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Effects of Molecular Dynamics on Electrical Conductance of Single Molecular Junction in Aqueous Solution: First Principles Calculations

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Effects of Molecular Dynamics on Electrical Conductance of Single Molecular Junction in Aqueous Solution: First Principles Calculations e-Journal of Surface Science and Nanotechnology 23 January 2010 e-J. Surf. Sci. Nanotech. Vol. 8 (2010) 38-43 Conference - ACSIN-10 - Effects of Molecular Dynamics on Electrical Conductance of Single Molecular Junction in Aqueous Solution: First Principles Calculations¤ Arihiro Tawara,y Tomofumi Tada, and Satoshi Watanabe Department of Materials Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan (Received 9 October 2009; Accepted 4 December 2009; Published 23 January 2010) The electronic transport in benzene-1,4-dithiolate molecule in aqueous solution sandwiched between gold elec- trodes have been investigated by the ab initio nonequilibrium Green’s function method combined with Car- Parrinello molecular dynamics. We have found that the C–S bond length shows clear negative correlation with the conductance both in aqueous solution and vacuum, whereas the Au–S and C–C bond lengths have little correlation. This originates from large local density of states around C–S bonds at the Fermi level. [DOI: 10.1380/ejssnt.2010.38] Keywords: Electrical transport; Benzene dithiolate (BDT); Water; Density functional calculations; Nonequilibrium Green’s function method; Molecular dynamics I. INTRODUCTION neither been understood enough nor explored in theoreti- cal fashion so far except for our previous calculation [32]. Recently, electronic transport properties of single In our previous study [32], we calculated a large number molecular junctions have been increasingly important and of conductances of a system consisting of a BDT molecule actively investigated in experimental and theoretical stud- and water molecules sandwiched between Au(100) sur- ies to deepen our understanding of nanoscale devices on faces in order to clarify bare effects of aqueous solution single molecule level. Benzene-1,4-dithiolate (BDT) be- on conductance at room temperature, using the ab ini- tween gold electrodes has been studied extensively as a tio NEGF-DFT method and Car-Parrinello molecular dy- benchmark molecule both in experimental [1–4] and the- namics (CPMD). Analyses of conductance histograms re- oretical [5–13] studies. In particular, theoretical inves- vealed the effects of the aqueous solution on the conduc- tigations on various effects such as adsorption configura- tance of the BDT: the peak of the conductance histogram tion [14–18], inelastic current [19–23] and limitation of the shifts downward by 0.01-0.02 G0 (5-10 %), which is at- density functional theory (DFT) [24–27] deepened our un- tributed to the electrostatic effects of the aqueous solu- derstanding on the transport properties of molecular junc- tion. We also found that subsidiary peaks in histograms tions. In experimental studies, conductance is mostly ob- emerge or disappear due to dynamical effects of the aque- served at room temperature and in solution, and the fluc- ous solution, which is correlated with the C–S stretching tuation of conductance is usually analyzed through his- mode of the BDT molecule. However, the analyses were tograms. Thus theoretical analyses based on conductance focused only on the C–S stretching, and the dynamical ef- histograms considering the fluctuations of the molecular fects induced by other modes have not been investigated junction are expected to provide a better understanding in the previous work [32]. In this paper, we assess the of the electronic transport through a single molecule. A correlations of conductance with Au–S and C–C lengths few such studies have already been reported for single as well as C–S length to understand the effects on con- molecular junctions in vacuum [28–30]. ductance in terms of the dynamical behavior of the BDT Several interesting studies on solution effects have also molecular junction further. been reported. In a mechanically controllable break junction experiment, Taniguchi et al. observed that the ¡ Au¡[Ni(dmit)2] ¡Au molecular junction shows almost II. COMPUTATIONAL METHOD the same conductance but different stability between the cases in a trichlorobenzene solution and in vacuum at Figure 1 shows the schematic of our computational room temperature [31]. Cao et al. studied the calculated model for the molecular junction adopted in our study, conductance histograms of a perylene tetracarboxylic di- where a BDT molecule is sandwiched between Au(100) imides molecule between gold electrodes in aqueous solu- surfaces. Fig. 1(a) and 1(b) show the unit cells of the sys- tion at different temperatures and showed a temperature tems with and without the aqueous solution (1.0 g/cm3, dependence of conductance due to water molecules [30]. 