J. Phys. Chem. C 2009, 113, 18353–18357
18353
Orientation of Decanethiol Molecules in Self-Assembled Monolayers Determined by Inelastic Electron Tunneling Spectroscopy Jian-Cai Leng,†,§ Li-Li Lin,† Xiu-Neng Song,‡ Zong-Liang Li,† and Chuan-Kui Wang*,† College of Physics and Electronics, Shandong Normal UniVersity, Jinan 250014, People’s Republic of China; Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNoVa, S-10691 Stockholm, Sweden; and College of Mathematics and Physics, Shandong Institute of Light Industry, Jinan 250353, People’s Republic of China ReceiVed: June 4, 2009; ReVised Manuscript ReceiVed: August 13, 2009
We present first-principles calculations for the inelastic electron tunneling spectroscopy (IETS) of decanethiolate molecules sandwiched between Au(111) surface and scanning tunneling microscope (STM) tip, as reported by Hallba¨ck et al. (Nano Lett. 2004, 4, 2393). It is demonstrated here that the IET spectra are very sensitive to the molecule-metal contact structure, orientation of the molecule adsorbed on the surface, and the distance between the carbon of the terminal methyl group and the STM tip. With correct assignation of the experimental spectral features, the orientation of the molecule and then the probable configuration of the molecular junction are determined. I. Introduction The possibility of using single molecules to build electronic devices has attracted much attention in recent decades.1-12 Many exciting developments have been made in the field by virtue of technological advances and in-depth understanding of electron transport in molecular junctions. It is known that the detailed geometrical configuration of metal-molecule-metal junctions plays a key role in the charge transport properties. Thus, resolving the configuration of molecular junctions is a key issue for the controlled formation of molecular devices with functions required. Recently, one of the most exciting developments in this field has been the application of inelastic electron tunneling spectroscopy (IETS) to molecular junctions, thanks to the pioneering work of Ho’s group, which found that the combination of IETS with scanning tunneling microscope (STM) makes the chemical fingerprinting of molecules adsorbed on a surface possible.13 The interplay between the experimental and theoretical works in this field is very important. With available experimental IET spectra for molecular junctions, theories are needed to make accurate assignments and to interpret features of the spectra in order to deduce structures of the molecular junctions. Inelastic electron transports in molecular junctions have been studied by several groups using either model calculations or first-principles simulations.14-21 For instance, using first-principles simulations, Luo’s group has calculated IET spectra of several molecular junctions and reproduced the experimental spectra very well.14,15 They concluded that IET spectra are very sensitive to the intramolecular conformation, molecule-metal contact geometry, and the molecule-metal bonding. Taking pentane monothiolate as a model system, Troisi et al. have shown a close relationship between the IET spectrum and the orientation of the molecule * To whom correspondence should be addressed. E-mail: ckwang@ sdnu.edu.cn. † College of Physics and Electronics, Shandong Normal University. § College of Mathematics and Physics, Shandong Institute of Light Industry. ‡ Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology.
adsorbed on a metal surface, and concluded that IETS can be used to establish the molecular orientation in junctions.22 The studies in this field have demonstrated that the IETS can be used not only to understand the influence of nuclear motion of molecules on electronic transport properties, but also as a powerful tool to determine the geometrical structure of molecular junctions. Self-assembled monolayers of alkanethiols are promised to have different applications and have been extensively studied.23-25 However, the accurate determination of the configuration of alkanethiols adsorbed on a surface is a long-standing and interesting problem. Recently, Ha¨llback et al. have presented IETS measurements using STM for a decanethiol self-assembled monolayer on Au(111).25 The possible resolution of the spectral feature related to molecular vibration modes is qualitatively suggested. In this work, we report our systematic studies on the IETS of the decanethiol molecule sandwiched by Au(111) surface and the STM tip. The probable configuration of the decanethiol junction related to the experiment is thus determined for the first time. II. Formalisms and Computational Details Utilizing the available knowledge in the field, we take the following strategy for this work. The effect of contact configuration on the IETS of the molecular junction is first investigated, and the favorable contact configuration is thus predicted in which the calculated IET spectrum is close to the counterpart in measurement. Second, with the favorable contact configuration, we change the orientation of the molecule adsorbed on a surface and obtain the IETS at one angle that is more similar to the experimental features. Third, in order to pursue the extensive agreement between the theoretical simulation and the measurement, we modify the distance between the carbon of the terminal methyl group and the STM tip. Finally, we fulfill our work for determining the configuration of the STM tip-decanethiol self-assembled monolayer-Au substrate junction. We consider a Au(111) surface parallel to the other electrode. In all calculations, the Au-S distance and the Au-Au bond
10.1021/jp9052264 CCC: $40.75 2009 American Chemical Society Published on Web 09/28/2009
18354
J. Phys. Chem. C, Vol. 113, No. 42, 2009
Leng et al.
