1
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Pitters J, Croshaw J, Achal R, Livadaru L, Ng S, Lupoiu R, Chutora T, Huff T, Walus K, Wolkow RA. Atomically Precise Manufacturing of Silicon Electronics. ACS NANO 2024; 18:6766-6816. [PMID: 38376086 PMCID: PMC10919096 DOI: 10.1021/acsnano.3c10412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/21/2024]
Abstract
Atomically precise manufacturing (APM) is a key technique that involves the direct control of atoms in order to manufacture products or components of products. It has been developed most successfully using scanning probe methods and has received particular attention for developing atom scale electronics with a focus on silicon-based systems. This review captures the development of silicon atom-based electronics and is divided into several sections that will cover characterization and atom manipulation of silicon surfaces with scanning tunneling microscopy and atomic force microscopy, development of silicon dangling bonds as atomic quantum dots, creation of atom scale devices, and the wiring and packaging of those circuits. The review will also cover the advance of silicon dangling bond logic design and the progress of silicon quantum atomic designer (SiQAD) simulators. Finally, an outlook of APM and silicon atom electronics will be provided.
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Affiliation(s)
- Jason Pitters
- Nanotechnology
Research Centre, National Research Council
of Canada, Edmonton, Alberta T6G 2M9, Canada
| | - Jeremiah Croshaw
- Department
of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Roshan Achal
- Department
of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Quantum
Silicon Inc., Edmonton, Alberta T6G 2M9, Canada
| | - Lucian Livadaru
- Department
of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Quantum
Silicon Inc., Edmonton, Alberta T6G 2M9, Canada
| | - Samuel Ng
- Department
of Electrical and Computer Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Robert Lupoiu
- School
of Engineering, Stanford University, Stanford, California 94305, United States
| | - Taras Chutora
- Department
of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Taleana Huff
- Canadian
Bank Note Company, Ottawa, Ontario K1Z 1A1, Canada
| | - Konrad Walus
- Department
of Electrical and Computer Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Robert A. Wolkow
- Department
of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Quantum
Silicon Inc., Edmonton, Alberta T6G 2M9, Canada
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2
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Wang X, Zahl P, Wang H, Altman EI, Schwarz UD. How Precisely Can Individual Molecules Be Analyzed? A Case Study on Locally Quantifying Forces and Energies Using Scanning Probe Microscopy. ACS NANO 2024; 18:4495-4506. [PMID: 38265359 DOI: 10.1021/acsnano.3c11219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Recent advances in scanning probe microscopy methodology have enabled the measurement of tip-sample interactions with picometer accuracy in all three spatial dimensions, thereby providing a detailed site-specific and distance-dependent picture of the related properties. This paper explores the degree of detail and accuracy that can be achieved in locally quantifying probe-molecule interaction forces and energies for adsorbed molecules. Toward this end, cobalt phthalocyanine (CoPc), a promising CO2 reduction catalyst, was studied on Ag(111) as a model system using low-temperature, ultrahigh vacuum noncontact atomic force microscopy. Data were recorded as a function of distance from the surface, from which detailed three-dimensional maps of the molecule's interaction with the tip for normal and lateral forces as well as the tip-molecule interaction potential were constructed. The data were collected with a CO molecule at the tip apex, which enabled a detailed visualization of the atomic structure. Determination of the tip-substrate interaction as a function of distance allowed isolation of the molecule-tip interactions; when analyzing these in terms of a Lennard-Jones-type potential, the atomically resolved equilibrium interaction energies between the CO tethered to the tip and the CoPc molecule could be recovered. Interaction energies peaked at less than 160 meV, indicating a physisorption interaction. As expected, the interaction was weakest at the aromatic hydrogens around the periphery of the molecule and strongest surrounding the metal center. The interaction, however, did not peak directly above the Co atom but rather in pockets surrounding it.
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Affiliation(s)
- Xinzhe Wang
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06511, United States
| | - Percy Zahl
- Center for Functional Nanomaterials, Brookhaven National Lab, Upton, New York 11973, United States
| | - Hailiang Wang
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Eric I Altman
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Udo D Schwarz
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06511, United States
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, United States
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3
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Nam S, Riegel E, Hörmann L, Hofmann OT, Gretz O, Weymouth AJ, Giessibl FJ. Exploring in-plane interactions beside an adsorbed molecule with lateral force microscopy. Proc Natl Acad Sci U S A 2024; 121:e2311059120. [PMID: 38170747 PMCID: PMC10786270 DOI: 10.1073/pnas.2311059120] [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: 07/12/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
Atomic force microscopy with a CO-functionalized tip can be used to directly image the internal structure of a planar molecule and to characterize chemical bonds. However, hydrogen atoms usually cannot be directly observed due to their small size. At the same time, these atoms are highly important, since they can direct on-surface chemical reactions. Measuring in-plane interactions at the sides of PTCDA (3,4,9,10-perylenetetracarboxylic dianhydride) molecules with lateral force microscopy allowed us to directly identify hydrogen atoms via their repulsive signature, which we confirmed with a model incorporating radially symmetric atomic interactions. Additional features were observed in the force data and could not be explained by H-bonding of the CO tip with the PTCDA sides. Instead, they are caused by electrostatic interaction of the large dipole of the metal apex, which we verified with density functional theory. This calculation allowed us to estimate the strength of the dipole at the metal tip apex. To further confirm that this dipole generally affects measurements on weakly polarized systems, we investigated the archetypical surface adsorbate of a single CO molecule. We determined the radially symmetric atomic interaction to be valid over a large solid angle of 5.4 sr, corresponding to 82°. We therefore find that in both the PTCDA and CO systems, the underlying interaction preventing direct observations of H-bonding and causing a collapse of the radially symmetric model is the dipole at the metal apex, which plays a significant role when approaching closer than standard imaging heights.
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Affiliation(s)
- Shinjae Nam
- Chair of Quantum Nanoscience, Faculty of Physics, University of Regensburg, 93053Regensburg, Germany
| | - Elisabeth Riegel
- Chair of Quantum Nanoscience, Faculty of Physics, University of Regensburg, 93053Regensburg, Germany
| | - Lukas Hörmann
- Simulation-Driven Material Discovery Group, Institute of Solid State Physics, Graz University of Technology, 8010Graz, Austria
| | - Oliver T. Hofmann
- Simulation-Driven Material Discovery Group, Institute of Solid State Physics, Graz University of Technology, 8010Graz, Austria
| | - Oliver Gretz
- Chair of Quantum Nanoscience, Faculty of Physics, University of Regensburg, 93053Regensburg, Germany
| | - Alfred J. Weymouth
- Chair of Quantum Nanoscience, Faculty of Physics, University of Regensburg, 93053Regensburg, Germany
| | - Franz J. Giessibl
- Chair of Quantum Nanoscience, Faculty of Physics, University of Regensburg, 93053Regensburg, Germany
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4
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Zhong Q, Mardyukov A, Solel E, Ebeling D, Schirmeisen A, Schreiner PR. On-Surface Synthesis and Real-Space Visualization of Aromatic P 3 N 3. Angew Chem Int Ed Engl 2023; 62:e202310121. [PMID: 37702299 DOI: 10.1002/anie.202310121] [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: 07/16/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/14/2023]
Abstract
On-surface synthesis is at the verge of emerging as the method of choice for the generation and visualization of unstable or unconventional molecules, which could not be obtained via traditional synthetic methods. A case in point is the on-surface synthesis of the structurally elusive cyclotriphosphazene (P3 N3 ), an inorganic aromatic analogue of benzene. Here, we report the preparation of this fleetingly existing species on Cu(111) and Au(111) surfaces at 5.2 K through molecular manipulation with unprecedented precision, i.e., voltage pulse-induced sextuple dechlorination of an ultra-small (about 6 Å) hexachlorophosphazene P3 N3 Cl6 precursor by the tip of a scanning probe microscope. Real-space atomic-level imaging of cyclotriphosphazene reveals its planar D3h -symmetric ring structure. Furthermore, this demasking strategy has been expanded to generate cyclotriphosphazene from a hexaazide precursor P3 N21 via a different stimulation method (photolysis) for complementary measurements by matrix isolation infrared and ultraviolet spectroscopy.
