1
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Li C, Kaspar C, Zhou P, Liu JC, Chahib O, Glatzel T, Häner R, Aschauer U, Decurtins S, Liu SX, Thoss M, Meyer E, Pawlak R. Strong signature of electron-vibration coupling in molecules on Ag(111) triggered by tip-gated discharging. Nat Commun 2023; 14:5956. [PMID: 37749099 PMCID: PMC10519934 DOI: 10.1038/s41467-023-41601-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 09/05/2023] [Indexed: 09/27/2023] Open
Abstract
Electron-vibration coupling is of critical importance for the development of molecular electronics, spintronics, and quantum technologies, as it affects transport properties and spin dynamics. The control over charge-state transitions and subsequent molecular vibrations using scanning tunneling microscopy typically requires the use of a decoupling layer. Here we show the vibronic excitations of tetrabromotetraazapyrene (TBTAP) molecules directly adsorbed on Ag(111) into an orientational glassy phase. The electron-deficient TBTAP is singly-occupied by an electron donated from the substrate, resulting in a spin 1/2 state, which is confirmed by a Kondo resonance. The TBTAP•- discharge is controlled by tip-gating and leads to a series of peaks in scanning tunneling spectroscopy. These occurrences are explained by combining a double-barrier tunneling junction with a Franck-Condon model including molecular vibrational modes. This work demonstrates that suitable precursor design enables gate-dependent vibrational excitations of molecules on a metal, thereby providing a method to investigate electron-vibration coupling in molecular assemblies without a decoupling layer.
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Affiliation(s)
- Chao Li
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland.
| | - Christoph Kaspar
- Institute of Physics, University of Freiburg, Hermann-Herder-Strasse 3, 79104, Freiburg, Germany
| | - Ping Zhou
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Jung-Ching Liu
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland
| | - Outhmane Chahib
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland
| | - Thilo Glatzel
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland
| | - Robert Häner
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Ulrich Aschauer
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
- Department of Chemistry and Physics of Materials, University of Salzburg, Jakob-Haringer-Strasse 2A, 5020 Salzburg, Austria
| | - Silvio Decurtins
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Shi-Xia Liu
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.
| | - Michael Thoss
- Institute of Physics, University of Freiburg, Hermann-Herder-Strasse 3, 79104, Freiburg, Germany
- EUCOR Centre for Quantum Science and Quantum Computing, University of Freiburg, Hermann-Herder-Str. 3, 79104, Freiburg, Germany
| | - Ernst Meyer
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland.
| | - Rémy Pawlak
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland.
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2
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Wang L, Tan JM, Chen Y, Chen MF, Wong MW. Dispersion-Corrected DFT-D4 Study of the Adsorption of Halobenzenes and 1,3,5-Trihalobenzenes on the Cu(111) Surface─Effect of Sigma Hole Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37473457 DOI: 10.1021/acs.langmuir.3c00918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Halogen bonds, characterized by directionality, tunability, hydrophobicity, and variable sizes, are ideal noncovalent interactions to design and control the formation of self-assembled nanostructures. The specific self-assembly cases formed by the halogen-bonding interaction have been well studied by scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations. However, there is a lack of systematic theoretical adsorption studies on halogenated molecules. In this work, the adsorption of halobenzenes and 1,3,5-trihalobenzenes on the Cu(111) surface was examined by dispersion-corrected DFT methods. The adsorption geometries, noncovalent molecule-surface interactions, electronic densities, and electrostatic potential maps were examined for their most stable adsorption sites using the DFT-D4 method. Our calculations revealed that the iodo compounds favor a different adsorption geometry from aryl chlorides and bromides. Down the halogen group (Cl to I), the adsorption energy increases and the distance between the halogen atom and Cu surface decreases, which indicates stronger molecule-surface interactions. This is supported by the changes in the density of states upon adsorption. Noncovalent interaction analysis was also employed to further understand the nature and relative strength of the molecule-surface interactions. Electrostatic potential maps revealed that the positive character of the halogen sigma hole becomes stronger upon adsorption. Thus, surface adsorption of the halogenated molecule will enhance the formation of intermolecular halogen bonds. The present theoretical findings are expected to contribute toward a more comprehensive understanding of halogen bonding on the Cu(111) surface.
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Affiliation(s)
- Lulu Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Jun Min Tan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Yingqian Chen
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Meng-Fu Chen
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
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3
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Carracedo-Cosme J, Romero-Muñiz C, Pou P, Pérez R. Molecular Identification from AFM Images Using the IUPAC Nomenclature and Attribute Multimodal Recurrent Neural Networks. ACS APPLIED MATERIALS & INTERFACES 2023; 15:22692-22704. [PMID: 37126486 PMCID: PMC10176476 DOI: 10.1021/acsami.3c01550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Spectroscopic methods─like nuclear magnetic resonance, mass spectrometry, X-ray diffraction, and UV/visible spectroscopies─applied to molecular ensembles have so far been the workhorse for molecular identification. Here, we propose a radically different chemical characterization approach, based on the ability of noncontact atomic force microscopy with metal tips functionalized with a CO molecule at the tip apex (referred as HR-AFM) to resolve the internal structure of individual molecules. Our work demonstrates that a stack of constant-height HR-AFM images carries enough chemical information for a complete identification (structure and composition) of quasiplanar organic molecules, and that this information can be retrieved using machine learning techniques that are able to disentangle the contribution of chemical composition, bond topology, and internal torsion of the molecule to the HR-AFM contrast. In particular, we exploit multimodal recurrent neural networks (M-RNN) that combine convolutional neural networks for image analysis and recurrent neural networks to deal with language processing, to formulate the molecular identification as an imaging captioning problem. The algorithm is trained using a data set─which contains almost 700,000 molecules and 165 million theoretical AFM images─to produce as final output the IUPAC name of the imaged molecule. Our extensive test with theoretical images and a few experimental ones shows the potential of deep learning algorithms in the automatic identification of molecular compounds by AFM. This achievement supports the development of on-surface synthesis and overcomes some limitations of spectroscopic methods in traditional solution-based synthesis.
