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Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy.

Jarvis SP - Int J Mol Sci (2015)

Bottom Line: In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed.Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure.In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds.

View Article: PubMed Central - PubMed

Affiliation: School of Physics & Astronomy, University of Nottingham, Nottingham NG7 2RD, UK. Samuel.Jarvis@nottingham.ac.uk.

ABSTRACT
A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions.

No MeSH data available.


Related in: MedlinePlus

Imaging internal bond structure with CO-mediated non-contact atomic force microscopy (NC-AFM). (A) Internal bond structure of perylene-tetracarboxylic-dianhydride (PTCDA) resolved with scanning tunnelling hydrogen microscopy (STHM) using a trapped hydrogen molecule in the scanning tunnelling microscope (STM) tunnel junction [14,16]; (B) First images of internal bond structure resolved with NC-AFM achieved via pick-up of a single CO molecule onto the tip apex (from [24], reprinted with permission from AAAS); (C) NC-AFM images showing molecular structure identification of cephalandole A adsorbed on NaCl (2 ML)/Cu(111). Red and blue coloured atoms correspond to oxygen and nitrogen, respectively (reprinted by permission from Macmillan Publishers Ltd.: Nature Chemistry [27], copyright 2010); (D) NC-AFM reveals bistable configurations of dibenzo[a,h]thianthrene (DBTH) adopting a “butterfly” arrangement. Yellow coloured atoms correspond to sulphur (reprinted with permission from [28], copyright 2012 by the American Physical Society); (E) Pauling bond order discrimination in hexabenzocoronene with NC-AFM (from [29], reprinted with permission from AAAS); (F) Inelastic tunnelling spectroscopy (IETS) image revealing chemical bonds with a CO-terminated tip (from [30], reprinted with permission from AAAS); (G) NC-AFM images of the different steps of a chemical reaction with submolecular resolution (from [31], reprinted with permission from AAAS); (H) STM (left) and NC-AFM (right) imaging of the structure and adsorption site of naphthalene tetracarboxylic diimide (NTCDI) on the Si(111)- surface at 77 K [32,33].
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ijms-16-19936-f001: Imaging internal bond structure with CO-mediated non-contact atomic force microscopy (NC-AFM). (A) Internal bond structure of perylene-tetracarboxylic-dianhydride (PTCDA) resolved with scanning tunnelling hydrogen microscopy (STHM) using a trapped hydrogen molecule in the scanning tunnelling microscope (STM) tunnel junction [14,16]; (B) First images of internal bond structure resolved with NC-AFM achieved via pick-up of a single CO molecule onto the tip apex (from [24], reprinted with permission from AAAS); (C) NC-AFM images showing molecular structure identification of cephalandole A adsorbed on NaCl (2 ML)/Cu(111). Red and blue coloured atoms correspond to oxygen and nitrogen, respectively (reprinted by permission from Macmillan Publishers Ltd.: Nature Chemistry [27], copyright 2010); (D) NC-AFM reveals bistable configurations of dibenzo[a,h]thianthrene (DBTH) adopting a “butterfly” arrangement. Yellow coloured atoms correspond to sulphur (reprinted with permission from [28], copyright 2012 by the American Physical Society); (E) Pauling bond order discrimination in hexabenzocoronene with NC-AFM (from [29], reprinted with permission from AAAS); (F) Inelastic tunnelling spectroscopy (IETS) image revealing chemical bonds with a CO-terminated tip (from [30], reprinted with permission from AAAS); (G) NC-AFM images of the different steps of a chemical reaction with submolecular resolution (from [31], reprinted with permission from AAAS); (H) STM (left) and NC-AFM (right) imaging of the structure and adsorption site of naphthalene tetracarboxylic diimide (NTCDI) on the Si(111)- surface at 77 K [32,33].

Mentions: The internal bond structure of a molecule (see reference [15] for an overview of submolecular resolution with various SPM techniques) was first observed by Temirov et al. [14] for perylene-tetracarboxylic-dianhydride (PTCDA) and tetracene, who introduced molecular hydrogen (H2) into an STM chamber during scanning. Due to the low temperature of the scan head (∼10 K), the H2 would spontaneously condense and trap itself within the tunnelling junction, significantly enhancing the resolution of the observed image (see Figure 1A). In this so-called scanning tunnelling hydrogen microscopy (STHM) mode of imaging, the position of the trapped H2 molecule is determined by the degree of Pauli repulsion felt within the small (<1 nm) tip-sample junction [16], causing the trapped molecule to effectively act as a transducer, modulating the STM signal via changes in the degree of Pauli repulsion. As will be described in more detail below, the effect of Pauli repulsion, which is largest when the tip is directly above the atoms and bonds of the molecule, is essential for achieving internal bond resolution. In addition to a H2 molecule, D2, CO, Xe and CH4 [17] have also all been shown to produce very similar results, demonstrating the general applicability of the STHM method.


Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy.