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Affiliation(s)
- Qigang Zhong
- Institute of Applied Physics, Justus Liebig University Giessen, Giessen, Germany
- Center for Materials Research (ZfM), Justus Liebig University Giessen, Giessen, Germany
| | - Artur Mardyukov
- Center for Materials Research (ZfM), Justus Liebig University Giessen, Giessen, Germany
- Institute of Organic Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Ephrath Solel
- Center for Materials Research (ZfM), Justus Liebig University Giessen, Giessen, Germany
- Institute of Organic Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Daniel Ebeling
- Institute of Applied Physics, Justus Liebig University Giessen, Giessen, Germany
- Center for Materials Research (ZfM), Justus Liebig University Giessen, Giessen, Germany
| | - André Schirmeisen
- Institute of Applied Physics, Justus Liebig University Giessen, Giessen, Germany
- Center for Materials Research (ZfM), Justus Liebig University Giessen, Giessen, Germany
| | - Peter R Schreiner
- Center for Materials Research (ZfM), Justus Liebig University Giessen, Giessen, Germany
- Institute of Organic Chemistry, Justus Liebig University Giessen, Giessen, Germany
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5
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Heggemann J, Ranawat YS, Krejčí O, Foster AS, Rahe P. Differences in Molecular Adsorption Emanating from the (2 × 1) Reconstruction of Calcite(104). J Phys Chem Lett 2023; 14:1983-1989. [PMID: 36794827 PMCID: PMC10100545 DOI: 10.1021/acs.jpclett.2c03243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Calcite, in the natural environment the most stable polymorph of calcium carbonate (CaCO3), not only is an abundant mineral in the Earth's crust but also forms a central constituent in the biominerals of living organisms. Intensive studies of calcite(104), the surface supporting virtually all processes, have been performed, and the interaction with a plethora of adsorbed species has been studied. Surprisingly, there is still serious ambiguity regarding the properties of the calcite(104) surface: effects such as a row-pairing or a (2 × 1) reconstruction have been reported, yet so far without physicochemical explanation. Here, we unravel the microscopic geometry of calcite(104) using high-resolution atomic force microscopy (AFM) data acquired at 5 K combined with density functional theory (DFT) and AFM image calculations. A (2 × 1) reconstruction of a pg-symmetric surface is found to be the thermodynamically most stable form. Most importantly, a decisive impact of the (2 × 1) reconstruction on adsorbed species is revealed for carbon monoxide.
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Affiliation(s)
- Jonas Heggemann
- Fachbereich
Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | | | - Ondřej Krejčí
- Department
of Applied Physics, Aalto University, Helsinki FI-00076, Finland
| | - Adam S. Foster
- Department
of Applied Physics, Aalto University, Helsinki FI-00076, Finland
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kanazawa 920-1192, Japan
| | - Philipp Rahe
- Fachbereich
Physik, Universität Osnabrück, 49076 Osnabrück, Germany
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6
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Carracedo-Cosme J, Romero-Muñiz C, Pou P, Pérez R. QUAM-AFM: A Free Database for Molecular Identification by Atomic Force Microscopy. J Chem Inf Model 2022; 62:1214-1223. [PMID: 35234034 PMCID: PMC9942089 DOI: 10.1021/acs.jcim.1c01323] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper introduces Quasar Science Resources-Autonomous University of Madrid atomic force microscopy image data set (QUAM-AFM), the largest data set of simulated atomic force microscopy (AFM) images generated from a selection of 685,513 molecules that span the most relevant bonding structures and chemical species in organic chemistry. QUAM-AFM contains, for each molecule, 24 3D image stacks, each consisting of constant-height images simulated for 10 tip-sample distances with a different combination of AFM operational parameters, resulting in a total of 165 million images with a resolution of 256 × 256 pixels. The 3D stacks are especially appropriate to tackle the goal of the chemical identification within AFM experiments by using deep learning techniques. The data provided for each molecule include, besides a set of AFM images, ball-and-stick depictions, IUPAC names, chemical formulas, atomic coordinates, and map of atom heights. In order to simplify the use of the collection as a source of information, we have developed a graphical user interface that allows the search for structures by CID number, IUPAC name, or chemical formula.
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Affiliation(s)
- Jaime Carracedo-Cosme
- Quasar
Science Resources S.L., Camino de las Ceudas 2, E-28232 Las Rozas de Madrid, Spain,Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Carlos Romero-Muñiz
- Departamento
de Física Aplicada I, Universidad
de Sevilla, E-41012 Seville, 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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7
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Zahl P, Yakutovich AV, Ventura-Macías E, Carracedo-Cosme J, Romero-Muñiz C, Pou P, Sadowski JT, Hybertsen MS, Pérez R. Hydrogen bonded trimesic acid networks on Cu(111) reveal how basic chemical properties are imprinted in HR-AFM images. NANOSCALE 2021; 13:18473-18482. [PMID: 34580697 DOI: 10.1039/d1nr04471k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High resolution non-contact atomic force microscopy measurements characterize assemblies of trimesic acid molecules on Cu(111) and the link group interactions, providing the first fingerprints utilizing CO-based probes for this widely studied paradigm for hydrogen bond driven molecular self assembly. The enhanced submolecular resolution offered by this technique uniquely reveals key aspects of the competing interactions. Accurate comparison between full-density-based modeled images and experiment allows to identify key structural elements in the assembly in terms of the electron-withdrawing character of the carboxylic groups, interactions of those groups with Cu atoms in the surface, and the valence electron density in the intermolecular region of the hydrogen bonds. This study of trimesic acid assemblies on Cu(111) combining high resolution atomic force microscopy measurements with theory and simulation forges clear connections between fundamental chemical properties of molecules and key features imprinted in force images with submolecular resolution.