22 H2O), respectively. We abbreviate the systems in the However, much room for discussion is left and further in- aqueous solution and in vacuum as “Aq” and “Vac”. The vestigations are needed in the electronic transport proper- BDT is assumed to be adsorbed at the hollow site of ties affected by solution. Even for the simple BDT molec- Au(100) surface shown in Fig. 1(c) with the distance be- ular junction, the solution effects on conductance have tween electrodes of 9.8 A.˚ The computational model and procedures are identical to those given in our previous study [32]. Here, the computational procedures are de- scribed briefly. The procedure consists of three steps as ¤This paper was presented at 10th International Conference on follows. Atomically Controlled Surfaces, Interfaces and Nanostructures (ACSIN-10), Granada Conference Centre, Spain, 21-25 September, Step I: We perform CPMD calculations using the 2009. CPMD code [33, 34] to obtain a large number of configu- yCorresponding author: [email protected] rations in the Aq/Vac systems. Note that water and BDT ISSN 1348-0391 °c 2010 The Surface Science Society of Japan (http://www.sssj.org/ejssnt) 38 e-Journal of Surface Science and Nanotechnology Volume 8 (2010) (a) Aq (b) Vac 10 0.22 Conductance (G 9 z 0.20 8 0.18 7 0.16 6 0.14 5 (Å) 0.12 z 4 0.10 3 0.08 2 0 ) 0.06 1 0 0.04 0.0 0.5 1.0 1.5 Time (ps) (c) FIG. 2: Calculated time evolution of oxygen positions (left vertical axis, black lines) and conductance (right vertical axis, 1st layer red points) of BDT in the aqueous solution. Here, the z-axis on top bridge is perpendicular to the Au(100) surface, and z = 0 and 9.8 A˚ + + j 2nd layer z correspond to the topmost layers of the Au(100) surfaces. + hollow i (a) (b) 60 60 FIG. 1: (a) Snapshot of the system with the aqueous solu- Aq Vac tion (Aq), (b) the system without the aqueous solution (Vac) 50 50 and (c) the top view of a Au(100) surface together with the 40 40 adsorption sites (hollow, bridge, and on-top). Au, S, C, O, 30 30 Counts Counts and H atoms are depicted with gold, yellow, gray, red, and 20 20 white, respectively, in the snapshots. The z direction is per- 10 10 pendicular to the Au(100) surface. The white squares define 0 0 the scattering region in conductance calculations with ATK. 0.0 0.1 0.2 0.3 0.0 0.1 0.2 0.3 Conductance (G ) Conductance (G ) 0 0 (c) (d) molecules are relaxed while Au atoms are fixed during the 60 60 Aq Vac dynamics. 50 50 Step II: We perform NEGF-DFT calculations using the 40 40 code Atomistix ToolKit (ATK) [35–38] to obtain zero-bias 30 30 Counts Counts conductances of BDT in Aq/Vac for hundreds of configu- 20 20 rations selected from the CPMD calculations in Step I. 10 10 Step III: We make conductance histograms using the 0 0 calculated conductance and analyze the Aq/Vac his- 0.0 0.1 0.2 0.3 0.0 0.1 0.2 0.3 Conductance (G ) Conductance (G ) tograms to characterize the effects of the aqueous solution 0 0 on conductance. Note that in the present study we use the same compu- FIG. 3: Calculated conductance histograms for the cases (a) tational data obtained in our previous work [32] to analyze in the aqueous solution (Aq) and (b) in vacuum (Vac). Fig- histogram in more detail. ure 3(a) is obtained from the calculated conductance shown as red points in Fig 2. The total number of samples is 400 in the Aq histogram (Fig. 3(a)) and 448 in the Vac one ( Fig. 3(b)). Figures 3(c) and 3(d) show conductance histograms obtained III. RESULTS AND DISCUSSION from 300 samples randomly selected from the histograms of Figs. 3(a) and 3(b), respectively. The bin sizes are 0.006 G0 in Figure 2 shows the time evolution of oxygen z-positions all the histograms. The light blue and black lines denote the of water molecules and conductance of BDT in water. Wa- respective Gaussian functions obtained by the fitting and the ter molecules confined in the nano-gapped space between sum of the Gaussians, respectively. the electrodes form three layers with each interlayer dis- tance of about 2.5 A,˚ and the uppermost and lowermost layers appear at about 2.5 A˚ apart from the gold surfaces. lines, we found two peaks in the histogram of Fig. 3(a) In Step II of our method, we picked up the CPMD con- and three in Fig. 3(b) as listed in Table I. The main figurations every 20 time-steps (1.94 fs) and calculated peaks are the 1st peak in the Aq histogram and the 3rd the zero-bias conductances for the selected configurations peak in the Vac, respectively. The downward shift of the using ATK to make conductance histograms. Figures 3(a) main peak in Aq is caused by the electrostatic effect of and (b) show the conductance histograms of the Aq and water molecules [32], i.e.
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