1
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Chahib O, Yin Y, Liu JC, Li C, Glatzel T, Ding F, Yuan Q, Meyer E, Pawlak R. Probing charge redistribution at the interface of self-assembled cyclo-P 5 pentamers on Ag(111). Nat Commun 2024; 15:6542. [PMID: 39095352 PMCID: PMC11297031 DOI: 10.1038/s41467-024-50862-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
Phosphorus pentamers (cyclo-P5) are unstable in nature but can be synthesized at the Ag(111) surface. Unlike monolayer black phosphorous, little is known about their electronic properties when in contact with metal electrodes, although this is crucial for future applications. Here, we characterize the atomic structure of cyclo-P5 assembled on Ag(111) using atomic force microscopy with functionalized tips and density functional theory. Combining force and tunneling spectroscopy, we find that a strong charge transfer induces an inward dipole moment at the cyclo-P5/Ag interface as well as the formation of an interface state. We probe the image potential states by field-effect resonant tunneling and quantify the increase of the local change of work function of 0.46 eV at the cyclo-P5 assembly. Our experimental approach suggest that the cyclo-P5/Ag interface has the characteristic ingredients of a p-type semiconductor-metal Schottky junction with potential applications in field-effect transistors, diodes, or solar cells.
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Affiliation(s)
- Outhmane Chahib
- Department of Physics, University of Basel, Basel, Switzerland
| | - Yuling Yin
- Institute of Technology for Carbon Neutrality, Shenzhen Institute of Advanced Technology, Shenzhen, People's Republic of China
- Faculty of Materials Science and Energy Engineering, Shenzhen University of Advanced Technology, Shenzhen, People's Republic of China
| | - Jung-Ching Liu
- Department of Physics, University of Basel, Basel, Switzerland
| | - Chao Li
- Department of Physics, University of Basel, Basel, Switzerland
| | - Thilo Glatzel
- Department of Physics, University of Basel, Basel, Switzerland
| | - Feng Ding
- Institute of Technology for Carbon Neutrality, Shenzhen Institute of Advanced Technology, Shenzhen, People's Republic of China
- Faculty of Materials Science and Energy Engineering, Shenzhen University of Advanced Technology, Shenzhen, People's Republic of China
| | - Qinghong Yuan
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai, People's Republic of China
| | - Ernst Meyer
- Department of Physics, University of Basel, Basel, Switzerland.
| | - Rémy Pawlak
- Department of Physics, University of Basel, Basel, Switzerland.
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2
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Kinikar A, Wang XY, Di Giovannantonio M, Urgel JI, Liu P, Eimre K, Pignedoli CA, Stolz S, Bommert M, Mishra S, Sun Q, Widmer R, Qiu Z, Narita A, Müllen K, Ruffieux P, Fasel R. Sterically Selective [3 + 3] Cycloaromatization in the On-Surface Synthesis of Nanographenes. ACS NANOSCIENCE AU 2024; 4:128-135. [PMID: 38644965 PMCID: PMC11027121 DOI: 10.1021/acsnanoscienceau.3c00062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 04/23/2024]
Abstract
Surface-catalyzed reactions have been used to synthesize carbon nanomaterials with atomically predefined structures. The recent discovery of a gold surface-catalyzed [3 + 3] cycloaromatization of isopropyl substituted arenes has enabled the on-surface synthesis of arylene-phenylene copolymers, where the surface activates the isopropyl substituents to form phenylene rings by intermolecular coupling. However, the resulting polymers suffered from undesired cross-linking when more than two molecules reacted at a single site. Here we show that such cross-links can be prevented through steric protection by attaching the isopropyl groups to larger arene cores. Upon thermal activation of isopropyl-substituted 8,9-dioxa-8a-borabenzo[fg]tetracene on Au(111), cycloaromatization is observed to occur exclusively between the two molecules. The cycloaromatization intermediate formed by the covalent linking of two molecules is prevented from reacting with further molecules by the wide benzotetracene core, resulting in highly selective one-to-one coupling. Our findings extend the versatility of the [3 + 3] cycloaromatization of isopropyl substituents and point toward steric protection as a powerful concept for suppressing competing reaction pathways in on-surface synthesis.
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Affiliation(s)
- Amogh Kinikar
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
| | - Xiao-Ye Wang
- Max Planck
Institute for Polymer Research, 55128 Mainz, Germany
- State
Key
Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Marco Di Giovannantonio
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
| | - José I. Urgel
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
| | - Pengcai Liu
- State
Key
Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Kristjan Eimre
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
| | - Carlo A. Pignedoli
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
| | - Samuel Stolz
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Condensed Matter Physics, Station 3, EPFL, 1015 Lausanne, Switzerland
| | - Max Bommert
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
| | - Shantanu Mishra
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
| | - Qiang Sun
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
| | - Roland Widmer
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
| | - Zijie Qiu
- Max Planck
Institute for Polymer Research, 55128 Mainz, Germany
| | - Akimitsu Narita
- Max Planck
Institute for Polymer Research, 55128 Mainz, Germany
| | - Klaus Müllen
- Max Planck
Institute for Polymer Research, 55128 Mainz, Germany
- Department
of Chemistry, Johannes Gutenberg-Universität
Mainz, 55128 Mainz, Germany
| | - Pascal Ruffieux
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
| | - Roman Fasel
- Empa, Swiss
Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
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3
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Brill L, Brandhoff J, Gruenewald M, Calcinelli F, Hofmann OT, Forker R, Fritz T. Partial restoration of aromaticity of pentacene-5,7,12,14-tetrone on Cu(111). NANOSCALE 2024; 16:2654-2661. [PMID: 38230573 PMCID: PMC10832359 DOI: 10.1039/d3nr04848a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024]
Abstract
The π-conjugation of organic molecules can be strongly influenced when functional groups are added to a molecule, for example when pentacene is converted into pentacene-5,7,12,14-tetrone (P4O) by substitution of four H-atoms with four O-atoms, leading to four CO double bonds. In fact, although free P4O resembles the parent hydrocarbon pentacene structurally at a first glance, its electronic properties differ drastically and can be more accurately described by three benzene units connected via four carbonyl groups. If P4O is deposited onto Cu(111), the electronic interaction across the interface has previously been reported to fully restore the π-conjugation through a weakening of the CO double bonds and a redistribution of electrons, both of which have been explained with the model of surface-induced aromatic stabilization. Here, we observe for the case of P4O on Cu(111) that the molecule does not exhibit full π-conjugation upon interaction with the surface, likely because of the special electronic nature of the hybridized P4O on Cu(111). Our results are derived from CO-functionalized noncontact atomic force microscopy measurements in combination with dispersion-corrected density functional theory calculations yielding bond lengths and molecular geometries. To characterize the aromaticity, we apply the harmonic oscillator model of aromaticity.
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Affiliation(s)
- Lorenz Brill
- Friedrich Schiller University Jena, Institute of Solid State Physics, Helmholtzweg 5, 07743 Jena, Germany.
| | - Jonas Brandhoff
- Friedrich Schiller University Jena, Institute of Solid State Physics, Helmholtzweg 5, 07743 Jena, Germany.
| | - Marco Gruenewald
- Friedrich Schiller University Jena, Institute of Solid State Physics, Helmholtzweg 5, 07743 Jena, Germany.
| | - Fabio Calcinelli
- Graz University of Technology, Institute of Solid State Physics, NAWI Graz, Petersgasse 16/II, 8010 Graz, Austria.
| | - Oliver T Hofmann
- Graz University of Technology, Institute of Solid State Physics, NAWI Graz, Petersgasse 16/II, 8010 Graz, Austria.
| | - Roman Forker
- Friedrich Schiller University Jena, Institute of Solid State Physics, Helmholtzweg 5, 07743 Jena, Germany.
| | - Torsten Fritz
- Friedrich Schiller University Jena, Institute of Solid State Physics, Helmholtzweg 5, 07743 Jena, Germany.