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Affiliation(s)
- Percy Zahl
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Aliaksandr V Yakutovich
- Swiss Federal Laboratories for Materials Science and Technology (Empa), nanotech@surfaces laboratory, CH-8600 Dübendorf, Switzerland
| | - Emiliano Ventura-Macías
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Jaime Carracedo-Cosme
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Quasar Science Resources S.L., Camino de las Ceudas 2, E-28232 Las Rozas, Madrid, Spain
| | - Carlos Romero-Muñiz
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Ctra. Utrera Km. 1, E-41013, Seville, 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.
| | - Jerzy T Sadowski
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Mark S Hybertsen
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - 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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8
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Giessibl FJ. Probing the Nature of Chemical Bonds by Atomic Force Microscopy. Molecules 2021; 26:4068. [PMID: 34279408 PMCID: PMC8271455 DOI: 10.3390/molecules26134068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/24/2021] [Accepted: 06/26/2021] [Indexed: 11/16/2022] Open
Abstract
The nature of the chemical bond is important in all natural sciences, ranging from biology to chemistry, physics and materials science. The atomic force microscope (AFM) allows to put a single chemical bond on the test bench, probing its strength and angular dependence. We review experimental AFM data, covering precise studies of van-der-Waals-, covalent-, ionic-, metallic- and hydrogen bonds as well as bonds between artificial and natural atoms. Further, we discuss some of the density functional theory calculations that are related to the experimental studies of the chemical bonds. A description of frequency modulation AFM, the most precise AFM method, discusses some of the experimental challenges in measuring bonding forces. In frequency modulation AFM, forces between the tip of an oscillating cantilever change its frequency. Initially, cantilevers were made mainly from silicon. Most of the high precision measurements of bonding strengths by AFM became possible with a technology transfer from the quartz watch technology to AFM by using quartz-based cantilevers ("qPlus force sensors"), briefly described here.
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Affiliation(s)
- Franz J Giessibl
- Chair for Quantum Nanoscience, Institute of Experimental and Applied Physics, University of Regensburg, D-93040 Regensburg, Germany
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9
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Carracedo-Cosme J, Romero-Muñiz C, Pérez R. A Deep Learning Approach for Molecular Classification Based on AFM Images. NANOMATERIALS 2021; 11:nano11071658. [PMID: 34202532 PMCID: PMC8306777 DOI: 10.3390/nano11071658] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/13/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022]
Abstract
In spite of the unprecedented resolution provided by non-contact atomic force microscopy (AFM) with CO-functionalized and advances in the interpretation of the observed contrast, the unambiguous identification of molecular systems solely based on AFM images, without any prior information, remains an open problem. This work presents a first step towards the automatic classification of AFM experimental images by a deep learning model trained essentially with a theoretically generated dataset. We analyze the limitations of two standard models for pattern recognition when applied to AFM image classification and develop a model with the optimal depth to provide accurate results and to retain the ability to generalize. We show that a variational autoencoder (VAE) provides a very efficient way to incorporate, from very few experimental images, characteristic features into the training set that assure a high accuracy in the classification of both theoretical and experimental images.
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Affiliation(s)
- Jaime Carracedo-Cosme
- Quasar Science Resources S.L., Camino de las Ceudas 2, E-28232 Las Rozas de Madrid, Spain;
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Carlos Romero-Muñiz
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Ctra. Utrera Km. 1, E-41013 Seville, Spain;
- Departamento de Física Aplicada I, Universidad de Sevilla, E-41012 Seville, 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
- Correspondence:
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10
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Omidian M, Leitherer S, Néel N, Brandbyge M, Kröger J. Electric-Field Control of a Single-Atom Polar Bond. PHYSICAL REVIEW LETTERS 2021; 126:216801. [PMID: 34114869 DOI: 10.1103/physrevlett.126.216801] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/07/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
We expose the polar covalent bond between a single Au atom terminating the apex of an atomic force microscope tip and a C atom of graphene on SiC(0001) to an external electric field. For one field orientation, the Au─C bond is strong enough to sustain the mechanical load of partially detached graphene, while for the opposite orientation, the bond breaks easily. Calculations based on density-functional theory and nonequilibrium Green's function methods support the experimental observations by unveiling bond forces that reflect the polar character of the bond. Field-induced charge transfer between the atomic orbitals modifies the polarity of the different electronegative reaction partners and the Au─C bond strength.
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Affiliation(s)
- M Omidian
- Institut für Physik, Technische Universität Ilmenau, D-98693 Ilmenau, Germany
| | - S Leitherer
- Center of Nanostructured Graphene, Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - N Néel
- Institut für Physik, Technische Universität Ilmenau, D-98693 Ilmenau, Germany
| | - M Brandbyge
- Center of Nanostructured Graphene, Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - J Kröger
- Institut für Physik, Technische Universität Ilmenau, D-98693 Ilmenau, Germany
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11
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Weymouth AJ, Riegel E, Simmet B, Gretz O, Giessibl FJ. Lateral Force Microscopy Reveals the Energy Barrier of a Molecular Switch. ACS NANO 2021; 15:3264-3271. [PMID: 33523628 DOI: 10.1021/acsnano.0c09965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Copper phthalocyanine (CuPc) is a small molecule often used in organic light emitting diodes where it is deposited on a conducting electrode. Previous scanning tunneling microscopy (STM) studies of CuPc on Cu(111) have shown that inelastic tunneling events can cause CuPc to switch between a ground state and two symmetrically equivalent metastable states in which the molecule is rotated. We investigated CuPc on Cu(111) and Ag(111) with STM and lateral force microscopy (LFM). Even without inelastic events, the presence of the tip can induce rotations and upon closer approach, causes the rotated states to be favored. Combining STM measurements at various temperatures and LFM measurements, we show that the long-range attraction of the tip changes the potential energy landscape of this molecular switch. We can also determine the geometry of the rotated and ground states. We compare our observations of CuPc on Cu(111) to CuPc on Ag(111). On Ag(111), CuPc appears flat and does not rotate. Stronger bonding typically involves shorter bond lengths, larger shifts of energy levels, and structural stability. Although the binding of CuPc to Cu(111) is stronger than that on Ag(111), the nonplanar geometry of CuPc on Cu(111) is accompanied by two metastable states which are not present on the Ag(111) surface.
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Affiliation(s)
| | | | | | - Oliver Gretz
- University of Regensburg, Regensburg 93053, Germany
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12
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Larson AM, Balema TA, Zahl P, Schilling AC, Stacchiola DJ, Sykes ECH. Hypothetical Efficiency of Electrical to Mechanical Energy Transfer during Individual Stochastic Molecular Switching Events. ACS NANO 2020; 14:16558-16564. [PMID: 32946215 DOI: 10.1021/acsnano.0c04082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
There are now many examples of single molecule rotors, motors, and switches in the literature that, when driven by photons, electrons, or chemical reactions, exhibit well-defined motions. As a step toward using these single molecule devices to perform useful functions, one must understand how they interact with their environment and quantify their ability to perform work on it. Using a single molecule rotary switch, we examine the transfer of electrical energy, delivered via electron tunneling, to mechanical motion and measure the forces the switch experiences with a noncontact q-plus atomic force microscope. Action spectra reveal that the molecular switch has two stable states and can be excited resonantly between them at a bias of 100 mV via a one-electron inelastic tunneling process which corresponds to an energy input of 16 zJ. While the electrically induced switching events are stochastic and no net work is done on the cantilever, by measuring the forces between the molecular switch and the AFM cantilever, we can derive the maximum hypothetical work the switch could perform during a single switching event, which is ∼55 meV, equal to 8.9 zJ, which translates to a hypothetical efficiency of ∼55% per individual inelastic tunneling electron-induced switching event. When considering the total electrical energy input, this drops to 1 × 10-7% due to elastic tunneling events that dominate the tunneling current. However, this approach constitutes a general method for quantifying and comparing the energy input and output of molecular-mechanical devices.
