Computational analysis of the competitive bonding and reactivity pattern of a bifunctional cyclooctyne on Si(001)


The chemoselective bonding of a bifunctional organic molecule on a semiconductor surface is analyzed with density functional theory (DFT). Periodic energy decomposition analysis is used to reveal the bonding characteristics of different adsorption modes and transition states for 5-ethoxymethyl-5-methylcyclooctyne on Si(001). This system has previously been experimentally proven to be a prototype model system for inorganic–organic hybrid interfaces. The molecule thereby poses challenges for a theoretical description of conformational flexibility and competitive adsorption behavior of the two functional groups. We find that adsorption via the strained triple bond is preferred over the ether group, thus confirming previous experiments. Bonding analysis in combination with static DFT as well as ab initio molecular dynamics methods thereby reveals the determining factors for this chemoselectivity and shows that the functional groups barely influence each other in their surface adsorption.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Part b reproduced with permission from Ref. [10]. Copyright John Wiley & Sons, Inc

Fig. 5
Fig. 6
Fig. 7
Fig. 8

Cyclooctyne data taken from Ref. [11]

Fig. 9
Fig. 10


  1. 1.

    Minimum mode following algorithms, such as the Dimer method, are based on the premise that there is only one low-frequency vibration, i.e., the one that is going to invert its curvature. Climbing-image NEB, on the contrary, only works if the frequencies of the imaginary vibration and the lowest real vibration are large enough so that the computation is unsusceptible to numerical noise. Both methods failed to convert to first-order saddle points in this system.


  1. 1.

    Wolkow RA (1999) Annu Rev Phys Chem 50:413

    CAS  Article  Google Scholar 

  2. 2.

    Teplyakov AV, Bent SF (2013) J Vac Sci Technol A 31:050810

    Article  Google Scholar 

  3. 3.

    Rosenow P, Jakob P, Tonner R (2016) J Phys Chem Lett 7:1422

    CAS  Article  Google Scholar 

  4. 4.

    Hossain MZ, Yamashita Y, Mukai K, Yoshinobu J (2004) Chem Phys Lett 388:27

    CAS  Article  Google Scholar 

  5. 5.

    Reutzel M, Münster N, Lipponer MA, Länger C, Höfer U, Koert U, Dürr M (2016) J Phys Chem C 120:26284

    CAS  Article  Google Scholar 

  6. 6.

    Mette G, Dürr M, Bartholomäus R, Koert U, Höfer U (2013) Chem Phys Lett 556:70

    CAS  Article  Google Scholar 

  7. 7.

    Mette G, Reutzel M, Bartholomäus R, Laref S, Tonner R, Dürr M, Koert U, Höfer U (2014) ChemPhysChem 15:3725

    CAS  Article  Google Scholar 

  8. 8.

    Reutzel M, Mette G, Stromberger P, Koert U, Dürr M, Höfer U (2015) J Phys Chem C 119:6018

    CAS  Article  Google Scholar 

  9. 9.

    Reutzel M, Lipponer M, Dürr M, Höfer U (2015) J Phys Chem Lett 6:3971

    CAS  Article  Google Scholar 

  10. 10.

    Pecher J, Schober C, Tonner R (2017) Chem Eur J 23:5459

    CAS  Article  Google Scholar 

  11. 11.

    Pecher L, Schmidt S, Tonner R (2017) J Phys Chem C 121:26840

    CAS  Article  Google Scholar 

  12. 12.

    Pecher L, Laref S, Raupach M, Tonner R (2017) Angew Chem Int Ed 56:15150

    CAS  Article  Google Scholar 

  13. 13.

    Kresse G, Hafner J (1993) Phys Rev B 47:558

    CAS  Article  Google Scholar 

  14. 14.

    Kresse G, Hafner J (1994) Phys Rev B 49:14251

    CAS  Article  Google Scholar 

  15. 15.

    Kresse G, Furthmüller J (1996) Phys Rev B 54:11169

    CAS  Article  Google Scholar 

  16. 16.

    Kresse G, Furthmüller J (1996) Comput Mater Sci 6:15

    CAS  Article  Google Scholar 

  17. 17.

    Blöchl PE (1994) Phys Rev B 50:17953

    Article  Google Scholar 

  18. 18.

    Kresse G, Joubert D (1999) Phys Rev B 59:1758

    CAS  Article  Google Scholar 

  19. 19.

    Perdew JP, Burke K, Enzerhof M (1996) Phys Rev Lett 77:3865

    CAS  Article  Google Scholar 

  20. 20.