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4
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Dou Z, Qian J, Li Y, Lin R, Wang J, Cheng P, Xu Z. Reducing molecular simulation time for AFM images based on super-resolution methods. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2021; 12:775-785. [PMID: 34386314 PMCID: PMC8329368 DOI: 10.3762/bjnano.12.61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Atomic force microscopy (AFM) has been an important tool for nanoscale imaging and characterization with atomic and subatomic resolution. Theoretical investigations are getting highly important for the interpretation of AFM images. Researchers have used molecular simulation to examine the AFM imaging mechanism. With a recent flurry of researches applying machine learning to AFM, AFM images obtained from molecular simulation have also been used as training data. However, the simulation is incredibly time consuming. In this paper, we apply super-resolution methods, including compressed sensing and deep learning methods, to reconstruct simulated images and to reduce simulation time. Several molecular simulation energy maps under different conditions are presented to demonstrate the performance of reconstruction algorithms. Through the analysis of reconstructed results, we find that both presented algorithms could complete the reconstruction with good quality and greatly reduce simulation time. Moreover, the super-resolution methods can be used to speed up the generation of training data and vary simulation resolution for AFM machine learning.
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Affiliation(s)
- Zhipeng Dou
- School of Physics, Beihang University, Beijing 100083, China
| | - Jianqiang Qian
- School of Physics, Beihang University, Beijing 100083, China
| | - Yingzi Li
- School of Physics, Beihang University, Beijing 100083, China
| | - Rui Lin
- School of Physics, Beihang University, Beijing 100083, China
| | - Jianhai Wang
- School of Physics, Beihang University, Beijing 100083, China
| | - Peng Cheng
- School of Physics, Beihang University, Beijing 100083, China
| | - Zeyu Xu
- School of Physics, Beihang University, Beijing 100083, China
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5
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Xu J, Zhu X, Tan S, Zhang Y, Li B, Tian Y, Shan H, Cui X, Zhao A, Dong Z, Yang J, Luo Y, Wang B, Hou JG. Determining structural and chemical heterogeneities of surface species at the single-bond limit. Science 2021; 371:818-822. [DOI: 10.1126/science.abd1827] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 12/07/2020] [Accepted: 01/14/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Jiayu Xu
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiang Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shijing Tan
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yao Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Li
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yunzhe Tian
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huan Shan
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xuefeng Cui
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Aidi Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhenchao Dong
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jinlong Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bing Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - J. G. Hou
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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6
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Liebig A, Hapala P, Weymouth AJ, Giessibl FJ. Quantifying the evolution of atomic interaction of a complex surface with a functionalized atomic force microscopy tip. Sci Rep 2020; 10:14104. [PMID: 32839507 PMCID: PMC7445177 DOI: 10.1038/s41598-020-71077-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/07/2020] [Indexed: 11/09/2022] Open
Abstract
Terminating the tip of an atomic force microscope with a CO molecule allows data to be acquired with a well-known and inert apex. Previous studies have shown conflicting results regarding the electrostatic interaction, indicating in some cases that the negative charge at the apex of the CO dominates, whereas in other cases the positive charge at the end of the metal tip dominates. To clarify this, we investigated [Formula: see text](111). [Formula: see text] is an ionic crystal and the (111) surface does not possess charge inversion symmetry. Far from the surface, the interaction is dominated by electrostatics via the negative charge at the apex. Closer to the surface, Pauli repulsion and CO bending dominate, which leads to an unexpected appearance of the complex 3-atom unit cell. We compare simulated data in which the electrostatics are modeled by point particles versus a charge density calculated by DFT. We also compare modeling Pauli repulsion via individual Lennard-Jones potentials versus a total charge density overlap. In doing so, we determine forcefield parameters useful for future investigations of biochemical processes.
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Affiliation(s)
- Alexander Liebig
- Institute of Experimental and Applied Physics, University of Regensburg, 93040, Regensburg, Germany.
| | - Prokop Hapala
- Department of Applied Physics, Aalto University, Aalto, Finland.,Institute of Physics, Czech Academy of Sciences, Cukrovarnická 10, 162 00, Prague 6, Czech Republic
| | - Alfred J Weymouth
- Institute of Experimental and Applied Physics, University of Regensburg, 93040, Regensburg, Germany
| | - Franz J Giessibl
- Institute of Experimental and Applied Physics, University of Regensburg, 93040, Regensburg, Germany.
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7
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Weymouth AJ, Riegel E, Gretz O, Giessibl FJ. Strumming a Single Chemical Bond. PHYSICAL REVIEW LETTERS 2020; 124:196101. [PMID: 32469591 DOI: 10.1103/physrevlett.124.196101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/02/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
Atomic force microscopy and scanning tunneling microscopy can image the internal structure of molecules adsorbed on surfaces. One reliable method is to terminate the tip with a nonreactive adsorbate, often a single CO molecule, and to collect data at a close distance where Pauli repulsion plays a strong role. Lateral force microscopy, in which the tip oscillates laterally, probes similar interactions but has the unique ability to pull the CO over a chemical bond, load it as a torsional spring, and release it as it snaps over with each oscillation cycle. This produces measurable energy dissipation. The dissipation has a characteristic decay length in the vertical direction of 4 pm, which is 13 times smaller than the decay length in typical STM or AFM experiments.
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Affiliation(s)
| | | | - Oliver Gretz
- University of Regensburg, 93053 Regensburg, Germany
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8
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Alldritt B, Hapala P, Oinonen N, Urtev F, Krejci O, Federici Canova F, Kannala J, Schulz F, Liljeroth P, Foster AS. Automated structure discovery in atomic force microscopy. SCIENCE ADVANCES 2020; 6:eaay6913. [PMID: 32133405 PMCID: PMC7043916 DOI: 10.1126/sciadv.aay6913] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/04/2019] [Indexed: 05/12/2023]
Abstract
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 nonplanar 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 applying 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.
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Affiliation(s)
- Benjamin Alldritt
- Department of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Prokop Hapala
- Department of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Niko Oinonen
- Department of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Fedor Urtev
- Department of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
- Department of Computer Science, Aalto University, 00076 Aalto, Espoo, Finland
| | - Ondrej Krejci
- Department of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Filippo Federici Canova
- Department of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
- Nanolayers Research Computing Ltd., London, UK
| | - Juho Kannala
- Department of Computer Science, Aalto University, 00076 Aalto, Espoo, Finland
| | - Fabian Schulz
- Department of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Peter Liljeroth
- Department of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
- Corresponding author. (P.L.); (A.S.F.)
| | - Adam S. Foster
- Department of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
- Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128, Germany
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Corresponding author. (P.L.); (A.S.F.)
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9
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Quantitative determination of atomic buckling of silicene by atomic force microscopy. Proc Natl Acad Sci U S A 2019; 117:228-237. [PMID: 31871150 DOI: 10.1073/pnas.1913489117] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The atomic buckling in 2D "Xenes" (such as silicene) fosters a plethora of exotic electronic properties such as a quantum spin Hall effect and could be engineered by external strain. Quantifying the buckling magnitude with subangstrom precision is, however, challenging, since epitaxially grown 2D layers exhibit complex restructurings coexisting on the surface. Here, we characterize using low-temperature (5 K) atomic force microscopy (AFM) with CO-terminated tips assisted by density functional theory (DFT) the structure and local symmetry of each prototypical silicene phase on Ag(111) as well as extended defects. Using force spectroscopy, we directly quantify the atomic buckling of these phases within 0.1-Å precision, obtaining corrugations in the 0.8- to 1.1-Å range. The derived band structures further confirm the absence of Dirac cones in any of the silicene phases due to the strong Ag-Si hybridization. Our method paves the way for future atomic-scale analysis of the interplay between structural and electronic properties in other emerging 2D Xenes.