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Affiliation(s)
- Amanda M Larson
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Tedros A Balema
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Percy Zahl
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Alex C Schilling
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Dario J Stacchiola
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - E Charles H Sykes
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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13
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Tschakert J, Zhong Q, Martin-Jimenez D, Carracedo-Cosme J, Romero-Muñiz C, Henkel P, Schlöder T, Ahles S, Mollenhauer D, Wegner HA, Pou P, Pérez R, Schirmeisen A, Ebeling D. Surface-controlled reversal of the selectivity of halogen bonds. Nat Commun 2020; 11:5630. [PMID: 33159060 PMCID: PMC7648107 DOI: 10.1038/s41467-020-19379-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/01/2020] [Indexed: 11/08/2022] Open
Abstract
Intermolecular halogen bonds are ideally suited for designing new molecular assemblies because of their strong directionality and the possibility of tuning the interactions by using different types of halogens or molecular moieties. Due to these unique properties of the halogen bonds, numerous areas of application have recently been identified and are still emerging. Here, we present an approach for controlling the 2D self-assembly process of organic molecules by adsorption to reactive vs. inert metal surfaces. Therewith, the order of halogen bond strengths that is known from gas phase or liquids can be reversed. Our approach relies on adjusting the molecular charge distribution, i.e., the σ-hole, by molecule-substrate interactions. The polarizability of the halogen and the reactiveness of the metal substrate are serving as control parameters. Our results establish the surface as a control knob for tuning molecular assemblies by reversing the selectivity of bonding sites, which is interesting for future applications.
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Affiliation(s)
- Jalmar Tschakert
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
| | - Qigang Zhong
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
| | - Daniel Martin-Jimenez
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
| | - Jaime Carracedo-Cosme
- Quasar Science Resources S.L., Camino de las Ceudas 2, E-28232, Las Rozas de Madrid, Spain
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Carlos Romero-Muñiz
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Ctra. Utrera Km. 1, E-41013, Seville, Spain
| | - Pascal Henkel
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Tobias Schlöder
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sebastian Ahles
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Doreen Mollenhauer
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Hermann A Wegner
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - 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
| | - André Schirmeisen
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
| | - Daniel Ebeling
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany.
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany.
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14
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Schneider S, Hoffmann-Vogel R. Electrostatic forces above graphene nanoribbons and edges interpreted as partly hydrogen-free. NANOSCALE 2020; 12:17895-17901. [PMID: 32844849 DOI: 10.1039/d0nr03348k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Graphene nanoribbons' electronic transport properties strongly depend on the type of edge, armchair, zigzag or other, and on edge functionalization that can be used for band-gap engineering. For only partly hydrogenated edges interesting magnetic properties are predicted. Electric charge accumulates at edges and corners. Scanning force microscopy has so far shown the centre of graphene nanoribbons with atomic resolution using a quartz crystal tuning fork sensor of high stiffness. Weak long-range electrostatic forces related to the charge accumulation on the edges of graphene nanoribbons could not be imaged so far. Here, we show the electrostatic forces at the corners and edges of graphene nanoribbons are amenable to measurement. We use soft cantilevers and a bimodal imaging technique to combine enhanced sensitivity to weak long-range electrostatic forces with the high resolution of the second-frequency shift. Additionally, in our work the edges of the nanoribbons are mainly hydrogen-free, opening to the route to investigations of partly hydrogenated magnetic nanoribbons.
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Affiliation(s)
- Sebastian Schneider
- Physikalisches Institut, Karlsruhe Institute of Technology, Karlsruhe, Germany
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15
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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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16
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Doležal J, Mutombo P, Nachtigallová D, Jelínek P, Merino P, Švec M. Mechano-Optical Switching of a Single Molecule with Doublet Emission. ACS NANO 2020; 14:8931-8938. [PMID: 32539338 PMCID: PMC7116298 DOI: 10.1021/acsnano.0c03730] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The ability to control the emission from single-molecule quantum emitters is an important step toward their implementation in optoelectronic technology. Phthalocyanine and derived metal complexes on thin insulating layers studied by scanning tunneling microscope-induced luminescence (STML) offer an excellent playground for tuning their excitonic and electronic states by Coulomb interaction and to showcase their high environmental sensitivity. Copper phthalocyanine (CuPc) has an open-shell electronic structure, and its lowest-energy exciton is a doublet, which brings interesting prospects in its application for optospintronic devices. Here, we demonstrate that the excitonic state of a single CuPc molecule can be reproducibly switched by atomic-scale manipulations permitting precise positioning of the molecule on the NaCl ionic crystal lattice. Using a combination of STML, AFM, and ab initio calculations, we show the modulation of electronic and optical bandgaps and the exciton binding energy in CuPc by tens of meV. We explain this effect by spatially dependent Coulomb interaction occurring at the molecule-insulator interface, which tunes the local dielectric environment of the emitter.
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Affiliation(s)
- Jiří Doležal
- Institute of Physics, Czech Academy of Sciences, Praha, Czech Republic
- Faculty of Mathematics and Physics, Charles University, Praha, Czech Republic
| | - Pingo Mutombo
- Institute of Physics, Czech Academy of Sciences, Praha, Czech Republic
- Department of Petrochemistry and Refining, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Pavel Jelínek
- Institute of Physics, Czech Academy of Sciences, Praha, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Pablo Merino
- Instituto de Ciencia de Materiales de Madrid, CSIC, Sor Juana Inés de la Cruz 3, E28049, Madrid, Spain
- Instituto de Física Fundamental, CSIC, Serrano 121, E28006, Madrid, Spain
| | - Martin Švec
- Institute of Physics, Czech Academy of Sciences, Praha, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Šlechtitelů 27, 78371 Olomouc, Czech Republic
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17
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Sokolović I, Reticcioli M, Čalkovský M, Wagner M, Schmid M, Franchini C, Diebold U, Setvín M. Resolving the adsorption of molecular O 2 on the rutile TiO 2(110) surface by noncontact atomic force microscopy. Proc Natl Acad Sci U S A 2020; 117:14827-14837. [PMID: 32527857 PMCID: PMC7334520 DOI: 10.1073/pnas.1922452117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Interaction of molecular oxygen with semiconducting oxide surfaces plays a key role in many technologies. The topic is difficult to approach both by experiment and in theory, mainly due to multiple stable charge states, adsorption configurations, and reaction channels of adsorbed oxygen species. Here we use a combination of noncontact atomic force microscopy (AFM) and density functional theory (DFT) to resolve [Formula: see text] adsorption on the rutile [Formula: see text](110) surface, which presents a longstanding challenge in the surface chemistry of metal oxides. We show that chemically inert AFM tips terminated by an oxygen adatom provide excellent resolution of both the adsorbed species and the oxygen sublattice of the substrate. Adsorbed [Formula: see text] molecules can accept either one or two electron polarons from the surface, forming superoxo or peroxo species. The peroxo state is energetically preferred under any conditions relevant for applications. The possibility of nonintrusive imaging allows us to explain behavior related to electron/hole injection from the tip, interaction with UV light, and the effect of thermal annealing.
