotated without further optimization, while the S-Au distance is kept to be 2.41 Å. The IET spectra of the molecular junctions with different β values are shown in Figure 3, together with the experimentally measured one. When β is 10° with the distance between the two electrodes being 1.040 nm, one can see that the largest spectral intensity is contributed by δS(CH2). In addition, νa(C-S) and νS(C-S) also have large contributions to the IETS. However, the modes between 100 and 175 meV have small contributions to the IETS. When β is increased to 25°, with the electrode distance 1.010 nm, one can see from Figure 3b that the IETS has a large discrepancy from that in Figure 3a, which clearly demonstrates the dependence of IETS on the orientation of the molecule relative to the electrode surface. More importantly, the profile of the calculated IETS in Figure 3b highly resembles the experimental one shown in Figure 3c (the lowest curve of Figure 3c in ref 7). Hihath et al. used a simple one-dimensional model to estimate the vibrational modes and assigned the calculated modes to some peaks in the measured IETS. On the basis of our first-principles calculations, we can assign in detail the peaks with vibrational modes. The spectral peak at 48 meV is related to δs(S-C-C), but not ν(C-S) as assigned by Hihath et al. The peak at 110 meV is contributed by the δr(CH2) and γt(CH2). The modes at 152 meV contain γw(CH2), γt(CH2), and δr(CH2), in which γw(CH2) is the dominant one. Furthermore, the peak at 185 meV is assigned to be δS(CH2), but not the ν(C-C) mode assigned by Hihath et al. Herein we pay attention to the νa(C-S) mode, which contains a combination of the C(2)-S(1) stretching and the C(8)-S(11) stretching that can be considered as quasi-antisymmetry with respect to the carbon atom C(5). The normal mode for three configurations of the molecular junction with different tilted angle β is displayed in Figure 4. It is seen from Figures 2 and 3 that, when β is increased from 0° to 10°, the νa(C-S) mode has a more active performance in the IET spectra. This manifestation may be explained qualitatively in terms of Troisi and Ratner’s propensity rules.28,30 It would nevertheless be mentioned that the proposed propensity rules are subject to some exceptions when small molecules are considered.30 The observation of the antisymmetry νa(C-S) mode in the small molecular
Figure 4. νa(C-S) mode of the extended 1,3-propanedithiol molecule with different titled angle β: 0° (a), 10° (b), and 25° (c).
Figure 5. Calculated IET spectrum of the molecular junction with β of -30° (a), together with the experiment result (b) (the middle curve of Figure 3c in ref 7). The configuration of the molecular junction is given in the inset. Vibration modes are assigned for the spectral peaks.
junction studied here could thus anyway be possible. However, as the molecule is titled, more tunneling paths can be formed. In our case, the probability of a tunneling path gold-S(11)-C(8)C(5)-C(2)-gold can become competitive with the path gold-S(11)-C(8)-C(5)-C(2)-S(1)-gold. For the shorter tunneling path, the νa(C-S) mode should provide certain intensity. Therefore, the increase of the relative intensity of the νa(C-S) mode can be interpreted as the involvement of additional tunneling paths. Up to now, one configuration of the single 1,3-propanedithiol molecular junction has been determined by comparing with the experimental IET spectrum. We now turn our attention to the configuration that can reproduce another experimental IET spectrum.7 The simulated IET spectrum together with the experimental result is shown in Figure 5. The inset shows the most probable configuration of the molecular junction, where β is - 30°, the S-Au bond length is 2.32 Å, and the electrode distance is 0.897 nm. From Figure 5, one can see that the profile of the simulated IETS is highly consistent with the experimental
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one (the middle curve of Figure 3c in ref 7). The δs(S-C-C) modes at 34 and 49 meV in our calculation correspond to the ν(C-S) mode as assigned by the simple one-dimensional model.7 The spectral peak contributed by the ν(S-Au) mode at 26 meV is not resolved by the simple one-dimensional model. Furthermore, the CH2 wagging and scissoring modes are responsible for the spectral peak at 179 meV, instead of the νa(C-C) mode assigned by Hihath et al.7 Our calculations demonstrate the extreme sensitivity of the IETS to the details of the bonding geometry. The delicate changes in the configuration of the single molecule junction can cause drastic changes in the IETS. When the strain in the junction is changed by separating the two electrodes, the tilt angle of the molecule, namely, the position of the electrode relative to the other, is changed. Therefore, the IET spectra from one junction to the next become different. It demonstrates yet again that the IETS technique is a power tool for determining the configuration of the single molecule junction. Our calculations further confirm that certain selection rules in IETS as shown in previous studies2,3,9,19,28 work quite well. It is known that longitudinal modes with the same direction of tunneling current have greater contribution to IETS than transverse modes because the longitudinal vibration has a larger coupling with metal. In Figure 3, the spectral peak contributed by the CH2 scissoring mode is found to be decreased with the increase of β, which results from weakening of its longitudinal component. In addition, ν(C-S) modes always have contribution to the spectrum because their longitudinal components remain. In conclusion, our study has demonstrated the high sensitivity of the IETS on the configuration of the molecular junction which opens up an opportunity for determining configuration changes in a single molecular junction. The first-principles simulations have revealed important details in IETS that are not accessible in the experiment. The excellent agreement between the theory and the experiment allows people to determine the probable configuration of the molecular junctions formed in the experiment. The great benefits of combining theoretical and experimental studies on IETS of molecular junctions have been further proven. Acknowledgment. This work is supported by National Nature Science Foundation of China under Grant Nos. 10804064 and 10974121 and Nature Science Foundation of Shandong Province under Grant No. Z2007A02.
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