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10
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Scheuerer P, Patera LL, Simbürger F, Queck F, Swart I, Schuler B, Gross L, Moll N, Repp J. Charge-Induced Structural Changes in a Single Molecule Investigated by Atomic Force Microscopy. PHYSICAL REVIEW LETTERS 2019; 123:066001. [PMID: 31491133 DOI: 10.1103/physrevlett.123.066001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/12/2019] [Indexed: 06/10/2023]
Abstract
Intramolecular structural relaxations occurring upon electron transfer are crucial in determining the rate of redox reactions. Here, we demonstrate that subangstrom structural changes occurring upon single-electron charging can be quantified by means of atomically resolved atomic force microscopy (AFM) for the case of single copper(II)phthalocyanine (CuPc) molecules deposited on an ultrathin NaCl film. Imaging the molecule in distinct charge states (neutral and anionic) reveals characteristic differences in the AFM contrast. In comparison to density functional theory simulations these changes in contrast can be directly related to relaxations of the molecule's geometric structure upon charging. The dominant contribution arises from a nonhomogeneous vertical relaxation of the molecule, caused by a change in the electrostatic interaction with the surface.
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Affiliation(s)
- Philipp Scheuerer
- Institute of Experimental and Applied Physics, University of Regensburg, 93053 Regensburg, Germany
| | - Laerte L Patera
- Institute of Experimental and Applied Physics, University of Regensburg, 93053 Regensburg, Germany
| | - Felix Simbürger
- Institute of Experimental and Applied Physics, University of Regensburg, 93053 Regensburg, Germany
| | - Fabian Queck
- Institute of Experimental and Applied Physics, University of Regensburg, 93053 Regensburg, Germany
| | - Ingmar Swart
- Institute of Experimental and Applied Physics, University of Regensburg, 93053 Regensburg, Germany
- Debye Institute for Nanomaterials Science, Utrecht University, PO Box 80 000, 3508 TA Utrecht, Netherlands
| | - Bruno Schuler
- IBM Research-Zurich, 8803 Rüschlikon, Switzerland
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Leo Gross
- IBM Research-Zurich, 8803 Rüschlikon, Switzerland
| | - Nikolaj Moll
- IBM Research-Zurich, 8803 Rüschlikon, Switzerland
| | - Jascha Repp
- Institute of Experimental and Applied Physics, University of Regensburg, 93053 Regensburg, Germany
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11
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Ellner M, Pou P, Pérez R. Molecular Identification, Bond Order Discrimination, and Apparent Intermolecular Features in Atomic Force Microscopy Studied with a Charge Density Based Method. ACS NANO 2019; 13:786-795. [PMID: 30605593 DOI: 10.1021/acsnano.8b08209] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We introduce an efficient method to simulate high-resolution atomic force microscopy (HR-AFM) images with CO probes. Our model explicitly takes into account the charge densities of the sample and the probe for the calculation of the short-range (SR) interaction and retains ab initio accuracy with only two parameters, that are essentially universal, independent of the number of chemical species and the complexity of the bonding topology. The application to molecular images shows a strong dependence on the stoichiometry and bonding configuration that precludes the chemical identification of individual atoms based on local force-distance curves. However, we have identified features in the 2D images and 3D force maps that reflect the highly anisotropic spatial decay of the molecular charge density and provide a way toward molecular identification. The model treats SR and electrostatics interactions on an equal footing and correctly pinpoints the Pauli repulsion as the underlying interaction responsible for the bond order discrimination in C60. Finally, we settle the controversy regarding the origin of the intermolecular features, discarding the effect of the charge redistribution associated with the H bonds, and linking them with the overlap of the wave functions of the atoms that constitute the bond. This overlap creates saddle regions in the potential energy landscape that are sensed by the probe.
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Affiliation(s)
- Michael Ellner
- Departamento de Física Teórica de la Materia Condensada , Universidad Autónoma de Madrid , E-28049 Madrid , Spain
| | - Pablo Pou
- Departamento de Física Teórica de la Materia Condensada , Universidad Autónoma de Madrid , E-28049 Madrid , Spain
- Condensed Matter Physics Center (IFIMAC) , Universidad Autónoma de Madrid , E-28049 Madrid , Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada , Universidad Autónoma de Madrid , E-28049 Madrid , Spain
- Condensed Matter Physics Center (IFIMAC) , Universidad Autónoma de Madrid , E-28049 Madrid , Spain
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12
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Mönig H. Copper-oxide tip functionalization for submolecular atomic force microscopy. Chem Commun (Camb) 2018; 54:9874-9888. [PMID: 30124700 DOI: 10.1039/c8cc05332d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Establishing submolecular imaging in real-space by non-contact atomic force microscopy (NC-AFM) has been a major breakthrough in the field of organic surface chemistry. The key for the drastically increased resolution in these experiments is to functionalize a metallic tip apex with an inert probe particle. However, due to their weak bonding at the metal apex, these probe particles show a pronounced dynamic lateral deflection in the measurements. This constitutes a major limitation of this approach as it involves image distortions, an overestimation of bond lengths, and even artificial bond-like contrast features where actually no bonds exist. In this contribution, recent progress by using an alternative approach by copper-oxide tip functionalization is reviewed. Copper-oxide tips (CuOx tips) consist of a bulk copper apex, terminated by a covalently connected single oxygen atom, which chemically passivates the tip. Such CuOx tips can be identified by contrast analysis at specific surface sites and allow for submolecular resolution. A comparative analysis of data recorded with flexible tips allows a detailed discussion of the contrast mechanisms and related artificial effects. It is concluded with an assessment of limitations, future challenges and opportunities in such experiments.
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Affiliation(s)
- Harry Mönig
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany.
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13
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Schulz F, Ritala J, Krejčí O, Seitsonen AP, Foster AS, Liljeroth P. Elemental Identification by Combining Atomic Force Microscopy and Kelvin Probe Force Microscopy. ACS NANO 2018; 12:5274-5283. [PMID: 29800512 PMCID: PMC6097802 DOI: 10.1021/acsnano.7b08997] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/25/2018] [Indexed: 05/23/2023]
Abstract
There are currently no experimental techniques that combine atomic-resolution imaging with elemental sensitivity and chemical fingerprinting on single molecules. The advent of using molecular-modified tips in noncontact atomic force microscopy (nc-AFM) has made it possible to image (planar) molecules with atomic resolution. However, the mechanisms responsible for elemental contrast with passivated tips are not fully understood. Here, we investigate elemental contrast by carrying out both nc-AFM and Kelvin probe force microscopy (KPFM) experiments on epitaxial monolayer hexagonal boron nitride (hBN) on Ir(111). The hBN overlayer is inert, and the in-plane bonds connecting nearest-neighbor boron and nitrogen atoms possess strong covalent character and a bond length of only ∼1.45 Å. Nevertheless, constant-height maps of both the frequency shift Δ f and the local contact potential difference exhibit striking sublattice asymmetry. We match the different atomic sites with the observed contrast by comparison with nc-AFM image simulations based on the density functional theory optimized hBN/Ir(111) geometry, which yields detailed information on the origin of the atomic-scale contrast.