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Affiliation(s)
- Igor Sokolović
- Institute of Applied Physics, Technische Universität Wien, 1040 Vienna, Austria
| | - Michele Reticcioli
- Institute of Applied Physics, Technische Universität Wien, 1040 Vienna, Austria
- Faculty of Physics, University of Vienna, 1090 Vienna, Austria
- Center for Computational Materials Science, University of Vienna, 1090 Vienna, Austria
| | - Martin Čalkovský
- Institute of Applied Physics, Technische Universität Wien, 1040 Vienna, Austria
- Institute of Physical Engineering, Brno University of Technology, 616 69 Brno, Czech Republic
| | - Margareta Wagner
- Institute of Applied Physics, Technische Universität Wien, 1040 Vienna, Austria
- Central European Institute of Technology, Brno University of Technology, 612 00 Brno, Czech Republic
| | - Michael Schmid
- Institute of Applied Physics, Technische Universität Wien, 1040 Vienna, Austria
| | - Cesare Franchini
- Faculty of Physics, University of Vienna, 1090 Vienna, Austria
- Center for Computational Materials Science, University of Vienna, 1090 Vienna, Austria
- Dipartimento di Fisica e Astronomia, Università di Bologna, 40127 Bologna, Italy
| | - Ulrike Diebold
- Institute of Applied Physics, Technische Universität Wien, 1040 Vienna, Austria
| | - Martin Setvín
- Institute of Applied Physics, Technische Universität Wien, 1040 Vienna, Austria;
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University, 180 00 Prague 8, Czech Republic
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18
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Fatayer S, Albrecht F, Zhang Y, Urbonas D, Peña D, Moll N, Gross L. Molecular structure elucidation with charge-state control. SCIENCE (NEW YORK, N.Y.) 2020; 365:142-145. [PMID: 31296763 DOI: 10.1126/science.aax5895] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/12/2019] [Indexed: 11/02/2022]
Abstract
The charge state of a molecule governs its physicochemical properties, such as conformation, reactivity, and aromaticity, with implications for on-surface synthesis, catalysis, photoconversion, and applications in molecular electronics. On insulating, multilayer sodium chloride (NaCl) films, we controlled the charge state of organic molecules and resolved their structures in neutral, cationic, anionic, and dianionic states by atomic force microscopy, obtaining atomic resolution and bond-order discrimination using carbon monoxide (CO)-functionalized tips. We detected changes in conformation, adsorption geometry, and bond-order relations for azobenzene, tetracyanoquinodimethane, and pentacene in multiple charge states. Moreover, for porphine, we investigate the charge state-dependent change of aromaticity and conjugation pathway in the macrocycle. This work opens the way to studying chemical-structural changes of individual molecules for a wide range of charge states.
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Affiliation(s)
| | | | - Yunlong Zhang
- ExxonMobil Research and Engineering Company, Annandale, NJ 08801, USA
| | | | - Diego Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Nikolaj Moll
- IBM Research-Zurich, Rueschlikon 8803, Switzerland
| | - Leo Gross
- IBM Research-Zurich, Rueschlikon 8803, Switzerland.
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19
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Berwanger J, Polesya S, Mankovsky S, Ebert H, Giessibl FJ. Atomically Resolved Chemical Reactivity of Small Fe Clusters. PHYSICAL REVIEW LETTERS 2020; 124:096001. [PMID: 32202857 DOI: 10.1103/physrevlett.124.096001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Small metal clusters have been investigated for decades due to their beneficial catalytic activity. It was found that edges are most reactive and the number of catalytic events increases with the cluster's size. However, a direct measurement of chemical reactivity of individual atoms within the clusters has not been reported yet. We combine the high-resolution capability of CO-terminated tips in scanning probe microscopy with their ability to probe chemical binding forces on single Fe atoms to study the chemical reactivity of atom-by-atom assembled Fe clusters from 1 to 15 atoms on the atomic scale. We find that the chemical reactivity of individual atoms within flat Fe clusters does not depend on the cluster size but on the coordination number of the investigated atom. Furthermore, we explain the atomic contrast of the investigated Fe clusters by relating the force spectra of individual atoms with atomic force microscopy images of the clusters.
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Affiliation(s)
- Julian Berwanger
- Institute of Experimental and Applied Physics, University of Regensburg, 93040 Regensburg, Germany
| | - Svitlana Polesya
- Department of Chemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Sergiy Mankovsky
- Department of Chemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Hubert Ebert
- Department of Chemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Franz J Giessibl
- Institute of Experimental and Applied Physics, University of Regensburg, 93040 Regensburg, Germany
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20
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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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21
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Sweetman A, Champness NR, Saywell A. On-surface chemical reactions characterised by ultra-high resolution scanning probe microscopy. Chem Soc Rev 2020; 49:4189-4202. [DOI: 10.1039/d0cs00166j] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The impact of high resolution scanning probe microscopy on imaging individual molecules with intramolecular resolution is reviewed.
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Affiliation(s)
- Adam Sweetman
- School of Physics and Astronomy
- University of Leeds
- Leeds
- UK
| | | | - Alex Saywell
- School of Physics and Astronomy
- University of Nottingham
- Nottingham
- UK
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22
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Cao D, Song Y, Peng J, Ma R, Guo J, Chen J, Li X, Jiang Y, Wang E, Xu L. Advances in Atomic Force Microscopy: Weakly Perturbative Imaging of the Interfacial Water. Front Chem 2019; 7:626. [PMID: 31572715 PMCID: PMC6751248 DOI: 10.3389/fchem.2019.00626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/30/2019] [Indexed: 11/17/2022] Open
Abstract
The structure and dynamics of interfacial water, determined by the water-interface interactions, are important for a wide range of applied fields and natural processes, such as water diffusion (Kim et al., 2013), electrochemistry (Markovic, 2013), heterogeneous catalysis (Over et al., 2000), and lubrication (Zilibotti et al., 2013). The precise understanding of water-interface interactions largely relies on the development of atomic-scale experimental techniques (Guo et al., 2014) and computational methods (Hapala et al., 2014b). Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields (Ichii et al., 2012; Shiotari and Sugimoto, 2017; Peng et al., 2018a). In this perspective, we review the recent progress in the noncontact atomic force microscopy (nc-AFM) imaging and AFM simulation techniques and discuss how the newly developed techniques are applied to study the properties of interfacial water. The nc-AFM with the quadrupole-like CO-terminated tip can achieve ultrahigh-resolution imaging of the interfacial water on different surfaces, trace the reconstruction of H-bonding network and determine the intrinsic structures of the weakly bonded water clusters and even their metastable states. In the end, we present an outlook on the directions of future AFM studies of interfacial water as well as the challenges faced by this field.
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Affiliation(s)
- Duanyun Cao
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China
| | - Yizhi Song
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China
| | - Jinbo Peng
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China.,Institute of Experimental and Applied Physics, University of Regensburg, Regensburg, Germany
| | - Runze Ma
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China
| | - Jing Guo
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Ji Chen
- School of Physics, Peking University, Beijing, China
| | - Xinzheng Li
- School of Physics, Peking University, Beijing, China.,Collaborative Innovation Center of Quantum Matter, Beijing, China
| | - Ying Jiang
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China.,Collaborative Innovation Center of Quantum Matter, Beijing, China.,CAS Center for Excellence in Topological Quantum Computation, University of Chinese Academy of Sciences, Beijing, China
| | - Enge Wang
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China.,Ceramics Division, Songshan Lake Materials Lab, Institute of Physics, Chinese Academy of Sciences, Guangdong, China.,School of Physics, Liaoning University, Shenyang, China
| | - Limei Xu
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China.,Collaborative Innovation Center of Quantum Matter, Beijing, China
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23
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Pozo I, Majzik Z, Pavliček N, Melle-Franco M, Guitián E, Peña D, Gross L, Pérez D. Revisiting Kekulene: Synthesis and Single-Molecule Imaging. J Am Chem Soc 2019; 141:15488-15493. [PMID: 31525873 PMCID: PMC6786662 DOI: 10.1021/jacs.9b07926] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Four decades after the first (and only) reported synthesis of kekulene, this emblematic cycloarene has been obtained again through an improved route involving the construction of a key synthetic intermediate, 5,6,8,9-tetrahydrobenzo[m]tetraphene, by means of a double Diels-Alder reaction between styrene and a versatile benzodiyne synthon. Ultra-high-resolution AFM imaging of single molecules of kekulene and computational calculations provide additional support for a molecular structure with a significant degree of bond localization in accordance with the resonance structure predicted by the Clar model.
