Characterization of single-molecule pentanedithiol junctions by inelastic electron tunneling spectroscopy and first-principles calculations $^{1}$Departamento de F´ısica de la Materia Condensada, Universidad Aut´ onoma de Madrid, 28049 Madrid, Spain $^{2}$Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, Donostia-San Sebasti´ an, Spain $^{3}$Instituto Madrile˜ no de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia),Campus Cantoblanco, 28049 Madrid, Spain $^{4}$Centro de F´ısica de Materiales CFM-MPC, Centro Mixto CSIC-UPV, Apdo. 1072, Donostia-San Sebasti´ an, Spain $^{5}$Depto. de F´ısica de Materiales UPV/EHU, Facultad de Qu´ımica, Apdo. 1072, Donostia-San Sebasti´ an, Spain (Dated: October 31, 2018) We study pentanedithiol molecular junctions formed by means of the break-junction technique with a scanning tunneling microscope at low temperatures. Using inelastic electron tunneling spec- troscopy and first-principles calculations, the response of the junction to elastic deformation is examined. We show that this procedure makes a detailed characterization of the molecular junction possible. In particular, our results indicate that tunneling takes place through just a single molecule. PACS numbers: 73.63.Rt, 73.40.-c, 31.10.+z, 63.22.-m, 68.37.Ef One of the most challenging aspects to reach ultimate miniaturization of electronic devices is the characteriza- tion of charge transport through individual molecules in contact with metallic electrodes [1]. However, from an ex- perimental point of view, it is very difficult to ensure that the junction consists of just a single molecule, and—even when such junctions are realized—it is hard to know the microscopic arrangement, e.g., how the molecule is bound to the electrodes or the pathway followed by the electrons in the molecule. A powerful tool for understanding elec- tron transport in nanoscopic devices is inelastic electron tunneling spectroscopy (IETS) [2–4]. This technique is based on the variations in the conductance caused by the excitation of vibrations by the traversing electrons. Some of the characteristic molecular vibrations have been identified in junctions comprising a relatively large num- ber of molecules in self-assembled monolayers of alka- nedithiol and other thiolated molecules [5–7]. In junc- tions of short molecules, like water or benzene, weakly bound to the electrodes, inelastic spectroscopy has been used to explore the molecular conformations in a single- molecule junction [8]. Recently, Hihath et al. [9] mea- sured IETS spectra of junctions with short alkanedithi- ols (propanedithiol) and showed that the average of spec- tra taken on the same conductance plateau were sensi- tive to changes in the configuration of the junction as a whole and were associated with a plastic deformation of the junction. However, the observed changes permit- ted neither to ensure the presence of a single molecule at the junction nor to discern its bonding configuration and state of strain, something that requires a detailed com- parison between individual spectra and first-principles calculations of the inelastic electronic transport process. Here, we report the evolution of IETS in single pen- tanedithiol molecules covalently bound to gold electrodes as the molecular junction is deformed elastically , i.e., with no change in molecular configuration. The measure- After rupture of a clean gold contact at low tempera- tures the current at a constant tip-substrate bias voltage decreases exponentially with a high apparent tunneling barrier of 3–4 eV, which is characteristic of vacuum tun- neling [13]. In contrast, the presence of the molecules on the substrate gives rise to plateaus in the conduc- tance, as shown in the inset of Fig. 1(a). The lowest conductance plateau before rupture is associated with a Single-molecule junctions are obtained by repeatedly forming and breaking the contact between an STM tip and a gold substrate covered with pentanedithiol molecules. The molecules were deposited on the sub- strate by immersion in a 1 mM solution of pentanedithiol molecules in toluene for 12 hours followed by washing and sonication in pure toluene, and drying in a stream of he- lium gas. Immediately after that, the sample was trans- ferred to the low temperature insert in helium gas atmo- sphere. Before immersion the substrate was treated with a piranha solution and flame annealed. The tip consisted of a freshly cut 99.99% purity gold wire. These deposition conditions are typical for the formation of self-assembled monolayers (SAM), and consequently we would expect a coverage close to a monolayer. During the process of con- tact formation and breaking the conductance of the junc- tion is measured by recording the current at a fixed bias voltage, of typically 25 mV, following a procedure simi- lar to the one used for the study of Au atomic contacts [10], single-atom chains [11, 12] and single-propanedithiol junctions [9]. ments are performed using a scanning tunneling micro- scope (STM) at low temperatures (4.2 K) and compared to first-principles calculations, which permits a unique identification of the main peaks in the vibrational spec- tra, as well as their variation with strain. This further allows us to conclude unambiguously that electrons tun- nel through just a single molecule suspended between the electrodes. arXiv:1001.2392v1 [cond-mat.mes-hall] 14 Jan 2010 Carlos R. Arroyo, 1 Thomas Frederiksen, 2 Gabino Rubio-Bollinger, 1 Marisela V´ elez, 1, 3 Andr´ es Arnau, 2, 4, 5 Daniel S´ anchez-Portal, 4,5 and Nicol´ as Agra¨ıt 1, 3