TF, DSP and AA acknowledge stimulating discussions with Magnus Paulsson. This work has been supported by the Spanish MICINN (MAT2008-01735, FIS2007-6671- C02-00 and MAT2007-62732, and Consolider-Ingenio 2010 CSD2007-0010), the CAM (“CITECNOMIK” P- ESP-000337-0505), the UPV/EHU (IT-366-07), and the Basque Depto. de Industria and the Diputaci´ on Foral de Guipuzcoa (“ETORTEK”), the EC (STREP “SURF- MOF” NMP4-CT-2006-032109, and FP7 ITN “FUN- MOLS” 212942). TF acknowledges support from the Danish FNU (Grant No. 272-07-0114). the backbone of the molecule and that the it is bound to the electrodes by the thiol groups. junction consists of a single molecule. Indeed, if there were more molecules in the junction contributing to the transport, they would certainly be in different states of strain due to irregularities of the electrodes and, thus, preclude the observation of clear frequency shifts. In conclusion, our results show that combining first- principles transport calculations and high resolution low temperature IETS it is possible to characterize the config- uration of single-molecule junctions. The agreement be- tween experiment and theory is excellent and, in addition to identifying the presence of pentanedithiol molecules, allows us to extract structural information of the molec- ular junction, e.g., its state of strain. Indeed, the IETS signal indicates that the electrons are passing through 5 [27] J. M. Soler, E. Artacho, J. D. Gale, A. Garcia, J. Jun- quera, P. Ordejon, and D. Sanchez-Portal, J. Phys.: Con- dens. Matter 14 , 2745 (2002). [26] M. Paulsson, T. Frederiksen, H. Ueba, N. Lorente, and M. Brandbyge, Phys. Rev. Lett. 100 , 226604 (2008). [25] The electronic structure calculations are based on the SIESTA density functional theory code [27] using the GGA-PBE functional for exchange-correlation, DZP for H, C, and S atoms and SZP for Au, a k -point mesh of 2 × 2 × 2, and 200 Ry cutoff for real-space integrations. The forces on the molecule and the Au adatoms were re- laxed until residual forces were smaller than 0.02 eV/ ˚ A. Intramolecular e-ph couplings were derived from finite differences [23] and the IETS, calculated within the low- est order expansion [18], were averaged over 10 × 10 k - points. [16] B. Ludoph and J.M. van Ruitenbeek, Phys. Rev. B 61 , 2273 (2000). [15] G. Rubio-Bollinger, S.R. Bahn, N. Agrait, K.W. Jacob- sen, and S. Vieira, Phys. Rev. Lett. 87 , 026101 (2001). [14] B. Xu and N. J. Tao, Science 301 , 1221 (2003). [13] G. Rubio-Bollinger, P. Joyez, and N. Agra¨ıt, Phys. Rev. Lett. 93 , 116803 (2004). [12] N. Agrait, A. Yeyati, and J. van Ruitenbeek, Phys. Rep. 377 , 81 (2003). [11] A. Yanson, G. Rubio Bollinger, H. van den Brom, N. Agra¨ıt, and J. van Ruitenbeek, Nature 395 , 783 (1998). [10] C. Untiedt, G. Rubio, S. Vieira, and N. Agra¨ıt, Phys. Rev. B 56 , 2154 (1997). [9] J. Hihath, C. R. Arroyo, G. Rubio-Bollinger, N. Tao, and N. Agra¨ıt, Nano Lett. 8 , 16731678 (2008). [8] M. Kiguchi, O. Tal, S. Wohlthat, F. Pauly, M. Krieger, D. Djukic, J.C. Cuevas, and J.M. van Ruitenbeek, Phys. Rev. Lett. 101 , 046801 (2008). [7] N. Okabayashi, Y. Konda, and T. Komeda, Phys. Rev. Lett. 100 , 217801 (2008). [6] J. G. Kushmerick, J. Lazorcik, C. H. Patterson, R. Shashidhar, D. S. Seferos, and G. C. Bazan, Nano Lett. 4 , 639 (2004). [5] W. Wang, T. Lee, I. Kretzschmar, and M. A. Reed, Nano Lett. 4 , 643 (2004). [4] R. H. M. Smit, Y. Noat, C. Untiedt, N. D. Lang, M. C. van Hemert, and J. M. van Ruitenbeek, Nature 419 , 906 (2002). [3] N. Agra¨ıt, C. Untiedt, G. Rubio-Bollinger, and S. Vieira, Phys. Rev. Lett. 88 , 216803 (2002). [2] B. C. Stipe, M. A. Rezaei, and W. Ho, Science 280 , 1732 (1998). [1] M. Ratner, Nature 435 , 575 (2005). [17] C. Untiedt, G.R. Bollinger, S. Vieira, and N. Agrait, Phys. Rev. B 62 , 9962 (2000). [18] M. Paulsson, T. Frederiksen, and M. Brandbyge, Phys. Rev. B 72 , 201101(R) (2005). [19] L. de la Vega, A. Mart´ın-Rodero, N. Agra¨ıt, and A. Levy Yeyati, Phys. Rev. B 73 , 075428 (2006). [20] T. Frederiksen, M. Brandbyge, N. Lorente, and A.-P. Jauho, Phys. Rev. Lett. 93 , 256601 (2004). [21] M. Paulsson and M. Brandbyge, Phys. Rev. B 76 , 115117 (2007). [22] M. Brandbyge, J. L. Mozos, P. Ordejon, J. Taylor, and K. Stokbro, Phys. Rev. B 65 , 165401 (2002). [23] T. Frederiksen, M. Paulsson, M. Brandbyge, and A.-P. Jauho, Phys. Rev. B 75 , 205413 (2007). [24] M. Paulsson, C. Krag, T. Frederiksen, and M. Brand- byge, Nano Lett. 9 , 117 (2009).