length are fixed to be 0.285 and 0.288 nm, respectively.14-16 All geometry optimizations are done at the density functional theory (DFT) level with the B3LYP26 functional and the LanL2DZ27 basis set, using the GAUSSIAN03 program package.28 The IET spectra are calculated by means of the QCME program, which implements a generalized quantum chemical mode for the elastic and inelastic transport in molecular junctions developed in Luo’s group.29 The formalisms are briefly described here and more details can be found elsewhere.14,16,30,31 The current density along molecular junctions is expressed as follows: jSD )
4em*kBT 3
III. Results and Discussion
×
p
∫
∞
0
{
}
1 + exp[(Ef - Ez + eVD)/kBT] ln |ζ(VD, Q)| 2nSnDdEz 1 + exp[(Ef - Ez)/kBT]
(1)
where nS and nD are the density of states of the source (S) and the drain (D), respectively, T is the device working temperature, m* is the electron effective mass, VD is the external voltage, and Q is vibrational normal mode. The transition matrix element from S to D, ζ(VD,Q), is determined by the following:
∑ ∑ VJS(Q)VDK(Q) ∑ gJKµ
ζ(VD, Q) )
J
K
(2)
µ
where VJS(Q) (VDK(Q)) represents the coupling energy between the site J(K) of the molecule and the S(D) in the site representation. J and K run over the molecular sites. As the carrier-conduction contribution from a scattering channelεµ, gµJK can be written as follows:
µ gJK )
{〈
Ψµ0 +
∑ a
〈Jµ0 +
|
∂Ψµ0 VV′′ µ Q K0 + ∂Qa a
{〈
zµ - εµ
〈Jµ0 +
∑ a
∑ a
∑ (∂Jµ0 /∂Qa)QV'Va |Ψµ0〉 a
Ψµ0 +
|
∂Ψµ0 V''V µ Q K0 + ∂Qa a
∑ a
〉
∂Kµ0 VV′′ Q × ∂Qa a
}
+
〉
∂Kµ0 V''V Q × ∂Qa a
∑ (∂Jµ0 /∂Qa)QV'Va | ∑ (∂Ψµ0 /∂Qa)QV'Va 〉 a
Three different contact conformations, a linear chain of three gold atoms at each side (cont1), a triangular structure with three gold atoms at each side (cont2), a triangular gold cluster at one side, and a parallelogram gold cluster at the other side (cont3) are constructed (see Figure 1). For cont2 and cont3, the sulfur atoms are placed above the middle of the triangle, while the carbons of the terminal methyl group are positioned above the middle of the triangle and the center of the parallelogram (i.e., the bridge site), respectively. The carbon of the terminal methyl group is at a distance of 0.351 nm away from the gold surface.22
a
zµ - pωa
}
(3)
where |J0µ〉 and |K0µ〉 are the electronic function of the molecular site J and K at equilibrium position, respectively, and ωa is the frequency for vibrational normal mode Qa. The electronic wave function expanded as Taylor series along the vibrational normal mode is truncated to the first order derivative with adopting the harmonic approximation. Here, parameter zµ is a complex variable, zµ ) Eµ + iΓµJK, where Eµ is the energy at which the scattering process is observed, ΓJK µ is the escape rate determined by the Fermi golden rule, 2 ΓµJK(Q) ) πnSVJS (Q)|〈J(Q)|µ(Q)〉| 2 + 2 (Q)|〈µ(Q)|K(Q)〉| 2 (4) πnDVDK
The calculated IET spectra of the decanethiolate junctions with three contact conformations at temperature 4.2 K are shown in Figure 2. One can see that the spectra in all cases consist of two groups that are located at about 25 mV and 150 mV. However, the spectral profile for a different contact configuration is noticeably different. The cont1 and cont2 configurations have different Au-S bonding strength that results in different intensity of vibronic feature in the ν(S-Au) mode. It thus further demonstrates that IETS is very sensitive to the bonding between the molecule and electrodes.15 The cont2 and cont3 have the same Au-S bonding, but different contact structure in terminal methyl group side, which produces quite different spectral profiles. The high sensitivity of the IETS on the contact structures is thus displayed. The spectral distributions on the right side are enlarged as insets in Figure 2 in order to assign the vibronic modes. One can see that both of the components and the relative intensities in the spectrum of this region are quite different among the three cases of contact conformations. For the case of cont1, there are only two modes w(CH2)and t(CH2) contributing to the inelastic current, while for the case of cont2, w(CH2) and ν(C-C) modes