Cooperative molecular dynamics in surface reactions


The controlled imprinting of surfaces with specified patterns is important in the development of nanoscale devices. Previously, such patterns were created using self-assembled physisorbed adsorbate molecules that can be stabilized on the surface by subsequent chemical bonding. Here we show a first step towards use of the bonding within a surface to propagate reactions for patterning, namely the cooperative reaction of adjacent silicon atoms. We exploit the double-bonded silicon dimer pairs present on the surface of Si(100)-2×1 and show that the halogenation of one silicon atom (induced by electrons or heat) results in cooperative halogenation of the neighbouring silicon atom with unit efficiency. The reactants used were two 1-halopentane molecules physisorbed over a pair of silicon atoms. This cooperative pair of halogenation reactions was shown by ab initio calculation to be sequential on a timescale of femtoseconds.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Experiment and theory for the cooperative reaction of a pair of fluoropentane molecules on a silicon surface.
Figure 2: Determining the identity of the reaction product atoms and the characteristics of the cooperative reaction.
Figure 3: Experimental results for the thermal cooperative reactions (360 K) of two pairs of fluoropentane molecules.
Figure 4: Calculated MEP for the cooperative bifluorination.


  1. 1

    Braunschweig, A. B., Huo, F. & Mirkin, C. A. Molecular printing. Nature Chem. 1, 353–358 (2009).

  2. 2

    McNab, I. R. & Polanyi, J. C. Patterned atomic reaction at surfaces. Chem. Rev. 106, 4321–4354 (2006).

  3. 3

    Harikumar, K. R. et al. Dipole-directed assembly of lines of 1,5-dichloropentane on silicon substrates by displacement of surface charge. Nature Nanotech. 3, 222–228 (2008).

  4. 4

    Lopinski, G. P., Wayner, D. D. M. & Wolkow, R. A. Self-directed growth of molecular nanostructures on silicon. Nature 416, 48–51 (2000).

  5. 5

    Maksymovych, P., Sorescu, D. C., Jordan, K. D. & Yates J. T. Collective reactivity of molecular chains self-assembled on a surface. Science 322, 1664–1667 (2008).

  6. 6

    Hass, K. C., Schneider, W. F., Curioni, A. & Andreoni, W. The chemistry of water on alumina surfaces: reaction dynamics from first principles. Science 282, 265–268 (1998).

  7. 7

    Qin, F., Magtoto, N. P. & Kelber, J. A. Moisture-induced instability at the Al2O3/Ni3Al(110) interface: interfacial chemistry. Mater. High Temp. 21, 193–204 (2004).

  8. 8

    Lee, H. S., An, K.-S., Kim, Y. & Choi, C. H., Surface SN2 reaction by H2O on chlorinated Si(100)-2×1 surface. J. Phys. Chem. B 109, 10909–10914 (2005).

  9. 9

    Jarvis, E. A. & Chaka, A. M. Oxidation mechanism and ferryl domain formation on the α-Fe2O3 (0001) surface. Surf. Sci. 601, 1909–1914 (2007).

  10. 10

    Somorjai, G. A. Introduction to Surface Chemistry and Catalysis 500 (Wiley, 1994).

  11. 11

    Dobrin, S. et al. Molecular dynamics of haloalkanes corral formation and surface halogenation at Si(111)-7×7. J. Chem. Phys. 125, 133407 (2006).

  12. 12

    Dobrin, S. et al. Self-assembled molecular corrals on a semiconductor surface. Surf. Sci. 600, L43–L47 (2006).

  13. 13

    Oura, K., Lifshits, V. G., Saranin, A. A., Zotov, A. V. & Katayama, M. Surface Science, an Introduction 181 (Springer, 2003).

  14. 14

    Bronikowski, M. J., Wang, Y., McEllistrem, M. T., Chen, D. & Hamers, R. J. Adsorption and dissociation of disilane on Si(001) studied by STM. Surf. Sci. 298, 50–62 (1993).

  15. 15

    Guo, H., Ji, W., Polanyi, J. C. & Yang, J. (S. Y.). Molecular dynamics of localized reaction, experiment and theory: methyl bromide on Si(111)-7×7. ACS Nano, 2, 699–706 (2008).

  16. 16

    Hahn, J. R. & Ho, W. Orbital specific chemistry: controlling the pathway in single-molecule dissociation. J. Chem. Phys. 122, 244704 (2005).

  17. 17

    Stroscio, J. A. & Celotta, R. J. Controlling the dynamics of a single atom in lateral atom manipulation. Science 306, 242–247 (2004).

  18. 18

    Quaade, U. J., Stokbro, K., Thirstrup, C. & Grey, F. Mechanism of single atom switch on silicon. Surf. Sci. 415, L1037–L1045 (1998).

  19. 19

    Nakayama, K. S. et al. Electronic structure of Si(001)-c(4×2) analyzed by scanning tunneling spectroscopy and ab initio simulations. Phys. Rev. B 73, 035330 (2006).