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Affiliation(s)
- Fabian Schulz
- Department
of Applied Physics, Aalto University School
of Science, P.O. Box 15100, FI-00076 Aalto, Finland
| | - Juha Ritala
- COMP
Center of Excellence, Department of Applied Physics, Aalto University School of Science,
P.O. Box 11100, FI-00076 Aalto, Finland
| | - Ondrej Krejčí
- COMP
Center of Excellence, Department of Applied Physics, Aalto University School of Science,
P.O. Box 11100, FI-00076 Aalto, Finland
| | - Ari Paavo Seitsonen
- Département
de Chimie, École Normale Supérieure, 24 rue Lhomond, F-75005 Paris, France
| | - Adam S. Foster
- COMP
Center of Excellence, Department of Applied Physics, Aalto University School of Science,
P.O. Box 11100, FI-00076 Aalto, Finland
- WPI
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Graduate
School Materials Science in Mainz, Staudinger Weg 9, D-55128 Mainz, Germany
| | - Peter Liljeroth
- Department
of Applied Physics, Aalto University School
of Science, P.O. Box 15100, FI-00076 Aalto, Finland
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14
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Affiliation(s)
- Ingmar Swart
- Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
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15
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Kawai S, Nakatsuka S, Hatakeyama T, Pawlak R, Meier T, Tracey J, Meyer E, Foster AS. Multiple heteroatom substitution to graphene nanoribbon. SCIENCE ADVANCES 2018; 4:eaar7181. [PMID: 29662955 PMCID: PMC5898832 DOI: 10.1126/sciadv.aar7181] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/23/2018] [Indexed: 05/20/2023]
Abstract
Substituting heteroatoms into nanostructured graphene elements, such as graphene nanoribbons, offers the possibility for atomic engineering of electronic properties. To characterize these substitutions, functionalized atomic force microscopy (AFM)-a tool to directly resolve chemical structures-is one of the most promising tools, yet the chemical analysis of heteroatoms has been rarely performed. We synthesized multiple heteroatom-substituted graphene nanoribbons and showed that AFM can directly resolve elemental differences and can be correlated to the van der Waals radii, as well as the modulated local electron density caused by the substitution. This elemental-sensitive measurement takes an important step in the analysis of functionalized two-dimensional carbon materials.
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Affiliation(s)
- Shigeki Kawai
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Corresponding author. (S.K.); (T.H.); (A.S.F.)
| | - Soichiro Nakatsuka
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo, Japan
| | - Takuji Hatakeyama
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo, Japan
- Corresponding author. (S.K.); (T.H.); (A.S.F.)
| | - Rémy Pawlak
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - Tobias Meier
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - John Tracey
- Department of Applied Physics, Aalto University, Espoo, Finland
| | - Ernst Meyer
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - Adam S. Foster
- Department of Applied Physics, Aalto University, Espoo, Finland
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
- Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany
- Corresponding author. (S.K.); (T.H.); (A.S.F.)
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16
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Strain-induced skeletal rearrangement of a polycyclic aromatic hydrocarbon on a copper surface. Nat Commun 2017; 8:16089. [PMID: 28726802 PMCID: PMC5524995 DOI: 10.1038/ncomms16089] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/23/2017] [Indexed: 11/17/2022] Open
Abstract
Controlling the structural deformation of organic molecules can drive unique reactions that cannot be induced only by thermal, optical or electrochemical procedures. However, in conventional organic synthesis, including mechanochemical procedures, it is difficult to control skeletal rearrangement in polycyclic aromatic hydrocarbons (PAHs). Here, we demonstrate a reaction scheme for the skeletal rearrangement of PAHs on a metal surface using high-resolution noncontact atomic force microscopy. By a combination of organic synthesis and on-surface cyclodehydrogenation, we produce a well-designed PAH—diazuleno[1,2,3-cd:1′,2′,3′-fg]pyrene—adsorbed flatly onto Cu(001), in which two azuleno moieties are highly strained by their mutual proximity. This local strain drives the rearrangement of one of the azuleno moieties into a fulvaleno moiety, which has never been reported so far. Our proposed thermally driven, strain-induced synthesis on surfaces will pave the way for the production of a new class of nanocarbon materials that conventional synthetic techniques cannot attain. Mechanical strains can induce chemical transformations otherwise inaccessible by conventional stimuli. Here, the authors show the unusual strain-induced transformation of a polycyclic aromatic hydrocarbon on a metal surface by means of atomic force microscopy.
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17
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Labidi H, Koleini M, Huff T, Salomons M, Cloutier M, Pitters J, Wolkow RA. Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface. Nat Commun 2017; 8:14222. [PMID: 28194036 PMCID: PMC5316802 DOI: 10.1038/ncomms14222] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 12/08/2016] [Indexed: 01/05/2023] Open
Abstract
The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed. Whether and under what circumstances chemical bonds could be imaged via force microscopy is a controversial topic. Here authors develop a particular combination of model surface, imaging procedures and simulation approach and discuss possible indications of chemical contrast in imaging data they obtain.
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Affiliation(s)
- Hatem Labidi
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada T6G 2J1.,National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada T6G 2M9
| | - Mohammad Koleini
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada T6G 2J1.,National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada T6G 2M9
| | - Taleana Huff
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada T6G 2J1
| | - Mark Salomons
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada T6G 2M9
| | - Martin Cloutier
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada T6G 2M9
| | - Jason Pitters
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada T6G 2M9
| | - Robert A Wolkow
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada T6G 2J1.,National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada T6G 2M9
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18
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Xin X, Gan LY, Van Hove MA, Ren X, Wang H, Guo CS, Zhao Y. Exploring Molecules beyond CO as Tip Functionalizations in High-Resolution Noncontact Atomic Force Microscopy: A First Principles Approach. ACS OMEGA 2016; 1:1004-1009. [PMID: 31457178 PMCID: PMC6640759 DOI: 10.1021/acsomega.6b00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/09/2016] [Indexed: 06/10/2023]
Abstract
Atomic resolution of molecules has been achieved using noncontact atomic force microscopy (AFM) with the key step to functionalize the tip apex by attaching suitable molecules so as to achieve high spatial resolution through a sharper tip. A few molecular terminations have been explored theoretically and experimentally, and they exhibit various imaging behaviors. Here, we explore the influence of the structures and chemical compositions of various molecular candidates as tips on the contrast of AFM images by a first principles approach. Our results reveal that the two end atoms of a linear molecule terminating nearest the sample dominate the imaging behaviors, for example, atomic resolution, sharpness, distortion, and so forth, whereas the symmetry of the termination plays an important role in the distortion of AFM images. These findings suggest that new tip terminations can be engineered by decoupling the three end atoms responsible for imaging behaviors from the tip structure behind them, which is attached to the macro tip apex.
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Affiliation(s)
- Xiaojun Xin
- Key
Laboratory of Advanced Technology of Materials (Ministry of Education),
Superconductivity and New Energy R&D Center and School of Physical Science and
Technology, Southwest Jiaotong University, Chengdu 610031, Sichuan, China
| | - Li-Yong Gan
- Key
Laboratory of Advanced Technology of Materials (Ministry of Education),
Superconductivity and New Energy R&D Center and School of Physical Science and
Technology, Southwest Jiaotong University, Chengdu 610031, Sichuan, China
| | - Michel A. Van Hove
- Institute
of Computational and Theoretical Studies and Department of Physics, Hong Kong Baptist University, Kowloon, Hong Kong Special Administrative
Region
| | - Xinguo Ren
- Key Laboratory of Quantum Information and Synergistic Innovation Center of
Quantum Information & Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Hongyan Wang
- Key
Laboratory of Advanced Technology of Materials (Ministry of Education),
Superconductivity and New Energy R&D Center and School of Physical Science and
Technology, Southwest Jiaotong University, Chengdu 610031, Sichuan, China
| | - Chun-Sheng Guo
- Key
Laboratory of Advanced Technology of Materials (Ministry of Education),
Superconductivity and New Energy R&D Center and School of Physical Science and
Technology, Southwest Jiaotong University, Chengdu 610031, Sichuan, China
| | - Yong Zhao
- Key
Laboratory of Advanced Technology of Materials (Ministry of Education),
Superconductivity and New Energy R&D Center and School of Physical Science and
Technology, Southwest Jiaotong University, Chengdu 610031, Sichuan, China
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19
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Yankowitz M, Watanabe K, Taniguchi T, San-Jose P, LeRoy BJ. Pressure-induced commensurate stacking of graphene on boron nitride. Nat Commun 2016; 7:13168. [PMID: 27762272 PMCID: PMC5462001 DOI: 10.1038/ncomms13168] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/08/2016] [Indexed: 11/21/2022] Open
Abstract
Combining atomically-thin van der Waals materials into heterostructures provides a powerful path towards the creation of designer electronic devices. The interaction strength between neighbouring layers, most easily controlled through their interlayer separation, can have significant influence on the electronic properties of these composite materials. Here, we demonstrate unprecedented control over interlayer interactions by locally modifying the interlayer separation between graphene and boron nitride, which we achieve by applying pressure with a scanning tunnelling microscopy tip. For the special case of aligned or nearly-aligned graphene on boron nitride, the graphene lattice can stretch and compress locally to compensate for the slight lattice mismatch between the two materials. We find that modifying the interlayer separation directly tunes the lattice strain and induces commensurate stacking underneath the tip. Our results motivate future studies tailoring the electronic properties of van der Waals heterostructures by controlling the interlayer separation of the entire device using hydrostatic pressure. Van der Waals heterostructures enable fabrication of materials with engineered functionalities. Here, the authors demonstrate precise control over the interaction between layers by application of pressure with a scanning tunnelling microscopy tip.