Jarvis SP - Int J Mol Sci (2015)

Imaging internal bond structure with CO-mediated non-contact atomic force microscopy (NC-AFM). (A) Internal bond structure of perylene-tetracarboxylic-dianhydride (PTCDA) resolved with scanning tunnelling hydrogen microscopy (STHM) using a trapped hydrogen molecule in the scanning tunnelling microscope (STM) tunnel junction [14,16]; (B) First images of internal bond structure resolved with NC-AFM achieved via pick-up of a single CO molecule onto the tip apex (from [24], reprinted with permission from AAAS); (C) NC-AFM images showing molecular structure identification of cephalandole A adsorbed on NaCl (2 ML)/Cu(111). Red and blue coloured atoms correspond to oxygen and nitrogen, respectively (reprinted by permission from Macmillan Publishers Ltd.: Nature Chemistry [27], copyright 2010); (D) NC-AFM reveals bistable configurations of dibenzo[a,h]thianthrene (DBTH) adopting a “butterfly” arrangement. Yellow coloured atoms correspond to sulphur (reprinted with permission from [28], copyright 2012 by the American Physical Society); (E) Pauling bond order discrimination in hexabenzocoronene with NC-AFM (from [29], reprinted with permission from AAAS); (F) Inelastic tunnelling spectroscopy (IETS) image revealing chemical bonds with a CO-terminated tip (from [30], reprinted with permission from AAAS); (G) NC-AFM images of the different steps of a chemical reaction with submolecular resolution (from [31], reprinted with permission from AAAS); (H) STM (left) and NC-AFM (right) imaging of the structure and adsorption site of naphthalene tetracarboxylic diimide (NTCDI) on the Si(111)- surface at 77 K [32,33].
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4581333&req=5

ijms-16-19936-f001: Imaging internal bond structure with CO-mediated non-contact atomic force microscopy (NC-AFM). (A) Internal bond structure of perylene-tetracarboxylic-dianhydride (PTCDA) resolved with scanning tunnelling hydrogen microscopy (STHM) using a trapped hydrogen molecule in the scanning tunnelling microscope (STM) tunnel junction [14,16]; (B) First images of internal bond structure resolved with NC-AFM achieved via pick-up of a single CO molecule onto the tip apex (from [24], reprinted with permission from AAAS); (C) NC-AFM images showing molecular structure identification of cephalandole A adsorbed on NaCl (2 ML)/Cu(111). Red and blue coloured atoms correspond to oxygen and nitrogen, respectively (reprinted by permission from Macmillan Publishers Ltd.: Nature Chemistry [27], copyright 2010); (D) NC-AFM reveals bistable configurations of dibenzo[a,h]thianthrene (DBTH) adopting a “butterfly” arrangement. Yellow coloured atoms correspond to sulphur (reprinted with permission from [28], copyright 2012 by the American Physical Society); (E) Pauling bond order discrimination in hexabenzocoronene with NC-AFM (from [29], reprinted with permission from AAAS); (F) Inelastic tunnelling spectroscopy (IETS) image revealing chemical bonds with a CO-terminated tip (from [30], reprinted with permission from AAAS); (G) NC-AFM images of the different steps of a chemical reaction with submolecular resolution (from [31], reprinted with permission from AAAS); (H) STM (left) and NC-AFM (right) imaging of the structure and adsorption site of naphthalene tetracarboxylic diimide (NTCDI) on the Si(111)- surface at 77 K [32,33].
Mentions: The internal bond structure of a molecule (see reference [15] for an overview of submolecular resolution with various SPM techniques) was first observed by Temirov et al. [14] for perylene-tetracarboxylic-dianhydride (PTCDA) and tetracene, who introduced molecular hydrogen (H2) into an STM chamber during scanning. Due to the low temperature of the scan head (∼10 K), the H2 would spontaneously condense and trap itself within the tunnelling junction, significantly enhancing the resolution of the observed image (see Figure 1A). In this so-called scanning tunnelling hydrogen microscopy (STHM) mode of imaging, the position of the trapped H2 molecule is determined by the degree of Pauli repulsion felt within the small (<1 nm) tip-sample junction [16], causing the trapped molecule to effectively act as a transducer, modulating the STM signal via changes in the degree of Pauli repulsion. As will be described in more detail below, the effect of Pauli repulsion, which is largest when the tip is directly above the atoms and bonds of the molecule, is essential for achieving internal bond resolution. In addition to a H2 molecule, D2, CO, Xe and CH4 [17] have also all been shown to produce very similar results, demonstrating the general applicability of the STHM method.

Bottom Line: In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed.Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure.In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds.

View Article: PubMed Central - PubMed

Affiliation: School of Physics & Astronomy, University of Nottingham, Nottingham NG7 2RD, UK. Samuel.Jarvis@nottingham.ac.uk.

ABSTRACT
A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions.

No MeSH data available.


Related in: MedlinePlus