  20. 20

    Hata, K., Shibata, Y. & Shigekawa, G. Fine electronic structure of the buckled dimers of Si(100) elucidated by atomically resolved scanning tunneling spectroscopy and bias-dependent imaging. Phys. Rev. B 64, 235310 (2001).

  21. 21

    Lastapis, M. et al. Picometer-scale electronic control of molecular dynamics inside a single molecule. Science 308, 1000–1003 (2005).

  22. 22

    Yoder, N. L. et al. Quantifying desorption of saturated hydrocarbons from silicon with quantum calculations and scanning tunneling microscopy. Phys. Rev. Lett. 97, 187601 (2006).

  23. 23

    Henkelman, G., Uberuaga, B. P. & Jónsson, H. A climbing image nudged elastic band method for finding saddle points and minimum energy paths. J. Chem. Phys. 113, 9901 (2000).

  24. 24

    Kresse, G. & Hafner, J. Ab initio molecular dynamics for liquid metals. Phys. Rev. B 47, 558–561 (1993).

  25. 25

    Kresse, G. & Furthmüller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. Rev. B 54, 11169–11186 (1996).

  26. 26

    Dobrin, S., Harikumar, K. R. & Polanyi, J. C. An STM study of the localized atomic reaction of 1,2- and 1,4-dibromobenzene at Si(111)-7×7. Surf. Sci. 561, 11–24 (2004).

  27. 27

    Bartmess, J. E. & Georgiadis, R. M. Empirical methods for determination of ionization gauge relative sensitivities for different gases. Vacuum 33, 149–153 (1983).

  28. 28

    Feenstra, R. M. & Stroscio, J. A. in Scanning Tunneling Microscopy (eds Kaiser, W. J. & Stroscio, J. A.) 96 (Academic Press, 1993).

  29. 29

    Perdew, J. P., Ernzerhof, M. & Burke, K. Rationale for mixing exact exchange with density functional approximations. J. Chem. Phys. 105, 9982 (1996).

  30. 30

    Heyd, J., Scuseria, G. E. & Ernzerhof, M. Hybrid functionals based on a screened Coulomb potential. J. Chem. Phys. 118, 8207–8215 (2003).

  31. 31

    Heyd, J., Scuseria, G. E. & Ernzerhof, M. Erratum: ‘Hybrid functionals based on a screened Coulomb potential’. J. Chem. Phys. 124, 2 19906 (2006).

  32. 32

    Paier, J. et al. Screened hybrid density functional applied to solids. J. Chem. Phys. 124, 154709 (2006).

  33. 33

    Paier, J. et al. Erratum: ‘Screened hybrid density functional applied to solids’. J. Chem. Phys. 125, 249901 (2006).

  34. 34

    Williams, H., Hofer, W. A., Cavar, E., Mikkelsen, A. & Lundgren, E. Density functional theory with hybrid functionals applied to defects in GaAs surfaces: effect of doping. Phys Rev B 78, 205309 (2008).

  35. 35

    Hofer, W. A. & Garcia-Lekue, A. Differential tunneling spectroscopy simulations: imaging surface states. Phys. Rev. B 71, 085401 (2005).

  36. 36

    Palotas, K. & Hofer, W. A., Multiple scattering in a vacuum barrier obtained from real-space wavefunctions. J. Phys. Condens. Matter, 17, 2705–2713 (2005).

  37. 37

    Hofer, W. A., Fisher, A. J., Lopinski, G. P. & Wolkow, R. A. Adsorption of benzene on Si(100)-(2×1): adsorption energies and STM image analysis by ab initio methods. Phys. Rev. B 63, 085314 (2001).

  38. 38

    Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Molec. Graph., 14, 33 (1996).

Download references


J.C.P. thanks the Natural Sciences and Engineering Research Council of Canada, Photonics Research Ontario (Ontario Centre of Excellence), Canadian Institute for Photonic Innovation and Xerox Research Centre Canada for their support of this work. H.L. is supported by the Engineering and Physical Sciences Research Council. W.A.H. thanks the Royal Society of London for support. J.C.P. and W.A.H. thank the Canadian Institute for Advanced Research for support. We thank Amir Zabet for permission to use Supplementary Fig. S3.

Author information

K.R.H., L.L., I.R.McN and J.C.P. were all involved in the concept and design of experiments and analysis of the data. H.L. and W.A.H. performed the DFT calculations and image simulations. All authors participated in interpreting the data and preparation of the manuscript.

Correspondence to John C. Polanyi.

Supplementary information

Supplementary information

Supplementary information (PDF 492 kb)

Supplementary information

Supplementary Movie S1 (MOV 129 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Harikumar, K., Leung, L., McNab, I. et al. Cooperative molecular dynamics in surface reactions. Nature Chem 1, 716–721 (2009).

Download citation

Further reading