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Affiliation(s)
- Matthew Yankowitz
- Physics Department, University of Arizona, Tucson, Arizona 85721, USA
| | - K Watanabe
- National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan
| | - T Taniguchi
- National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan
| | - Pablo San-Jose
- Instituto de Ciencia de Materiales de Madrid (ICMM-CSIC), Cantoblanco, 28049 Madrid, Spain
| | - Brian J LeRoy
- Physics Department, University of Arizona, Tucson, Arizona 85721, USA
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20
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Kawai S, Sadeghi A, Okamoto T, Mitsui C, Pawlak R, Meier T, Takeya J, Goedecker S, Meyer E. Organometallic Bonding in an Ullmann-Type On-Surface Chemical Reaction Studied by High-Resolution Atomic Force Microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5303-5311. [PMID: 27531252 DOI: 10.1002/smll.201601216] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/13/2016] [Indexed: 05/25/2023]
Abstract
The on-surface Ullmann-type chemical reaction synthesizes polymers by linking carbons of adjacent molecules on solid surfaces. Although an organometallic compound is recently identified as the reaction intermediate, little is known about the detailed structure of the bonded organometallic species and its influence on the molecule and the reaction. Herein atomic force microscopy at low temperature is used to study the reaction with 3,9-diiododinaphtho[2,3-b:2',3'-d]thiophene (I-DNT-VW), which is polymerized on Ag(111) in vacuum. Thermally sublimated I-DNT-VW picks up a Ag surface atom, forming a CAg bond at one end after removing an iodine. The CAg bond is usually short-lived, and a CAgC organometallic bond immediately forms with an adjacent molecule. The existence of the bonded Ag atoms strongly affects the bending angle and adsorption height of the molecular unit. Density functional theory calculations reveal the bending mechanism, which reveals that charge from the terminus of the molecule is transferred via the Ag atom into the organometallic bond and strengths the local adsorption to the substrate. Such deformations vanish when the Ag atoms are removed by annealing and CC bonds are established.
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Affiliation(s)
- Shigeki Kawai
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1, Namiki, Tsukuba, Ibaraki, 305-0044, Japan.
- PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama, 332-0012, Japan.
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056, Basel, Switzerland.
| | - Ali Sadeghi
- Department of Physics, Shahid Beheshti University, G. C., Evin, 19839, Tehran, Iran.
| | - Toshihiro Okamoto
- PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama, 332-0012, Japan.
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
| | - Chikahiko Mitsui
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Rémy Pawlak
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056, Basel, Switzerland
| | - Tobias Meier
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056, Basel, Switzerland
| | - Jun Takeya
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Stefan Goedecker
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056, Basel, Switzerland
| | - Ernst Meyer
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056, Basel, Switzerland
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21
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van der Heijden NJ, Hapala P, Rombouts JA, van der Lit J, Smith D, Mutombo P, Švec M, Jelinek P, Swart I. Characteristic Contrast in Δfmin Maps of Organic Molecules Using Atomic Force Microscopy. ACS NANO 2016; 10:8517-8525. [PMID: 27508403 DOI: 10.1021/acsnano.6b03644] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Scanning tunneling microscopy and atomic force microscopy can provide detailed information about the geometric and electronic structure of molecules with submolecular spatial resolution. However, an essential capability to realize the full potential of these techniques for chemical applications is missing from the scanning probe toolbox: chemical recognition of organic molecules. Here, we show that maps of the minima of frequency shift-distance curves extracted from 3D data cubes contain characteristic contrast. A detailed theoretical analysis based on density functional theory and molecular mechanics shows that these features are characteristic for the investigated species. Structurally similar but chemically distinct molecules yield significantly different features. We find that the van der Waals and Pauli interaction, together with the specific adsorption geometry of a given molecule on the surface, accounts for the observed contrast.
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Affiliation(s)
- Nadine J van der Heijden
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University , P.O. Box 80000, 3508 TA Utrecht, The Netherlands
| | - Prokop Hapala
- Institute of Physics, Czech Academy of Sciences , Cukrovarnická 10, 1862 53 Prague, Czech Republic
| | - Jeroen A Rombouts
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Joost van der Lit
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University , P.O. Box 80000, 3508 TA Utrecht, The Netherlands
| | - Daniël Smith
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University , P.O. Box 80000, 3508 TA Utrecht, The Netherlands
| | - Pingo Mutombo
- Institute of Physics, Czech Academy of Sciences , Cukrovarnická 10, 1862 53 Prague, Czech Republic
| | - Martin Švec
- Institute of Physics, Czech Academy of Sciences , Cukrovarnická 10, 1862 53 Prague, Czech Republic
| | - Pavel Jelinek
- Institute of Physics, Czech Academy of Sciences , Cukrovarnická 10, 1862 53 Prague, Czech Republic
| | - Ingmar Swart
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University , P.O. Box 80000, 3508 TA Utrecht, The Netherlands
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22
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Sweetman A, Jarvis SP, Rashid MA. Modelling of 'sub-atomic' contrast resulting from back-bonding on Si(111)-7×7. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:937-945. [PMID: 27547610 PMCID: PMC4979881 DOI: 10.3762/bjnano.7.85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 06/09/2016] [Indexed: 06/06/2023]
Abstract
It has recently been shown that 'sub-atomic' contrast can be observed during NC-AFM imaging of the Si(111)-7×7 substrate with a passivated tip, resulting in triangular shaped atoms [Sweetman et al. Nano Lett. 2014, 14, 2265]. The symmetry of the features, and the well-established nature of the dangling bond structure of the silicon adatom means that in this instance the contrast cannot arise from the orbital structure of the atoms, and it was suggested by simple symmetry arguments that the contrast could only arise from the backbonding symmetry of the surface adatoms. However, no modelling of the system has been performed in order to understand the precise origin of the contrast. In this paper we provide a detailed explanation for 'sub-atomic' contrast observed on Si(111)-7×7 using a simple model based on Lennard-Jones potentials, coupled with a flexible tip, as proposed by Hapala et al. [Phys. Rev. B 2014, 90, 085421] in the context of interpreting sub-molecular contrast. Our results show a striking similarity to experimental results, and demonstrate how 'sub-atomic' contrast can arise from a flexible tip exploring an asymmetric potential created due to the positioning of the surrounding surface atoms.