are resolved. In the case of cont3, four resolved modes, ν(C-C),w(CH2), t(CH2), and δs(CH2), have contribution to the IETS. Unfortunately, the general intensity of the vibronic spectrum in the right group is rather lower than that in the left group, which is a distinct discrepancy in comparison with the experimental results (see Figure 5). Nevertheless, on the basis of the theoretical experience and experimental results,22,25 we choose cont3 to more carefully study. Considering the available conclusion that the relative intensity of spectral peaks is closely dependent on the molecular orientation and junction width,16,22 we thus first set a molecular orientation for studying the orientation effect. The sulfur atom is set at the zero point and the Z axis of coordinates is perpendicular to the metal surface. The orientation of the molecule is defined by the tilting angle θ between the S-C bonding and the Z axis (see Figure 3). The molecule can be tilting around X axis in the YOZ plane. The IET spectra for the molecular junction of cont3 with the tilting angle θ ) 10°, 20°, 30°, and 40° are shown in Figure 4. One can see that the relative intensities of spectral peaks are closely dependent on the molecular orientation. More interestingly, the intensity of the main spectral peak in the right group is stronger than that in the left group for larger tilting angles, which gives the same spectral profile as that in the experiment. Moreover, a new vibronic mode ν(S-C) is resolved here for larger tilting angles. The intensity of the spectral peak contributed by the scissor mode δs(CH2) becomes stronger for the larger tilting angle. When the molecule is tilted, the δs(CH2)mode characterized as a
Orientation of Decanethiol in Self-Assembled MLs
J. Phys. Chem. C, Vol. 113, No. 42, 2009 18355
Figure 1. Structures of the decanethiol molecular junctions. (a) A linear chain of three gold atoms at each side (cont1), (b) a triangular structure with three gold atoms at each side (cont2), and (c) a triangular gold cluster at one side and a parallelogram gold cluster at the other side.
transverse mode is active because a longitudinal component along the direction of the tunneling current appears. In fact, the ratio between the longitudinal and transverse components of each mode is adjusted when the orientation of the molecule is changed, which gives a large influence on the IETS profile. This provides an explanation for the significant modification of the details of the IET spectra with the tilting angle. From Figure 4, one can also see that the frequencies of the assigned modes have little variation with the tilting angle, as the whole molecular junction holds to be almost unchanged. In comparison with the experimental IET spectrum, we speculate that the configuration of molecular junctions with a 20° tilting angle is the probable one that needs to be studied further. By adjusting the distance between the carbon of the terminal methyl group and the gold surface, the IET spectra of the decanethiolate junction having the cont3 configuration with a
20° tilting angle, together with the experimental spectrum found by Hallba¨ck et al. at temperature 77 K, are shown in Figure 5. It is shown again that the IETS is very sensitive to the junctionwidth. When the distance is changed, the conformation of the molecular junction is modified, which induces the shift of the frequencies of the vibrational normal modes. Among the simulations, we find that when the distance is 0.309 nm, the theoretical IETS is consistent with the experimental counterpart in view of the relative intensities of spectral peaks, and the kinds of modes contributed to the peaks. It is seen that the broaden peak at 33 mV in the experiment is contributed by theν(S - Au), ν(S - C), δs(C - C - C)and δs(S - C - C) modes, and the broaden peak at 153 mV is related to the contribution from ν(C - C), t(CH2) and w(CH2). Furthermore, the shoulder appeared at the end of the 153 mV peak is related to the δs(CH2) mode. It is worth noting that the assignation is consistent with the prediction given
18356
J. Phys. Chem. C, Vol. 113, No. 42, 2009
Leng et al.