    Perdew JP, Burke K, Enzerhof M (1997) Phys Rev Lett 78:1396

    CAS  Article  Google Scholar 

  21. 21.

    Grimme S, Antony J, Ehrlich S, Krieg H (2010) J Chem Phys 132:154104

    Article  Google Scholar 

  22. 22.

    Grimme S, Ehrlich S, Goerigk L (2010) J Comput Chem 32:1456

    Article  Google Scholar 

  23. 23.

    Boyd DRJ (1955) J Chem Phys 23:922

    CAS  Article  Google Scholar 

  24. 24.

    Jónsson H, Mills G, Jacobsen KW (1998) In: Berne BJ, Ciccotti G, Coker DF (eds) Classical and quantum dynamics in condensed phase simulations. World Scientific, Singapore, p 385

    Google Scholar 

  25. 25.

    Henkelman G, Uberuaga BP, Jónsson H (2000) J Chem Phys 113:9901

    CAS  Article  Google Scholar 

  26. 26.

    Henkelman G, Jónsson H (1999) J Chem Phys 111(15):7010

    CAS  Article  Google Scholar 

  27. 27.

    Raupach M, Tonner R (2015) J Chem Phys 142:194105

    Article  Google Scholar 

  28. 28.

    te Velde G, Baerends EJ (1991) Phys Rev B 44:7788

    Article  Google Scholar 

  29. 29.

    BAND (2016) SCM, theoretical chemistry, Vrije Universiteit, Amsterdam, The Netherlands. Accessed 20 Feb 2018

  30. 30.

    Verlet L (1967) Phys Rev 159:98

    CAS  Article  Google Scholar 

  31. 31.

    Swope WC, Andersen HC, Berens PH, Wilson KR (1982) J Chem Phys 76:637

    CAS  Article  Google Scholar 

  32. 32.

    Nosé S (1984) Mol Phys 52:255

    Article  Google Scholar 

  33. 33.

    Nosé S (1984) J Chem Phys 81:511

    Article  Google Scholar 

  34. 34.

    Random decimal fraction generator. Accessed 20 Feb 2018

  35. 35.

    Pecher J, Tonner R (2017) ChemPhysChem 18:34

    CAS  Article  Google Scholar 

  36. 36.

    Pecher J, Mette G, Dürr M, Tonner R (2017) ChemPhysChem 18:357

    CAS  Article  Google Scholar 

  37. 37.

    Weigend F, Ahlrichs R (2005) Phys Chem Chem Phys 7:3297

    CAS  Article  Google Scholar 

  38. 38.

    Riplinger C, Neese F (2013) J Chem Phys 138:034106

    Article  Google Scholar 

  39. 39.

    Riplinger C, Sandhoefer B, Hansen A, Neese F (2013) J Chem Phys 139:134101

    Article  Google Scholar 

  40. 40.

    Kim S-W, Lee J-H, Kim H-J, Cho J-H (2013) Chem Phys Lett 557:159

    CAS  Article  Google Scholar 

  41. 41.

    Kuze N, Kuroki N, Takeuchi H, Egawa T, Konaka S (1993) J Mol Struct 301:81

    CAS  Article  Google Scholar 

  42. 42.

    Ess DH, Jones GO, Houk KN (2008) Org Lett 10:1633

    CAS  Article  Google Scholar 

  43. 43.

    Schoenebeck F, Ess DH, Jones GO, Houk KN (2009) J Am Chem Soc 131:8121

    CAS  Article  Google Scholar 

  44. 44.

    Chenoweth K, Chenoweth D, Goddard WA III (2009) Org Biomol Chem 7:5255

    CAS  Article  Google Scholar 

  45. 45.

    Pigge FC (2016) Curr Org Chem 20:1902

    CAS  Article  Google Scholar 

Download references


We thank HRZ Marburg, LOEWE-CSC Frankfurt and HLRS Stuttgart for providing computational resources and Jan-Niclas Luy (Marburg) for preliminary work.


We thank the Deutsche Forschungsgemeinschaft (DFG) for funding via SFB 1083

Author information



Corresponding author

Correspondence to Ralf Tonner.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Published as part of the special collection of articles “First European Symposium on Chemical Bonding”.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (pdf 2757 KB)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Pecher, L., Tonner, R. Computational analysis of the competitive bonding and reactivity pattern of a bifunctional cyclooctyne on Si(001). Theor Chem Acc 137, 48 (2018).

Download citation


  • Energy decomposition analysis
  • Surface chemistry
  • Semiconductors
  • ab initio molecular dynamics
  • Density functional theory