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Affiliation(s)
- Adam Sweetman
- The School of Physics and Astronomy, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Samuel P Jarvis
- The School of Physics and Astronomy, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Mohammad A Rashid
- The School of Physics and Astronomy, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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23
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Yuan D, Han Z, Czap G, Chiang CL, Xu C, Ho W, Wu R. Quantitative Understanding of van der Waals Interactions by Analyzing the Adsorption Structure and Low-Frequency Vibrational Modes of Single Benzene Molecules on Silver. J Phys Chem Lett 2016; 7:2228-2233. [PMID: 27232051 DOI: 10.1021/acs.jpclett.6b00894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The combination of a sub-Kelvin scanning tunneling microscope and density functional calculations incorporating van der Waals (vdW) corrections has been used successfully to probe the adsorption structure and low-frequency vibrational modes of single benzene molecules on Ag(110). The inclusion of optimized vdW functionals and improved C6-based vdW dispersion schemes in density functional theory is crucial for obtaining the correct adsorption structure and low-energy vibrational modes. These results demonstrate the emerging capability to quantitatively probe the van der Waals interactions between a physisorbed molecule and an inert substrate.
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Affiliation(s)
- Dingwang Yuan
- Center for High Resolution Electron Microscopy, College of Materials Science and Engineering, Hunan University , Changsha 410082, China
- Department of Physics and Astronomy, University of California , Irvine, California 92697-4575, United States
| | - Zhumin Han
- Department of Physics and Astronomy, University of California , Irvine, California 92697-4575, United States
| | - Gregory Czap
- Department of Physics and Astronomy, University of California , Irvine, California 92697-4575, United States
| | - Chi-Lun Chiang
- Department of Physics and Astronomy, University of California , Irvine, California 92697-4575, United States
| | - Chen Xu
- Department of Physics and Astronomy, University of California , Irvine, California 92697-4575, United States
| | - W Ho
- Department of Physics and Astronomy, University of California , Irvine, California 92697-4575, United States
- Department of Chemistry, University of California , Irvine, California 92697-2025, United States
| | - Ruqian Wu
- Department of Physics and Astronomy, University of California , Irvine, California 92697-4575, United States
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24
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Hapala P, Švec M, Stetsovych O, van der Heijden NJ, Ondráček M, van der Lit J, Mutombo P, Swart I, Jelínek P. Mapping the electrostatic force field of single molecules from high-resolution scanning probe images. Nat Commun 2016; 7:11560. [PMID: 27230940 PMCID: PMC4894979 DOI: 10.1038/ncomms11560] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/08/2016] [Indexed: 01/06/2023] Open
Abstract
How electronic charge is distributed over a molecule determines to a large extent its chemical properties. Here, we demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with submolecular resolution. We exploit the fact that distortions typically observed in high-resolution atomic force microscopy images are for a significant part caused by the electrostatic force acting between charges of the tip and the molecule of interest. By finding a geometrical transformation between two high-resolution AFM images acquired with two different tips, the electrostatic force field or potential over individual molecules and self-assemblies thereof can be reconstructed with submolecular resolution. The chemical properties of molecules are largely determined by the distribution of charge across them. Here, the authors demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with sub-molecular resolution.
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Affiliation(s)
- Prokop Hapala
- Department of Thin Films and Nanostructures, Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Cukrovarnická 10, 162 00 Prague, Czech Republic
| | - Martin Švec
- Department of Thin Films and Nanostructures, Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Cukrovarnická 10, 162 00 Prague, Czech Republic
| | - Oleksandr Stetsovych
- Department of Thin Films and Nanostructures, Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Cukrovarnická 10, 162 00 Prague, Czech Republic
| | - Nadine J van der Heijden
- Department of Chemistry, Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, PO Box 80 000, 3508 TA Utrecht, The Netherlands
| | - Martin Ondráček
- Department of Thin Films and Nanostructures, Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Cukrovarnická 10, 162 00 Prague, Czech Republic
| | - Joost van der Lit
- Department of Chemistry, Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, PO Box 80 000, 3508 TA Utrecht, The Netherlands
| | - Pingo Mutombo
- Department of Thin Films and Nanostructures, Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Cukrovarnická 10, 162 00 Prague, Czech Republic
| | - Ingmar Swart
- Department of Chemistry, Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, PO Box 80 000, 3508 TA Utrecht, The Netherlands
| | - Pavel Jelínek
- Department of Thin Films and Nanostructures, Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Cukrovarnická 10, 162 00 Prague, Czech Republic
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25
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Sakai Y, Lee AJ, Chelikowsky JR. First-Principles Atomic Force Microscopy Image Simulations with Density Embedding Theory. NANO LETTERS 2016; 16:3242-3246. [PMID: 27050710 DOI: 10.1021/acs.nanolett.6b00741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present an efficient first-principles method for simulating noncontact atomic force microscopy (nc-AFM) images using a "frozen density" embedding theory. Frozen density embedding theory enables one to efficiently compute the tip-sample interaction by considering a sample as a frozen external field. This method reduces the extensive computational load of first-principles AFM simulations by avoiding consideration of the entire tip-sample system and focusing on the tip alone. We demonstrate that our simulation with frozen density embedding theory accurately reproduces full density functional theory simulations of freestanding hydrocarbon molecules while the computational time is significantly reduced. Our method also captures the electronic effect of a Cu(111) substrate on the AFM image of pentacene and reproduces the experimental AFM image of Cu2N on a Cu(100) surface. This approach is applicable for theoretical imaging applications on large molecules, two-dimensional materials, and materials surfaces.
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Affiliation(s)
- Yuki Sakai
- Center for Computational Materials, Institute for Computational Engineering and Sciences, ‡Department of Chemical Engineering, §Department of Physics, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Alex J Lee
- Center for Computational Materials, Institute for Computational Engineering and Sciences, ‡Department of Chemical Engineering, §Department of Physics, The University of Texas at Austin , Austin, Texas 78712, United States
| | - James R Chelikowsky
- Center for Computational Materials, Institute for Computational Engineering and Sciences, ‡Department of Chemical Engineering, §Department of Physics, The University of Texas at Austin , Austin, Texas 78712, United States
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26
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Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy. Nat Chem 2016; 8:678-83. [DOI: 10.1038/nchem.2506] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 03/16/2016] [Indexed: 12/25/2022]
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27
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Ellner M, Pavliček N, Pou P, Schuler B, Moll N, Meyer G, Gross L, Peréz R. The Electric Field of CO Tips and Its Relevance for Atomic Force Microscopy. NANO LETTERS 2016; 16:1974-1980. [PMID: 26840626 DOI: 10.1021/acs.nanolett.5b05251] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Metal tips decorated with CO molecules have paved the way for an impressively high resolution in atomic force microscopy (AFM). Although Pauli repulsion and the associated CO tilting play a dominant role at short distances, experiments on polar and metallic systems show that electrostatic interactions are necessary to understand the complex contrast observed and its distance evolution. Attempts to describe those interactions in terms of a single electrostatic dipole replacing the tip have led to contradictory statements about its nature and strength. Here, we solve this puzzle with a comprehensive experimental and theoretical characterization of the AFM contrast on Cl vacancies. Our model, based on density functional theory (DFT) calculations, reproduces the complex evolution of the contrast between both the Na cation and Cl anion sites, and the positively charged vacancy as a function of tip height, and highlights the key contribution of electrostatic interactions for tip-sample distances larger than 500 pm. For smaller separations, Pauli repulsion and the associated CO tilting start to dominate the contrast. The electrostatic field of the CO-metal tip can be represented by the superposition of the fields from the metal tip and the CO molecule. The long-range behavior is defined by the metal tip that contributes the field of a dipole with its positive pole at the apex. At short-range, the CO exhibits an opposite field that prevails. The interplay of these fields, with opposite sign and rather different spatial extension, is crucial to describe the contrast evolution as a function of the tip height.
