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Journal of Chemical Physics / Volume 136 / Issue 1 / ARTICLES / Surfaces, Interfaces, and Materials

J. Chem. Phys. 136, 014703 (2012); http://dx.doi.org/10.1063/1.3671455 (12 pages)

Identification of the atomic scale structures of the gold-thiol interfaces of molecular nanowires by inelastic tunneling spectroscopy

Firuz Demir and George Kirczenow

Department of Physics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada

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(Received 8 November 2011; accepted 30 November 2011; published online 5 January 2012)

We examine theoretically the effects of the bonding geometries at the gold-thiol interfaces on the inelastic tunneling spectra of propanedithiolate (PDT) molecules bridging gold electrodes and show that inelastic tunneling spectroscopy combined with theory can be used to determine these bonding geometries experimentally. With the help of density functional theory, we calculate the relaxed geometries and vibrational modes of extended molecules each consisting of one or two PDT molecules connecting two gold nanoclusters. We formulate a perturbative theory of inelastic tunneling through molecules bridging metal contacts in terms of elastic transmission amplitudes, and use this theory to calculate the inelastic tunneling spectra of the gold-PDT-gold extended molecules. We consider PDT molecules with both trans and gauche conformations bound to the gold clusters at top, bridge, and hollow bonding sites. Comparing our results with the experimental data of Hihath et al. [Nano Lett. 8, 1673 (2008)]10.1021/nl080580e, we identify the most frequently realized conformation in the experiment as that of trans molecules top-site bonded to both electrodes. We find the switching from the 42 meV vibrational mode to the 46 meV mode observed in the experiment to be due to the transition of trans molecules from mixed top-bridge to pure top-site bonding geometries. Our results also indicate that gauche molecular conformations and hollow site bonding did not contribute significantly to the experimental inelastic tunneling spectra. For pairs of PDT molecules connecting the gold electrodes in parallel we find total elastic conductances close to twice those of single molecules bridging the contacts with similar bonding conformations and small splittings of the vibrational mode energies for the modes that are the most sensitive to the molecule-electrode bonding geometries.

© 2012 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. THEORY
    1. Calculation of the low energy conformations and vibrational normal modes
    2. Calculations of the elastic conductances in the limit of low bias
    3. Perturbative theory of the IETS of molecular wires
  3. RESULTS
    1. Low energy conformations of the extended molecules
    2. Elastic conductances in the limit of low bias
    3. Inelastic tunneling spectroscopy of the gold-sulfur interface
      1. Top and bridge site bonding of trans PDT molecules
      2. Hollow site bonding
      3. Gauche molecular conformations
      4. Parallel transport through pairs of molecules
  4. CONCLUSIONS

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KEYWORDS and PACS

Keywords

density functional theory, electrical conductivity, electrodes, gold, interface phonons, interface structure, metal clusters, MIM structures, molecular configurations, nanowires, organic compounds, tunnelling spectra

PACS

  • 68.35.Ct

    Interface structure and roughness

  • 68.35.Ja

    Surface and interface dynamics and vibrations

  • 73.40.Rw

    Metal-insulator-metal structures

  • 61.46.Km

    Structure of nanowires and nanorods (long, free or loosely attached, quantum wires and quantum rods, but not gate-isolated embedded quantum wires)

  • 63.22.Gh

    Nanotubes and nanowires

  • 61.46.Bc

    Structure of clusters (e.g., metcars; not fragments of crystals; free or loosely aggregated or loosely attached to a substrate)

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3671455

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
    Y. Hu, Y. Zhu, H. Gao, and H. Guo, Phys. Rev. Lett. 95, 156803 (2005).

    A. Bilić, J. R. Reimers, and N. S. Hush, J. Chem. Phys. 122, 094708 (2005)JCPSA6000122000009094708000001.

    F. Demir and G. Kirczenow, J. Chem. Phys. 134, 121103 (2011)JCPSA6000134000012121103000001.

    X. H. Qiu, G. V. Nazin, and W. Ho, Phys. Rev. Lett. 92, 206102 (2004).

    L. H. Yu, Z. K. Keane, J. W. Ciszek, L. Cheng, M. P. Stewart, J. M. Tour, and D. Natelson, Phys. Rev. Lett. 93, 266802 (2004).

    W. Y. Wang and C. A. Richter, Appl. Phys. Lett. 89, 153105 (2006)APPLAB000089000015153105000001.

    J. J. Parks, A. R. Champagne, G. R. Hutchison, S. Flores-Torres, H. D. Abruna, and D. C. Ralph, Phys. Rev. Lett. 99, 026601 (2007).

    L. H. Yu, C. D. Zangmeister, and J. G. Kushmerick, Phys. Rev. Lett. 98, 206803 (2007).

    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).

