Submolecular Resolution Imaging of Molecules by Atomic Force Microscopy: The Influence of the Electrostatic Force

Lit, Joost van der; Cicco, Francesca Di; Hapala, Prokop; Jelı́nek, Pavel; Swart, Ingmar

doi:10.1103/physrevlett.116.096102

Cited by 56 publications

(63 citation statements)

References 43 publications

(55 reference statements)

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“…In systems where this is a problem, considering several experimental configurations of the same molecule, as done here, makes identification significantly easier. More generally, we are looking at including multiple channels of information for a single configuration by using an image descriptor incorporating tip-dependent electrostatic information available via other tip terminations 51,24,45 . This could be also be extended to incorporate simultaneous fitting to Kelvin Probe Force Microscopy data 52,53,54,55 , further improving the uniqueness of predictions.…”

Section: Discussionmentioning

confidence: 99%

“…Instead, the characteristic topology of interatomic potentials (saddle ridges between nearby atoms, vertexes between those ridges, contrast inversion) can be clearly determined from AFM data as a fingerprint of typical chemical groups or bonding configurations. The electrostatic force has a rather small contribution to vertical force in contact, but often considerably distorts the image laterally 24,45 .…”

Section: Introductionmentioning

confidence: 99%

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Automated structure discovery in atomic force microscopy

et al. 2020

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Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar aromatic molecules, due to difficulties with interpretation of highly distorted AFM images originating from non-planar molecules. Here we develop a deep learning infrastructure that matches a set of AFM images with a unique descriptor characterizing the molecular configuration, allowing us to predict the molecular structure directly. We apply this methodology to resolve several distinct adsorption configurations of 1S-camphor on Cu(111) based on low-temperature AFM measurements. This approach will open the door to apply high-resolution AFM to a large variety of systems for which routine atomic and chemical structural resolution on the level of individual objects/molecules would be a major breakthrough.CO-AFM now offers an unprecedented window into molecular structure on surfaces -aside from the detailed resolution of the results of molecular assembly 11,12 , it is possible to study bond order 13 , charge distributions 14,15 and the individual steps of on-surface chemical reactions 16,17,18,19 .As yet, most CO-AFM studies have been focused on planar molecular systems, where the experimental image requires almost no interpretation 10,5,20 . Even where understanding is not immediately obvious, such as due to controversies over the nature of observed bonds 21 , efficient models have been developed 22,12,23,24,25 that explain the contrast mechanism in terms of the tip-surface interaction and CO lateral flexibility. However, the further the systems studied are from two-dimensional molecules containing only hydrogen and carbon, the more complex and time consuming (if not impossible) the interpretation process becomes 17,26,27,28,29 . While recent measurements using rigid O-terminated copper tips makes interpreting images of flat systems even easier 30,31 , the rigidity also means even less atoms can be characterized when moving to 3D systems. In recent years, CO-AFM has moved towards measuring truly unknown structures 29,32,33,34 , where it has overcome many of the limitations of techniques such as nuclear magnetic resonance and mass spectrometry. It is clear that this trend is going to continue, and potentially even accelerate, in particular for innovative studies, e.g. in life sciences or biochemistry 6,7 , demonstrated manifestly in the first CO-AFM images of DNA 35 . Reliable interpretation of such data becomes a vast exploration through all possible molecules, configurations and imaging parameters to find agreement. This is impractical in anything beyond very simple systems, severely limiting the ultimate power of the technique.In this work, we couple a systematic software approach with detailed experimental CO-AFM imaging to understand and predict AFM images for molecules of any size, configuration or orientation without prior knowledge of the system being studied. We use the late...

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Automated structure discovery in atomic force microscopy

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“…Lennard-Jones parameters are the same that were used in recent literature 59 . The atomic positions were taken from the DFT-calculated geometries.…”

Section: Supplementary Note 2: Comparison Of Afm Data To Simulated Afmentioning

confidence: 99%

Synthesis and characterization of triangulene

et al. 2017

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* These authors contributed equally to this workTriangulene, the smallest triplet ground state polybenzenoid (also known as Clar's hydrocarbon), has been an enigmatic molecule ever since its existence was first hypothesized isomers (2, also denoted as dihydrotriangulenes) as precursor molecules. Compound 2 was deposited on Cu(111), NaCl(100), and Xe(111) surfaces to generate triangulene (1) by means of atomic manipulation. STM/AFM is an ideal combination to study on-surface synthesis ranging from individual molecules 9, 10 to graphene nanoribbons 11,12 . The chemical structure of reactants and products can be resolved by means of AFM with functionalized tips 13 . Even molecules too elusive to be studied by other means 14,15 can be stabilized by using an ultrathin insulating film as a decoupling 2 layer. A decoupling layer also facilitates studying the frontier molecular orbitals of the free molecule by means of STM and scanning tunnelling spectroscopy (STS) 16 .Figure 2 presents STM and AFM images of four different molecular species of compound 2 adsorbed on NaCl. As expected, different isomers of dihydrotriangulene are observed. This observation can be discussed by a comparison of Fig. 2e and Fig. 2f, showing the non-equivalent isomers 2a and 2b which we found on the surface, respectively. Because the former isomer is prochiral with respect to adsorption, we also observed its surface enantiomer (see Supplementary Fig. 5). Note that 2a is about three times more abundant than the highly symmetric 2b, although two Clar sextets can be drawn for both species. This difference can be rationalized by the resonance energy of its aromatic Remarkably, the ketone 3 in Fig. 2g represents an oxidized structure of 2 that was already reported by Clar and Stewart 1. A comparison of STM and AFM data reveals that in the STM images a tiny sharp kink arises at the position of a single CH 2 group. In contrast, a ketone group leads to a fainter bulge in STM images (Figs. 2c, d) and a lower contrast of the hexagon involved. The central carbon of the three adjacent CH 2 group in 3 adopts the expected tetrahedral bond angle for sp 3 carbon leading to sharp ridges in both STM and AFM mode (Figs. 2c, g) because of strong tilting of the CO molecule at the tip apex.We dehydrogenated promising candidates (2a and 2b molecules) to obtain triangulene by means of atomic manipulation 14,15,19 . To this end, we first positioned the tip above a molecule. Then, we opened the feedback loop and retracted the tip by 0.5 to 0.7 nm to limit the tunnelling current to a few picoamperes. Finally, we increased the voltage to values ranging from 3.5 to 4.1 V for several seconds. In many cases, this procedure also resulted in a lateral displacement of the molecule. When a subsequent STM image indicated a change in the appearance of the molecule, we recorded AFM 3 images to obtain its structure. Using this procedure, we did not observe any changes in the molecular structure other than the removal of single hydrogens from a CH 2 groups throughout our experiment...

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“…From DFT calculations the lateral stretching in the graphene network induced by the substitutional dopant is only about 1% in compression to the nearest-neighbor distance. Thus these distortions are imaging artifacts and are most likely due to the electrostatic interaction between the dopant atom, which has a partial positive charge, and the dipole moment of the tip [42,43,47,48]. A Bader charge analysis shows that the N atom has a charge of 1.27e, where 73% of that charge is extracted from the 3 neighboring C atoms donating 0.3e each to the N atom.…”

Section: Referencementioning

confidence: 99%