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Affiliation(s)
- Michael Ellner
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid , E-28049 Madrid, Spain
| | | | - Pablo Pou
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid , E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , E-28049 Madrid, Spain
| | | | - Nikolaj Moll
- IBM Research-Zurich, 8803 Rüschlikon, Switzerland
| | | | - Leo Gross
- IBM Research-Zurich, 8803 Rüschlikon, Switzerland
| | - Rubén Peréz
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid , E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , E-28049 Madrid, Spain
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28
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van der Lit J, Di Cicco F, Hapala P, Jelinek P, Swart I. Submolecular Resolution Imaging of Molecules by Atomic Force Microscopy: The Influence of the Electrostatic Force. PHYSICAL REVIEW LETTERS 2016; 116:096102. [PMID: 26991186 DOI: 10.1103/physrevlett.116.096102] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Indexed: 05/24/2023]
Abstract
The forces governing the contrast in submolecular resolution imaging of molecules with atomic force microscopy (AFM) have recently become a topic of intense debate. Here, we show that the electrostatic force is essential to understand the contrast in atomically resolved AFM images of polar molecules. Specifically, we image strongly polarized molecules with negatively and positively charged tips. A contrast inversion is observed above the polar groups. By taking into account the electrostatic forces between tip and molecule, the observed contrast differences can be reproduced using a molecular mechanics model. In addition, we analyze the height dependence of the various force components contributing to the high-resolution AFM contrast.
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Affiliation(s)
- Joost van der Lit
- Debye Institute for Nanomaterials Science, Utrecht University, P.O. Box 80.000, 3508 TA Utrecht, The Netherlands
| | - Francesca Di Cicco
- Debye Institute for Nanomaterials Science, Utrecht University, P.O. Box 80.000, 3508 TA Utrecht, The Netherlands
| | - Prokop Hapala
- Institute of Physics, Academy of Sciences of the Czech Republic Cukrovarnicka 10, 1862 53 Prague, Czech Republic
| | - Pavel Jelinek
- Institute of Physics, Academy of Sciences of the Czech Republic Cukrovarnicka 10, 1862 53 Prague, Czech Republic
| | - Ingmar Swart
- Debye Institute for Nanomaterials Science, Utrecht University, P.O. Box 80.000, 3508 TA Utrecht, The Netherlands
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29
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Mönig H, Hermoso DR, Díaz Arado O, Todorović M, Timmer A, Schüer S, Langewisch G, Pérez R, Fuchs H. Submolecular Imaging by Noncontact Atomic Force Microscopy with an Oxygen Atom Rigidly Connected to a Metallic Probe. ACS NANO 2016; 10:1201-9. [PMID: 26605698 DOI: 10.1021/acsnano.5b06513] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In scanning probe microscopy, the imaging characteristics in the various interaction channels crucially depend on the chemical termination of the probe tip. Here we analyze the contrast signatures of an oxygen-terminated copper tip with a tetrahedral configuration of the covalently bound terminal O atom. Supported by first-principles calculations we show how this tip termination can be identified by contrast analysis in noncontact atomic force and scanning tunneling microscopy (NC-AFM, STM) on a partially oxidized Cu(110) surface. After controlled tip functionalization by soft indentations of only a few angstroms in an oxide nanodomain, we demonstrate that this tip allows imaging an organic molecule adsorbed on Cu(110) by constant-height NC-AFM in the repulsive force regime, revealing its internal bond structure. In established tip functionalization approaches where, for example, CO or Xe is deliberately picked up from a surface, these probe particles are only weakly bound to the metallic tip, leading to lateral deflections during scanning. Therefore, the contrast mechanism is subject to image distortions, artifacts, and related controversies. In contrast, our simulations for the O-terminated Cu tip show that lateral deflections of the terminating O atom are negligible. This allows a detailed discussion of the fundamental imaging mechanisms in high-resolution NC-AFM experiments. With its structural rigidity, its chemically passivated state, and a high electron density at the apex, we identify the main characteristics of the O-terminated Cu tip, making it a highly attractive complementary probe for the characterization of organic nanostructures on surfaces.
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Affiliation(s)
- Harry Mönig
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
- Center for Nanotechnology (CeNTech) , Heisenbergstrasse 11, 48149 Münster, Germany
| | | | - Oscar Díaz Arado
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
- Center for Nanotechnology (CeNTech) , Heisenbergstrasse 11, 48149 Münster, Germany
| | | | - Alexander Timmer
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
- Center for Nanotechnology (CeNTech) , Heisenbergstrasse 11, 48149 Münster, Germany
| | - Simon Schüer
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
- Center for Nanotechnology (CeNTech) , Heisenbergstrasse 11, 48149 Münster, Germany
| | - Gernot Langewisch
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
- Center for Nanotechnology (CeNTech) , Heisenbergstrasse 11, 48149 Münster, Germany
| | | | - Harald Fuchs
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
- Center for Nanotechnology (CeNTech) , Heisenbergstrasse 11, 48149 Münster, Germany
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30
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Schuler B, Fatayer S, Mohn F, Moll N, Pavliček N, Meyer G, Peña D, Gross L. Reversible Bergman cyclization by atomic manipulation. Nat Chem 2016; 8:220-4. [DOI: 10.1038/nchem.2438] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/11/2015] [Indexed: 12/25/2022]
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31
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Jain SK, Juričić V, Barkema GT. Probing Crystallinity of Graphene Samples via the Vibrational Density of States. J Phys Chem Lett 2015; 6:3897-3902. [PMID: 26722890 DOI: 10.1021/acs.jpclett.5b01489] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The purity of graphene samples is of crucial importance for their experimental and practical use. In this regard, the detection of the defects is of direct relevance. Here, we show that structural defects in graphene samples give rise to clear signals in the vibrational density of states (VDOS) at specific peaks at high and low frequencies. These can be used as an independent probe of the defect density. In particular, we consider grain boundaries made of pentagon-heptagon pairs, and show that they lead to a shift of the characteristic vibrational D mode toward higher frequency; this distinguishes these line defects from Stone-Wales point defects, which do not lead to such a shift. Our findings may be instrumental for the detection of structural lattice defects using experimental techniques that can directly measure VDOS, such as inelastic electron tunneling and inelastic neutron spectroscopy.
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Affiliation(s)
- Sandeep K Jain
- Institute for Theoretical Physics, Universiteit Utrecht , Leuvenlaan 4, 3584 CE Utrecht, The Netherlands
| | - Vladimir Juričić
- Institute for Theoretical Physics, Universiteit Utrecht , Leuvenlaan 4, 3584 CE Utrecht, The Netherlands
| | - Gerard T Barkema
- Institute for Theoretical Physics, Universiteit Utrecht , Leuvenlaan 4, 3584 CE Utrecht, The Netherlands
- Institut-Lorentz, Universiteit Leiden , Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
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32
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Jarvis SP. Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy. Int J Mol Sci 2015; 16:19936-59. [PMID: 26307976 PMCID: PMC4581333 DOI: 10.3390/ijms160819936] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 07/24/2015] [Accepted: 07/30/2015] [Indexed: 11/25/2022] Open
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.
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Affiliation(s)
- Samuel Paul Jarvis
- School of Physics & Astronomy, University of Nottingham, Nottingham NG7 2RD, UK.