    M. Rahimi and A. Troisi, Phys. Rev. B 79, 113413 (2009).

    H. Song, Y. Kim, J. Ku, Y. H. Jang, H. Jeong, and T. Lee, Appl. Phys. Lett. 94, 103110 (2009)APPLAB000094000010103110000001.

    N. Okabayashi, M. Paulsson, H. Ueba, Y. Konda, and T. Komeda, Phys. Rev. Lett. 104, 077801 (2010).

    C. R. Arroyo, T. Frederiksen, G. Rubio-Bollinger, M. Vélez, A. Arnau, D. Sánchez-Portal, and N. Agraät, Phys. Rev. B 81, 075405 (2010).

    H. Song, Y. Kim, H. Jeong, M. A. Reed, and T. Lee, J. Appl. Phys. 109, 102419 (2011)JAPIAU000109000010102419000001.

    E. G. Emberly and G. Kirczenow, Phys. Rev. B 61, 5740 (2000).

    V. May, Phys. Rev. B 66, 245411 (2002).

    A. Troisi, M. A. Ratner, and A. Nitzan, J. Chem. Phys. 118, 6072 (2003)JCPSA6000118000013006072000001.

    M. Čížek, M. Thoss, and W. Domcke, Phys. Rev. B 70, 125406 (2004).

    A. Pecchia, G. Romano, and A. Di Carlo, Phys. Rev. B 75, 035401 (2007).

    N. Sergueev, D. Roubtsov, and H. Guo, Phys. Rev. Lett. 95, 146803 (2005).

    A. Troisi and M. A. Ratner, Phys. Rev. B 72, 033408 (2005).

    A. Troisi and M. A. Ratner, J. Chem. Phys 125, 214709 (2006)JCPSA6000125000021214709000001.

    N. Jean and S. Sanvito, Phys. Rev. B 73, 094433 (2006).

    M. Paulsson, T. Frederiksen, H. Ueba, N. Lorente, and M. Brandbyge, Phys. Rev. Lett. 100, 226604 (2008).

    T. Frederiksen, M. Paulsson, M. Brandbyge, and A. Jauho, Phys. Rev. B 75, 205413 (2007).

    A. Gagliardi, G. C. Solomon, A. Pecchia, T. Frauenheim, A. D. Carlo, N. S. Hush, and J. R. Reimers, Phys. Rev. B 75, 174306 (2007).

    R. Härtle, C. Benesch, and M. Thoss, Phys. Rev. B 77, 205314 (2008).

    M. Kula and Y. J. Luo, J. Chem. Phys. 128, 064705 (2008)JCPSA6000128000006064705000001.

    M. C. Lüffe, J. Koch, and F. von Oppen, Phys. Rev. B 77, 125306 (2008).

    T. Shimazaki and Y. Asai, Phys. Rev. B 77, 115428 (2008).

    J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 78, 1396 (1997).

    D. M. Cardamone and G. Kirczenow, Phys. Rev. B 77, 165403 (2008).

    E. G. Emberly and G. Kirczenow, Phys. Rev. Lett. 87, 269701 (2001).

    E. G. Emberly and G. Kirczenow, Phys. Rev. B 64, 235412 (2001).

    J. G. Kushmerick, D. B. Holt, J. C. Yang, J. Naciri, M. H. Moore, and R. Shashidhar, Phys. Rev. Lett. 89, 086802 (2002).

    G. Kirczenow, P. G. Piva, and R. A. Wolkow, Phys. Rev. B 72, 245306 (2005).

    P. G. Piva, R. A. Wolkow, and G. Kirczenow, Phys. Rev. Lett. 101, 106801 (2008).

    G. Kirczenow, P. G. Piva, and R. A. Wolkow, Phys. Rev. B 80, 035309 (2009).

    J. Buker and G. Kirczenow, Phys. Rev. B 78, 125107 (2008).

    H. Dalgleish and G. Kirczenow, Phys. Rev. B 72, 155429 (2005).

    G. Kirczenow, Phys. Rev. B 75, 045428 (2007).

    L. de la Vega, A. Martín-Rodero, N. Agraït, and A. L. Yeyati, Phys. Rev. B 73, 075428 (2006).

    E. Castaño and G. Kirczenow, Phys. Rev. B 41, 5055 (1990).

    S. N. Yaliraki and M. A. Ratner, J. Chem. Phys. 109, 5036 (1998)JCPSA6000109000012005036000001.

    M. Magoga and C. Joachim, Phys. Rev. B 59, 16011 (1999).

    N. D. Lang and Ph. Avouris, Phys. Rev. B 62, 7325 (2000).

    R. Liu, S.-H. Ke, H. U. Baranger, and W. Yang, J. Chem. Phys. 122, 044703 (2005)JCPSA6000122000004044703000001.


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