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Affiliation(s)
- Iago Pozo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Zsolt Majzik
- IBM Research-Zürich , 8803 Rüschlikon , Switzerland
| | | | - Manuel Melle-Franco
- CICECO, Aveiro Institute of Materials, Department of Chemistry , University of Aveiro , 3810-193 Aveiro , Portugal
| | - Enrique Guitián
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Diego Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Leo Gross
- IBM Research-Zürich , 8803 Rüschlikon , Switzerland
| | - Dolores Pérez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
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24
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Kaiser K, Scriven LM, Schulz F, Gawel P, Gross L, Anderson HL. An sp-hybridized molecular carbon allotrope, cyclo[18]carbon. Science 2019; 365:1299-1301. [DOI: 10.1126/science.aay1914] [Citation(s) in RCA: 277] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/02/2019] [Indexed: 01/25/2023]
Abstract
Carbon allotropes built from rings of two-coordinate atoms, known as cyclo[n]carbons, have fascinated chemists for many years, but until now they could not be isolated or structurally characterized because of their high reactivity. We generated cyclo[18]carbon (C18) using atom manipulation on bilayer NaCl on Cu(111) at 5 kelvin by eliminating carbon monoxide from a cyclocarbon oxide molecule, C24O6. Characterization of cyclo[18]carbon by high-resolution atomic force microscopy revealed a polyynic structure with defined positions of alternating triple and single bonds. The high reactivity of cyclocarbon and cyclocarbon oxides allows covalent coupling between molecules to be induced by atom manipulation, opening an avenue for the synthesis of other carbon allotropes and carbon-rich materials from the coalescence of cyclocarbon molecules.
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Martin-Jimenez D, Ahles S, Mollenhauer D, Wegner HA, Schirmeisen A, Ebeling D. Bond-Level Imaging of the 3D Conformation of Adsorbed Organic Molecules Using Atomic Force Microscopy with Simultaneous Tunneling Feedback. PHYSICAL REVIEW LETTERS 2019; 122:196101. [PMID: 31144947 DOI: 10.1103/physrevlett.122.196101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Indexed: 06/09/2023]
Abstract
The chemical structure and orientation of molecules on surfaces can be visualized using low temperature atomic force microscopy with CO-functionalized tips. Conventionally, this is done in constant-height mode by measuring the frequency shift of the oscillating force sensor. However, this method is unsuitable for analyzing 3D objects. We are using the tunneling current to track the topography while simultaneously obtaining submolecular resolution from the frequency shift signal. Thereby, the conformation of 3D molecules and the adsorption sites on the atomic lattice can be reliably determined.
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Affiliation(s)
- Daniel Martin-Jimenez
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Sebastian Ahles
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Doreen Mollenhauer
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Hermann A Wegner
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Andre Schirmeisen
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Daniel Ebeling
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
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26
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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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27
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Nazriq NKM, Minamitani E, Yamada TK. CO-tip manipulation using repulsive interactions. NANOTECHNOLOGY 2018; 29:495701. [PMID: 30207541 DOI: 10.1088/1361-6528/aae0df] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the interactions between a tip apex and a target atom or molecule is crucial for the manipulation of individual molecules with precise control by using scanning tunnelling microscopy (STM) and atomic force microscopy. Herein, we demonstrate the manipulation of target CO molecules on a Cu(111) substrate using a CO-functionalized W tip with atomic-scale accuracy. All experiments were performed in a home-built ultra-high vacuum STM system at 5 K. The CO-tip was fabricated by picking up a single CO molecule from a Cu(111) surface. In contrast to a metal tip, repulsive interactions occur between the CO-tip and the target CO molecule. This repulsive interaction promises perfect lateral hopping without any vertical hopping. Hopping events were directly monitored as sudden current drops in the simultaneously measured I-z curves. A larger barrier height between the CO-tip and the target CO (∼9.5 eV) was found from the slope of the I-z curve, which decreases the electron tunnelling probability between the tip and sample. Therefore, electron-driven manipulation cannot be a major trigger for the CO-CO repulsive manipulation. The CO-tip is able to manipulate only the target CO molecule, even when another CO molecule was located ∼0.5 nm away. Statistical measurements revealed that the nearest neighbour atop site is the energetically stable position after hopping. However, if the CO target has another CO molecule in a neighbouring position (denoted as a 'pair'), the target CO hops more than twice as far. This means that the CO-tip experiences a larger repulsive interaction from the pair. These observations of CO-tip manipulation are useful for the design of two-dimensional artificial molecular networks as well as for developing a better understanding of catalytic oxidation processes.
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Affiliation(s)
- Nana K M Nazriq
- Department of Materials Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
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28
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Neves MMPDS, Martín-Yerga D. Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging. BIOSENSORS 2018; 8:E100. [PMID: 30373209 PMCID: PMC6316691 DOI: 10.3390/bios8040100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023]
Abstract
Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.
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Affiliation(s)
| | - Daniel Martín-Yerga
- Department of Chemical Engineering, KTH Royal Institute of Technology, 100-44 Stockholm, Sweden.
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29
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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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30
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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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31
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Lee J, Tallarida N, Chen X, Jensen L, Apkarian VA. Microscopy with a single-molecule scanning electrometer. SCIENCE ADVANCES 2018; 4:eaat5472. [PMID: 29963637 PMCID: PMC6025905 DOI: 10.1126/sciadv.aat5472] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/17/2018] [Indexed: 05/13/2023]
Abstract
The vibrational spectrum of a single carbon monoxide molecule, adsorbed on the tip apex of a scanning tunneling microscope, is used to image electrostatic fields with submolecular spatial resolution. The method takes advantage of the vibrational Stark effect to image local electrostatic fields and the single-molecule sensitivity of tip-enhanced Raman scattering (TERS) to optically relay the signal. We apply the method to single metalloporphyrins adsorbed on Au(111) to image molecular charges, intramolecular polarization, local photoconductivity, atomically resolved hydrogen bonds, and surface electron density waves.
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Affiliation(s)
- Joonhee Lee
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Corresponding author. (J.L.); (L.J.); (V.A.A.)
| | - Nicholas Tallarida
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Xing Chen
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Lasse Jensen
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Corresponding author. (J.L.); (L.J.); (V.A.A.)
| | - V. Ara Apkarian
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Corresponding author. (J.L.); (L.J.); (V.A.A.)
