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      Chemical structure imaging of a single molecule by atomic force microscopy at room temperature

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          Abstract

          Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)–(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule.

          Abstract

          Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface, usually at low temperatures. Here, the authors demonstrate that the chemical structure of a single molecule strongly adsorbed onto a silicon surface can be determined at room temperature.

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          Most cited references16

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          Real-space identification of intermolecular bonding with atomic force microscopy.

          We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.
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            Atomic-scale distribution of water molecules at the mica-water interface visualized by three-dimensional scanning force microscopy.

            We have developed a method referred to as three-dimensional scanning force microscopy (3D-SFM) which enables us to visualize water distribution at a solid-liquid interface with an atomic-scale resolution in less than 1 min. The 3D-SFM image obtained at a mica-water interface visualizes 3D distributions of adsorbed water molecules above the center of hexagonal cavities and the laterally distributed hydration layer. The atomically resolved 3D-SFM image showing mirror symmetry suggests the existence of surface relaxation of the cleaved mica surface next to the aqueous environment.
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              Imaging the charge distribution within a single molecule.

              Scanning tunnelling microscopy and atomic force microscopy can be used to study the electronic and structural properties of surfaces, as well as molecules and nanostructures adsorbed on surfaces, with atomic precision, but they cannot directly probe the distribution of charge in these systems. However, another form of scanning probe microscopy, Kelvin probe force microscopy, can be used to measure the local contact potential difference between the scanning probe tip and the surface, a quantity that is closely related to the charge distribution on the surface. Here, we use a combination of scanning tunnelling microscopy, atomic force microscopy and Kelvin probe force microscopy to examine naphthalocyanine molecules (which have been used as molecular switches) on a thin insulating layer of NaCl on Cu(111). We show that Kelvin probe force microscopy can map the local contact potential difference of this system with submolecular resolution, and we use density functional theory calculations to verify that these maps reflect the intramolecular distribution of charge. This approach could help to provide fundamental insights into single-molecule switching and bond formation, processes that are usually accompanied by the redistribution of charge within or between molecules.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Pub. Group
                2041-1723
                16 July 2015
                2015
                : 6
                : 7766
                Affiliations
                [1 ]Graduate School of Engineering, Osaka University , 2-1, Yamada-Oka, Suita, Osaka 565-0871, Japan.
                [2 ]The Institute of Scientific and Industrial Research, Osaka University , 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
                [3 ]Institute of Physics, Academy of Sciences of the Czech Republic , Cukrovarnická 10/112, Prague 16200, Czech Republic.
                [4 ]Department of Advanced Materials Science, University of Tokyo 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8561, Japan.
                Author notes
                Article
                ncomms8766
                10.1038/ncomms8766
                4518281
                26178193
                8c2a7beb-61b0-459a-bdb0-bb3998443450
                Copyright © 2015, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 28 March 2015
                : 05 June 2015
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