Figure 2. Calculated IET spectra of the decanethiol molecular junctions for different contact structures: (a) for cont1, (b) for cont2, and (c) for cont3. The spectra at regions of about 150 mV are enlarged as insets. Figure 4. Calculated IET spectra of the decanethiol molecular junction with the contact structure of cont3 as a function of the tilting angle θ.
Figure 5. Calculated IET spectra of the decanethiol molecular junction with the contact structure of cont3 and θ ) 20° as a function of the distance of the carbon in the terminal methyl group away from the STM tip. The experimental spectrum from ref 25 is also shown. Figure 3. The decanethiol sandwiched between Au(111) surface and the STM tip in the S-C bonding perpendicular orientation and in the orientations titled 20°. The θ is defined by the S-C bonding and the Z axis. The cases of the molecule rotated around the X axis in the YOZ plane are considered.
by Hallba¨ck et al.25 However, there exists a discrepancy for the simulated spectrum at 0.309 nm and the measured one in which the right broaden peak is located at 164 mV, whereas it is at 153 mV for the measurement. The position of the right broad peak of the simulated spectrum at 0.351 nm coincides with that of the measurement, but there exists a discrepancy for the left broaden peak, especially, the ν(S-C) mode gives a new peak in the simulated spectrum. In short, further work is needed to improve the simulation, for example, considering the temperature effect. However, more information for the measured IET spectrum is required for determining the conformation of the molecular junction.
experiment of Ha¨llback et al. demonstrate a cont3 structure with a 20° titled angle and a 3.09 Å distance from the terminal carbon away from the STM tip. The use of IETS is demonstrated to be a powerful technique for providing detailed information on molecular electronic devices. In addition, our theoretical methods are now used to simulate IET spectra for several new single molecule IETS measurements.32-34 Acknowledgment. This work was supported by the National Nature Science Foundation of China under Grant Nos. 10674084 and 10804064 and Nature Science Foundation of Shandong Province under Grant No. Z2007A02. The authors are thankful for the support of the Swedish International Development Agency (SIDA) (348-2006-6679). Fruitful discussions with Professor Yi Luo in KTH, Sweden, are gratefully acknowledged.
IV. Conclusion
References and Notes
In conclusion, we have paid special attention to the study of IET spectra of the decanethiolate molecular junction and have shown that theoretical simulation has not only reproduced the experimental spectra, but also provided reliable and detailed information about the configuration of the molecular junction that is not otherwise accessible by experiment alone. The theoretical simulation shows that the molecular conformation and contact configuration of the molecular junction in the
(1) Aviram, A.; Ratner, M.A. Chem. Phys. Lett. 1974, 29, 277. (2) Bumm, L. A.; Arnold, J. J.; Cygan, M. T.; Dunbar, T. D.; Burgin, T. P.; Jones II., L.; Allara, D. L.; Tour, J. M.; Weiss, P. S. Science 1996, 271, 1705. (3) Reed, M. A.; Zhou, C.; Muller, C. J.; Burgin, T. P.; Tour, J. M. Science 1997, 278, 252. (4) Frank, S.; Poncharal, P.; Wang, Z. L.; de Heer, W. A. Science 1998, 280, 1744. (5) Chen, J.; Reed, M. A.; Rawlett, A. M.; Tour, J. M. Science 1999, 286, 1550.