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32
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The effect of hydration number on the interfacial transport of sodium ions. Nature 2018; 557:701-705. [DOI: 10.1038/s41586-018-0122-2] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/05/2018] [Indexed: 11/08/2022]
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Mönig H, Amirjalayer S, Timmer A, Hu Z, Liu L, Díaz Arado O, Cnudde M, Strassert CA, Ji W, Rohlfing M, Fuchs H. Quantitative assessment of intermolecular interactions by atomic force microscopy imaging using copper oxide tips. NATURE NANOTECHNOLOGY 2018; 13:371-375. [PMID: 29632397 DOI: 10.1038/s41565-018-0104-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 02/22/2018] [Indexed: 05/10/2023]
Abstract
Atomic force microscopy is an impressive tool with which to directly resolve the bonding structure of organic compounds1-5. The methodology usually involves chemical passivation of the probe-tip termination by attaching single molecules or atoms such as CO or Xe (refs 1,6-9). However, these probe particles are only weakly connected to the metallic apex, which results in considerable dynamic deflection. This probe particle deflection leads to pronounced image distortions, systematic overestimation of bond lengths, and in some cases even spurious bond-like contrast features, thus inhibiting reliable data interpretation8-12. Recently, an alternative approach to tip passivation has been used in which slightly indenting a tip into oxidized copper substrates and subsequent contrast analysis allows for the verification of an oxygen-terminated Cu tip13-15. Here we show that, due to the covalently bound configuration of the terminal oxygen atom, this copper oxide tip (CuOx tip) has a high structural stability, allowing not only a quantitative determination of individual bond lengths and access to bond order effects, but also reliable intermolecular bond characterization. In particular, by removing the previous limitations of flexible probe particles, we are able to provide conclusive experimental evidence for an unusual intermolecular N-Au-N three-centre bond. Furthermore, we demonstrate that CuOx tips allow the characterization of the strength and configuration of individual hydrogen bonds within a molecular assembly.
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Affiliation(s)
- Harry Mönig
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany.
- Center for Nanotechnology, Münster, Germany.
| | - Saeed Amirjalayer
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Center for Nanotechnology, Münster, Germany
| | - Alexander Timmer
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Center for Nanotechnology, Münster, Germany
| | - Zhixin Hu
- Center for Joint Quantum Studies and Department of Physics, Tianjin University, Tianjin, China
| | - Lacheng Liu
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Center for Nanotechnology, Münster, Germany
| | - Oscar Díaz Arado
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Center for Nanotechnology, Münster, Germany
| | - Marvin Cnudde
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Center for Nanotechnology, Münster, Germany
| | - Cristian Alejandro Strassert
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Center for Nanotechnology, Münster, Germany
| | - Wei Ji
- Department of Physics and Beijing Key Laboratory of Optoelectronic Functional Materials & Micro-Nano Devices, Renmin University of China, Beijing, China
| | - Michael Rohlfing
- Institut für Festkörpertheorie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Harald Fuchs
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Center for Nanotechnology, Münster, Germany
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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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35
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Gross L, Schuler B, Pavliček N, Fatayer S, Majzik Z, Moll N, Peña D, Meyer G. Rasterkraftmikroskopie für die molekulare Strukturaufklärung. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201703509] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Leo Gross
- IBM Research - Zürich; 8803 Rüschlikon Schweiz
| | - Bruno Schuler
- IBM Research - Zürich; 8803 Rüschlikon Schweiz
- Molecular Foundry; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
| | | | | | | | | | - Diego Peña
- Centro de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; Santiago de Compostela 15782 Spanien
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36
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Gross L, Schuler B, Pavliček N, Fatayer S, Majzik Z, Moll N, Peña D, Meyer G. Atomic Force Microscopy for Molecular Structure Elucidation. Angew Chem Int Ed Engl 2018; 57:3888-3908. [DOI: 10.1002/anie.201703509] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/14/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Leo Gross
- IBM Research-Zurich; 8803 Rüschlikon Switzerland
| | - Bruno Schuler
- IBM Research-Zurich; 8803 Rüschlikon Switzerland
- Current address: Molecular Foundry; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
| | | | | | - Zsolt Majzik
- IBM Research-Zurich; 8803 Rüschlikon Switzerland
| | - Nikolaj Moll
- IBM Research-Zurich; 8803 Rüschlikon Switzerland
| | - Diego Peña
- Centro de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; Santiago de Compostela 15782 Spain
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37
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Miller H, Zhou Z, Shepherd J, Wollman AJM, Leake MC. Single-molecule techniques in biophysics: a review of the progress in methods and applications. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:024601. [PMID: 28869217 DOI: 10.1088/1361-6633/aa8a02] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.
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Affiliation(s)
- Helen Miller
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom
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38
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Weakly perturbative imaging of interfacial water with submolecular resolution by atomic force microscopy. Nat Commun 2018; 9:122. [PMID: 29317638 PMCID: PMC5760619 DOI: 10.1038/s41467-017-02635-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/15/2017] [Indexed: 11/11/2022] Open
Abstract
Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields but the disturbance of the probes on the hydrogen-bonding structure of water has remained an intractable problem. Here, we report submolecular-resolution imaging of the water clusters on a NaCl(001) surface within the nearly noninvasive region by a qPlus-based noncontact atomic force microscopy. Comparison with theoretical simulations reveals that the key lies in probing the weak high-order electrostatic force between the quadrupole-like CO-terminated tip and the polar water molecules at large tip–water distances. This interaction allows the imaging and structural determination of the weakly bonded water clusters and even of their metastable states with negligible disturbance. This work may open an avenue for studying the intrinsic structure and dynamics of ice or water on surfaces, ion hydration, and biological water with atomic precision. Scanning probe microscopy has been extensively applied to probe interfacial water but the probes tend to disturb the structure of water easily. Here, the authors report submolecular-resolution imaging of water clusters within the nearly non-invasive region by qPlus noncontact atomic force microscopy.
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Tallarida N, Lee J, Apkarian VA. Tip-Enhanced Raman Spectromicroscopy on the Angstrom Scale: Bare and CO-Terminated Ag Tips. ACS NANO 2017; 11:11393-11401. [PMID: 28980800 DOI: 10.1021/acsnano.7b06022] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The tip is key to the successful execution of tip-enhanced Raman scattering (TERS) measurements in the single molecule limit. We show that nanoscopically smooth silver tips, batch produced through field-directed sputter sharpening, reliably attain TERS with enhancement factors that reach 1013, as measured by the Raman spectra of single CO molecules attached to the tip apex. We validate the bare tips by demonstrating spectromicroscopy with submolecular spatial resolution and underscore that TERS is a near-field effect that does not obey simple selection rules. As a more gainful analytical approach, we introduce TERS-relayed molecular force microscopy using CO-terminated tips. By taking advantage of the large Stark tuning rate of the CO stretch, molecular structure and charges can be imaged with atomic resolution. As illustration, we image a single Ag atom adsorbed on Au(111) and show that the adatom carries +0.2e charge.