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33
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Gross L, Schuler B, Mohn F, Moll N, Repp J, Meyer G. Atomic Resolution on Molecules with Functionalized Tips. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-15588-3_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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34
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Moreno C, Stetsovych O, Shimizu TK, Custance O. Imaging three-dimensional surface objects with submolecular resolution by atomic force microscopy. NANO LETTERS 2015; 15:2257-62. [PMID: 25756297 DOI: 10.1021/nl504182w] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Submolecular imaging by atomic force microscopy (AFM) has recently been established as a stunning technique to reveal the chemical structure of unknown molecules, to characterize intramolecular charge distributions and bond ordering, as well as to study chemical transformations and intermolecular interactions. So far, most of these feats were achieved on planar molecular systems because high-resolution imaging of three-dimensional (3D) surface structures with AFM remains challenging. Here we present a method for high-resolution imaging of nonplanar molecules and 3D surface systems using AFM with silicon cantilevers as force sensors. We demonstrate this method by resolving the step-edges of the (101) anatase surface at the atomic scale by simultaneously visualizing the structure of a pentacene molecule together with the atomic positions of the substrate and by resolving the contour and probe-surface force field on a C60 molecule with intramolecular resolution. The method reported here holds substantial promise for the study of 3D surface systems such as nanotubes, clusters, nanoparticles, polymers, and biomolecules using AFM with high resolution.
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Affiliation(s)
- César Moreno
- †National Institute for Materials Science (NIMS), 1-2-1 Sengen, 305-0047 Tsukuba, Ibaraki Japan
- ‡International Center for Young Scientists, NIMS, 1-2-1 Sengen, 305-0047 Tsukuba, Ibaraki Japan
| | - Oleksandr Stetsovych
- †National Institute for Materials Science (NIMS), 1-2-1 Sengen, 305-0047 Tsukuba, Ibaraki Japan
- §Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnicka 10, Prague, Czech Rebublic
| | - Tomoko K Shimizu
- †National Institute for Materials Science (NIMS), 1-2-1 Sengen, 305-0047 Tsukuba, Ibaraki Japan
- §JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Oscar Custance
- †National Institute for Materials Science (NIMS), 1-2-1 Sengen, 305-0047 Tsukuba, Ibaraki Japan
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35
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Telychko M, Berger J, Majzik Z, Jelínek P, Švec M. Graphene on SiC(0001) inspected by dynamic atomic force microscopy at room temperature. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2015; 6:901-6. [PMID: 25977861 PMCID: PMC4419658 DOI: 10.3762/bjnano.6.93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
We investigated single-layer graphene on SiC(0001) by atomic force and tunneling current microscopy, to separate the topographic and electronic contributions from the overall landscape. The analysis revealed that the roughness evaluated from the atomic force maps is very low, in accord with theoretical simulations. We also observed that characteristic electron scattering effects on graphene edges and defects are not accompanied by any out-of-plane relaxations of carbon atoms.
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Affiliation(s)
- Mykola Telychko
- Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, CZ-16200 Prague, Czech Republic
- Charles University, Faculty of Mathematics and Physics, V Holešovičkách 2, Praha 8, Czech Republic
| | - Jan Berger
- Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, CZ-16200 Prague, Czech Republic
- Department of Physical Electronics, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, CZ-11519 Prague, Czech Republic
| | - Zsolt Majzik
- Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, CZ-16200 Prague, Czech Republic
| | - Pavel Jelínek
- Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, CZ-16200 Prague, Czech Republic
| | - Martin Švec
- Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, CZ-16200 Prague, Czech Republic
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36
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Hapala P, Temirov R, Tautz FS, Jelínek P. Origin of High-Resolution IETS-STM Images of Organic Molecules with Functionalized Tips. PHYSICAL REVIEW LETTERS 2014; 113:226101. [PMID: 25494078 DOI: 10.1103/physrevlett.113.226101] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 05/27/2023]
Abstract
Recently, the family of high-resolution scanning probe imaging techniques using decorated tips has been complemented by a method based on inelastic electron tunneling spectroscopy (IETS). The new technique resolves the inner structure of organic molecules by mapping the vibrational energy of a single carbon monoxide (CO) molecule positioned at the apex of a scanning tunneling microscope (STM) tip. Here, we explain high-resolution IETS imaging by extending a model developed earlier for STM and atomic force microscopy (AFM) imaging with decorated tips. In particular, we show that the tip decorated with CO acts as a nanoscale sensor that changes the energy of its frustrated translation mode in response to changes of the local curvature of the surface potential. In addition, we show that high resolution AFM, STM, and IETS-STM images can deliver information about the charge distribution within molecules deposited on a surface. To demonstrate this, we extend our mechanical model by taking into account electrostatic forces acting on the decorated tip in the surface Hartree potential.
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Affiliation(s)
- Prokop Hapala
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Cukrovarnická 10, 162 00 Prague, Czech Republic
| | - Ruslan Temirov
- Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 52425 Jülich, Germany and Jülich Aachen Research Alliance (JARA)-Fundamentals of Future Information Technology, 52425 Jülich, Germany
| | - F Stefan Tautz
- Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 52425 Jülich, Germany and Jülich Aachen Research Alliance (JARA)-Fundamentals of Future Information Technology, 52425 Jülich, Germany
| | - Pavel Jelínek
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Cukrovarnická 10, 162 00 Prague, Czech Republic and Graduate School of Engineering, Osaka University 2-1, Yamada-Oka, Suita, Osaka 565-0871, Japan
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37
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Moll N, Schuler B, Kawai S, Xu F, Peng L, Orita A, Otera J, Curioni A, Neu M, Repp J, Meyer G, Gross L. Image distortions of a partially fluorinated hydrocarbon molecule in atomic force microscopy with carbon monoxide terminated tips. NANO LETTERS 2014; 14:6127-6131. [PMID: 25247477 DOI: 10.1021/nl502113z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The underlying mechanisms of image distortions in atomic force microscopy (AFM) with CO-terminated tips are identified and studied in detail. AFM measurements of a partially fluorinated hydrocarbon molecule recorded with a CO-terminated tip are compared with state-of-the-art ab initio calculations. The hydrogenated and fluorinated carbon rings in the molecule appear different in size, which primarily originates from the different extents of their π-electrons. Further, tilting of the CO at the tip, induced by van der Waals forces, enlarges the apparent size of parts of the molecule by up to 50%. Moreover, the CO tilting in response to local Pauli repulsion causes a significant sharpening of the molecule bonds in AFM imaging.
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Affiliation(s)
- Nikolaj Moll
- IBM Research - Zurich , Säumerstrasse 4, 8803 Rüschlikon, Switzerland
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Hämäläinen SK, van der Heijden N, van der Lit J, den Hartog S, Liljeroth P, Swart I. Intermolecular contrast in atomic force microscopy images without intermolecular bonds. PHYSICAL REVIEW LETTERS 2014; 113:186102. [PMID: 25396382 DOI: 10.1103/physrevlett.113.186102] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 05/19/2023]
Abstract
Intermolecular features in atomic force microscopy images of organic molecules have been ascribed to intermolecular bonds. A recent theoretical study [P. Hapala et al., Phys. Rev. B 90, 085421 (2014)] showed that these features can also be explained by the flexibility of molecule-terminated tips. We probe this effect by carrying out atomic force microscopy experiments on a model system that contains regions where intermolecular bonds should and should not exist between close-by molecules. Intermolecular features are observed in both regions, demonstrating that intermolecular contrast cannot be directly interpreted as intermolecular bonds.
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Affiliation(s)
- Sampsa K Hämäläinen
- Department of Applied Physics, Aalto University School of Science, P.O. Box 15100, 00076 Aalto, Finland
| | - Nadine van der Heijden
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, P.O. Box 80000, 3508 TA Utrecht, The Netherlands
| | - Joost van der Lit
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, P.O. Box 80000, 3508 TA Utrecht, The Netherlands
| | - Stephan den Hartog
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, P.O. Box 80000, 3508 TA Utrecht, The Netherlands
| | - Peter Liljeroth
- Department of Applied Physics, Aalto University School of Science, P.O. Box 15100, 00076 Aalto, Finland
| | - Ingmar Swart
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, P.O. Box 80000, 3508 TA Utrecht, The Netherlands
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