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

Abstract

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.

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

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Cyclooctyne data taken from Ref. [11]

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Notes

  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.

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Acknowledgements

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

Funding

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

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Correspondence to Ralf Tonner.

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The authors declare that they have no conflict of interest.

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

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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). https://doi.org/10.1007/s00214-018-2212-5

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Keywords

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