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Affiliation(s)
- Nicholas Tallarida
- Department of Chemistry, University of California at Irvine , Irvine, California 92697-2025, United States
| | - Joonhee Lee
- Department of Chemistry, University of California at Irvine , Irvine, California 92697-2025, United States
| | - Vartkess Ara Apkarian
- Department of Chemistry, University of California at Irvine , Irvine, California 92697-2025, United States
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Buchmann K, Hauptmann N, Foster AS, Berndt R. Submolecular resolution in scanning probe images of Sn-phthalocyanines on Cu(1 0 0) using metal tips. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:394004. [PMID: 28677588 DOI: 10.1088/1361-648x/aa7dbd] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single Sn-phthalocyanine (SnPc) molecules adsorb on Cu(1 0 0) with the Sn ion above (Sn-up) or below (Sn-down) the molecular plane. Here we use a combination of atomic force microscopy (AFM), scanning tunnelling microscopy (STM) and first principles calculations to understand the adsorption configuration and origin of observed contrast of molecules in the Sn-down state. AFM with metallic tips images the pyrrole nitrogen atoms in these molecules as attractive features while STM reveals a chirality of the electronic structure of the molecules close to the Fermi level [Formula: see text] which is not observed in AFM. Using density functional theory calculations, the origin of the submolecular contrast is analysed and, while the electrostatic forces turn out to be negligible, the van der Waals interaction between the phenyl rings of SnPc and the substrate deform the molecule, push the pyrrole nitrogen atoms away from the substrate and thus induce the observed submolecular contrast. Simulated STM images reproduce the chirality of the electronic structure near [Formula: see text].
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Affiliation(s)
- Kristof Buchmann
- Institut für Experimentelle und Angewandte Physik, Christian-Albrechts-Universität zu Kiel, D-24098 Kiel, Germany
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Jelínek P. High resolution SPM imaging of organic molecules with functionalized tips. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:343002. [PMID: 28749786 DOI: 10.1088/1361-648x/aa76c7] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
One of the most remarkable and exciting achievements in the field of scanning probe microscopy (SPM) in the last years is the unprecedented sub-molecular resolution of both atomic and electronic structures of single molecules deposited on solid state surfaces. Despite its youth, the technique has already brought many new possibilities to perform different kinds of measurements, which cannot be accomplished by other techniques. This opens new perspectives in advanced characterization of physical and chemical processes and properties of molecular structures on surfaces. Here, we discuss the history and recent progress of the high resolution imaging with a functionalized probe by means of atomic force microscopy (AFM), scanning tunnelling microscopy (STM) and inelastic electron tunneling spectroscopy (IETS). We describe the mechanisms responsible for the high-resolution AFM, STM and IETS-STM contrast. The complexity of this technique requires new theoretical approaches, where a relaxation of the functionalized probe is considered. We emphasise the similarities of the mechanism driving high-resolution SPM with other imaging methods. We also summarise briefly significant achievements and progress in different branches. Finally we provide brief perspectives and remaining challenges of the further refinement of these high-resolution methods.
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Affiliation(s)
- Pavel Jelínek
- Institute of Physics, Czech Academy of Sciences, Cukrovarnická 10, 162 00, Prague, Czech Republic
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Kawai S, Nishiuchi T, Kodama T, Spijker P, Pawlak R, Meier T, Tracey J, Kubo T, Meyer E, Foster AS. Direct quantitative measurement of the C═O⋅⋅⋅H-C bond by atomic force microscopy. SCIENCE ADVANCES 2017; 3:e1603258. [PMID: 28508080 PMCID: PMC5429039 DOI: 10.1126/sciadv.1603258] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/14/2017] [Indexed: 05/05/2023]
Abstract
The hydrogen atom-the smallest and most abundant atom-is of utmost importance in physics and chemistry. Although many analysis methods have been applied to its study, direct observation of hydrogen atoms in a single molecule remains largely unexplored. We use atomic force microscopy (AFM) to resolve the outermost hydrogen atoms of propellane molecules via very weak C═O⋅⋅⋅H-C hydrogen bonding just before the onset of Pauli repulsion. The direct measurement of the interaction with a hydrogen atom paves the way for the identification of three-dimensional molecules such as DNAs and polymers, building the capabilities of AFM toward quantitative probing of local chemical reactivity.
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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
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Tomohiko Nishiuchi
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Takuya Kodama
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Peter Spijker
- Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, PO Box 11100, FI-00076 Aalto, Finland
| | - 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
- Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, PO Box 11100, FI-00076 Aalto, Finland
| | - Takashi Kubo
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Ernst Meyer
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - Adam S. Foster
- Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, PO Box 11100, FI-00076 Aalto, Finland
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
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Zint S, Ebeling D, Schlöder T, Ahles S, Mollenhauer D, Wegner HA, Schirmeisen A. Imaging Successive Intermediate States of the On-Surface Ullmann Reaction on Cu(111): Role of the Metal Coordination. ACS NANO 2017; 11:4183-4190. [PMID: 28346826 DOI: 10.1021/acsnano.7b01109] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The in-depth knowledge about on-surface reaction mechanisms is crucial for the tailor-made design of covalently bonded organic frameworks, for applications such as nanoelectronic or -optical devices. Latest developments in atomic force microscopy, which rely on functionalizing the tip with single CO molecules at low temperatures, allow to image molecular systems with submolecular resolution. Here, we are using this technique to study the complete reaction pathway of the on-surface Ullmann-type coupling between bromotriphenylene molecules on a Cu(111) surface. All steps of the Ullmann reaction, i.e., bromotriphenylenes, triphenylene radicals, organometallic intermediates, and bistriphenylenes, were imaged with submolecular resolution. Together with density functional theory calculations with dispersion correction, our study allows to address the long-standing question of how the organometallic intermediates are coordinated via Cu surface or adatoms.
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Affiliation(s)
- Sören Zint
- Institute of Applied Physics (IAP), Justus Liebig University Giessen , Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Daniel Ebeling
- Institute of Applied Physics (IAP), Justus Liebig University Giessen , Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | | | | | | | | | - André Schirmeisen
- Institute of Applied Physics (IAP), Justus Liebig University Giessen , Heinrich-Buff-Ring 16, 35392 Giessen, Germany
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Pavliček N, Gross L. Generation, manipulation and characterization of molecules by atomic force microscopy. Nat Rev Chem 2017. [DOI: 10.1038/s41570-016-0005] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Hauptmann N, Robles R, Abufager P, Lorente N, Berndt R. AFM Imaging of Mercaptobenzoic Acid on Au(110): Submolecular Contrast with Metal Tips. J Phys Chem Lett 2016; 7:1984-1990. [PMID: 27183144 DOI: 10.1021/acs.jpclett.6b00684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A self-assembled monolayer of mercaptobenzoic acid (MBA) on Au(110) is investigated with scanning tunneling and atomic force microscopy (STM and AFM) and density functional calculations. High-resolution AFM images obtained with metallic tips show clear contrasts between oxygen atoms and phenyl moieties. The contrast above the oxygen atoms is due to attractive covalent interactions, which is different than previously reported high-resolution images, where Pauli repulsion dominated the image contrast. We show that the bonding of MBA to the substrate occurs mainly through dispersion interactions, whereas the thiol-Au bond contributes only a quarter of the adsorption energy. No indication of Au adatoms mediating the thiol-Au interaction was found in contrast to other thiol-bonded systems. However, MBA lifts the Au(110)-(2 × 1) reconstruction.
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Affiliation(s)
- Nadine Hauptmann
- Institut für Experimentelle und Angewandte Physik, Christian-Albrechts-Universität zu Kiel , 24098 Kiel, Germany
| | - Roberto Robles
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Paula Abufager
- Instituto de Física de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), and Universidad Nacional de Rosario, Avenida Pellegrini 250, 2000 Rosario, Argentina
| | - Nicolas Lorente
- Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5 and Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Richard Berndt
- Institut für Experimentelle und Angewandte Physik, Christian-Albrechts-Universität zu Kiel , 24098 Kiel, Germany
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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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