Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding

James Lawrence; Gabriele C. Sosso; Luka Đorđević; Harry Pinfold; Davide Bonifazi; Giovanni Costantini

doi:10.1038/s41467-020-15898-2

Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding

James Lawrence, Gabriele C. Sosso^*, Luka Đorđević, Harry Pinfold, Davide Bonifazi, Giovanni Costantini

^*Corresponding author for this work

Chemistry

Research output: Contribution to journal › Article › peer-review

25 Citations (Scopus)

Abstract

Scanning tunnelling microscopy (STM) is commonly used to identify on-surface molecular self-assembled structures. However, its limited ability to reveal only the overall shape of molecules and their relative positions is not always enough to fully solve a supramolecular structure. Here, we analyse the assembly of a brominated polycyclic aromatic molecule on Au(111) and demonstrate that standard STM measurements cannot conclusively establish the nature of the intermolecular interactions. By performing high-resolution STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, determining that halogen bonding governs the assemblies. This is supported by density functional theory calculations that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron density topology analysis that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramolecular structures, and we predict its increasing use in molecular nanoscience at surfaces.

Original language	English
Article number	2103
Journal	Nature Communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-15898-2
Publication status	Published - 1 Dec 2020

Bibliographical note

Funding Information:
G.C. acknowledges financial support from the University of Warwick and from the EU through the ERC Grant “VISUAL-MS” (Project ID: 308115). D.B. gratefully acknowledges the EU through the MSCA-RISE project “INFUSION” (Project ID: 734834), the ERC Grant “COLORLANDS” (Project ID: 280183), and Cardiff University. We thank Dr. Benson Kariuki, Deborah Romito and Nicolas Biot for the X-ray analysis, Dr. Robert L. Jenkins for the help with NMR experiments, Thomas Williams for his support with MALDI-HRMS analysis, and the Analytical Service at the School of Chemistry, Cardiff University. G.C.S. is grateful to the Centre for Scientific Computing at the University of Warwick for providing computational resources. G.C.S. also acknowledges the use of Athena at HPC Midlands+ (funded by the EPSRC on grant EP/P020232/) in this research, as part of the HPC Midlands+ consortium.

Publisher Copyright:
© 2020, The Author(s).

ASJC Scopus subject areas

General Chemistry
General Biochemistry,Genetics and Molecular Biology
General Physics and Astronomy

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Cite this

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abstract = "Scanning tunnelling microscopy (STM) is commonly used to identify on-surface molecular self-assembled structures. However, its limited ability to reveal only the overall shape of molecules and their relative positions is not always enough to fully solve a supramolecular structure. Here, we analyse the assembly of a brominated polycyclic aromatic molecule on Au(111) and demonstrate that standard STM measurements cannot conclusively establish the nature of the intermolecular interactions. By performing high-resolution STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, determining that halogen bonding governs the assemblies. This is supported by density functional theory calculations that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron density topology analysis that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramolecular structures, and we predict its increasing use in molecular nanoscience at surfaces.",

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note = "Funding Information: G.C. acknowledges financial support from the University of Warwick and from the EU through the ERC Grant “VISUAL-MS” (Project ID: 308115). D.B. gratefully acknowledges the EU through the MSCA-RISE project “INFUSION” (Project ID: 734834), the ERC Grant “COLORLANDS” (Project ID: 280183), and Cardiff University. We thank Dr. Benson Kariuki, Deborah Romito and Nicolas Biot for the X-ray analysis, Dr. Robert L. Jenkins for the help with NMR experiments, Thomas Williams for his support with MALDI-HRMS analysis, and the Analytical Service at the School of Chemistry, Cardiff University. G.C.S. is grateful to the Centre for Scientific Computing at the University of Warwick for providing computational resources. G.C.S. also acknowledges the use of Athena at HPC Midlands+ (funded by the EPSRC on grant EP/P020232/) in this research, as part of the HPC Midlands+ consortium. Publisher Copyright: {\textcopyright} 2020, The Author(s).",

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Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding

Abstract

Bibliographical note

ASJC Scopus subject areas

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