Orientation of Decanethiol in Self-Assembled MLs (6) Cui, X. D.; Primak, A.; Zarate, X.; Tomfohr, J.; Sankey, O. F.; Moore, A. L.; Moore, T. A.; Gust, D.; Harris, D.; Lindsay, S. M. Science 2001, 294, 571. (7) Smit, R. H.; Noat, Y.; Untiedt, C.; Lang, N. D.; Hemert, M. C.; Ruitenbeek, J. M. Nature 2002, 419, 906. (8) Nitzan, A.; Ratner, M. A. Science 2003, 300, 1384. (9) Xu, B.-Q.; Tao, T. J. Science 2003, 301, 1221. (10) Dadosh, T.; Gordin, Y.; Krahne, R.; Khivrich, I.; Mahalu, D.; Frydman, V.; Sperling, J.; Yacoby, A.; Bar, J. I. Nature 2005, 436, 677. (11) Zhao, A. D.; Li, Q. X.; Chen, L.; Xiang, H. J.; Wang, W. H.; Pan, S.; Wang, B.; Xiao, X. D.; Yang, J. L.; Hong, J. G.; Zhu, Q. S. Science 2005, 309, 1542. (12) Wu, S. M.; Gonza´lez, M. T.; Huber, R.; Grunder, S.; Mayor, M.; Scho¨nenberger, C.; Calame, M. Nat. Nanotechnol. 2008, 3, 569. (13) Ho, W. J. Chem. Phys. 2002, 117, 11033, and references therein. (14) Jiang, J.; Kula, M.; Lu, W.; Luo, Y. Nano Lett. 2005, 5, 1551. (15) Kula, M.; Jiang, J.; Luo, Y. Nano Lett. 2006, 6, 1693. (16) Jiang, J.; Kula, M.; Luo, Y. J. Chem. Phys. 2006, 124, 034708. (17) Pecchia, A.; Carlo, A. D.; Gagliardi, A.; Sanna, S.; Frauenheim, T.; Gutierrez, R. Nano Lett. 2004, 4, 2109. (18) Chen, Y. C.; Zwolak, M.; Ventra, M.; Di, Nano Lett. 2005, 5, 621. (19) Sergueev, N.; Demkov, A. A.; Guo, H. Phys. ReV. B. 2007, 75, 233418. (20) Troisi, A.; Ratner, M. A. Phys. ReV. B. 2005, 72, 33408. (21) Paulsson, M.; Frederiksen, T.; Brandbyge, M. Nano Lett. 2006, 6, 258. (22) Troisi, A.; Ratner, M. A. Phys. Chem. Chem. Phys. 2007, 9, 2421. (23) Poirier, G. E. Chem. ReV 1997, 97, 1117, and references therein. (24) Wang, W.; Lee, T.; Reed, M. A. Phys. ReV. B 2003, 68, 035416. (25) Hallba¨ck, A. S.; Oncel, N.; Huskens, J.; Zandvliet, H. J. W.; Poelsema, B. Nano Lett. 2004, 4, 2393. (26) Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
J. Phys. Chem. C, Vol. 113, No. 42, 2009 18357 (27) Hay, P. J.; Wadt, W. R. J. Chem. Phys. 1985, 82, 270. (28) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al- Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, ReVision C.02; Gaussian, Inc., Wallingford CT, 2004. (29) Jiang, J.; Wang, C. -K.; Luo, Y. QCME: Quantum Chemistry for Molecular Electronics; Royal Institute of Technology: Stockholm, Sweden, 2006. (30) Wang, C.-K.; Fu, Y.; Luo, Y. Phys. Chem. Chem. Phys. 2001, 3, 5017. (31) Kula, M.; Luo, Y. J. Chem. Phys. 2008, 124, 064705. (32) Osorio, E. A.; O’Neill, K.; Sthur-Hansen, N.; Nielsen, O. F.; Bjørnholm, T.; der Zant, H. S. J. AdV. Mater. 2007, 19, 281. (33) Kiguchi, M.; Stadler, R.; Kristensen, I. S.; Djukic, D.; van Ruitenbeek, J. M. Phys. ReV. Lett. 2007, 98, 146802. (34) Hihath, J.; Arroyo, C. R.; Rubio-Bollinger, G.; Tao, N. J.; Agraı¨t, N. Nano Lett. 2008, 8, 1673.
JP9052264