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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 de la Materia Condensada, Universidad de Sevilla, P.O. Box 1065, 41080 Sevilla, 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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4
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Kang F, Sun L, Gao W, Sun Q, Xu W. On-Surface Synthesis of a Carbon Nanoribbon Composed of 4-5-6-8-Membered Rings. ACS NANO 2023; 17:8717-8722. [PMID: 37125847 DOI: 10.1021/acsnano.3c01915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
From the structure point of view, there are a number of ways of tiling a carbon sheet with different polygons, resulting in prospects of tailoring electronic structures of low-dimensional carbon nanomaterials. However, up to now, the experimental fabrication of such structures embedded with periodic nonhexagon carbon polygons, especially ones with more than three kinds, is still very challenging, leaving their potential properties unexplored. Here we report the bottom-up synthesis of a nanoribbon composed of 4-5-6-8-membered rings via lateral fusion of polyfluorene chains on Au(111). Scanning probe microscopy unequivocally determines both the geometric structure and the electronic properties of such a nanoribbon, revealing its semiconducting property with a bandgap of ∼1.4 eV on Au(111). We expect that this work could be helpful for designing and synthesizing complicated carbon nanoribbons.
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Affiliation(s)
- Faming Kang
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China
| | - Luye Sun
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China
| | - Wenze Gao
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China
| | - Qiang Sun
- Materials Genome Institute, Shanghai University, Shanghai 200444, P. R. China
| | - Wei Xu
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China
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5
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Barragán A, Lois S, Sarasola A, Vitali L. Empowering non-covalent hydrogen, halogen, and [S-N] 2 bonds in synergistic molecular assemblies on Au(111). NANOSCALE 2022; 14:17895-17899. [PMID: 36458674 DOI: 10.1039/d2nr05984c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Non-covalent bonds are fundamental for designing self-assembled organic structures with potentially high responsiveness to mechanical, light, and thermal stimuli. The weak intermolecular interaction allows triggering charge-transport, energy-conversion, enzymatic, and catalytic activity, to name a few. Here, we discuss the synergistic action that multiple highly-directional and purely electrostatic bonds have in assembling one molecular specie, namely 4,7-dibromobenzo[c]-1,2,5-thiadiazole (2Br-BTD), in two different patterns on the Au(111) surface. We find, using scanning tunneling microscopy (STM) and density functional theory (DFT), that multiple secondary-interactions strengthen the electrostatic attraction between the pnicogen and chalcogen atoms forming [S-N]2 heterocycles, the building block of the two networks. Among these interactions, there are halogen-halogen bonds that form characteristic supra-molecular synthons of 3, 4, or 6 molecules. However, not all these nodal structures contribute to the cohesion of the system. In such cases, other secondary bonds involving hydrogen or nitrogen compensate for the eventual deficiency.
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Affiliation(s)
- Ana Barragán
- Donostia International Physics Center (DIPC), E-20018 San Sebastián, Spain.
- Advanced Polymers and Materials: Physics, Chemistry and Technology, Chemistry Faculty (UPV/EHU), Paseo M. Lardizabal 3, 20018 San Sebastian, Spain
- Centro de Física de Materiales, Centro Mixto CSIC-UPV/EHU, Paseo M Lardizabal 5, 20018 San Sebastian, Spain
| | - Sara Lois
- Donostia International Physics Center (DIPC), E-20018 San Sebastián, Spain.
- Departamento de Física Aplicada, Universidad del País Vasco (UPV/EHU), E-20018 San Sebastián, Spain.
| | - Ane Sarasola
- Donostia International Physics Center (DIPC), E-20018 San Sebastián, Spain.
- Departamento de Física Aplicada, Universidad del País Vasco (UPV/EHU), E-20018 San Sebastián, Spain.
| | - Lucia Vitali
- Donostia International Physics Center (DIPC), E-20018 San Sebastián, Spain.
- Advanced Polymers and Materials: Physics, Chemistry and Technology, Chemistry Faculty (UPV/EHU), Paseo M. Lardizabal 3, 20018 San Sebastian, Spain
- Centro de Física de Materiales, Centro Mixto CSIC-UPV/EHU, Paseo M Lardizabal 5, 20018 San Sebastian, Spain
- Ikerbasque Research Foundation for Science, Plaza Euskadi, 5, Bilbao 48009, Spain
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6
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Evolution of Br⋯Br contacts in enantioselective molecular recognition during chiral 2D crystallization. Nat Commun 2022; 13:5850. [PMID: 36195587 PMCID: PMC9532412 DOI: 10.1038/s41467-022-33446-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/19/2022] [Indexed: 11/25/2022] Open
Abstract
Halogen-mediated interactions play an important role in molecular recognition and crystallization in many chemical and biological systems, whereas their effect on homochiral versus heterochiral recognition and crystallization has rarely been explored. Here we demonstrate the evolution of Br⋯Br contacts in chiral recognition during 2D crystallization. On Ag(100), type I contacts prevail at low coverage and lead to homochiral recognition and the formation of 2D conglomerates; whereas type II contacts mediating heterochiral recognition are suppressed at medium coverage and appear in the racemates induced by structural transitions at high coverage. On Ag(111), type I contacts dominate the 2D crystallization and generate 2D conglomerates exclusively. DFT calculations suggest that the energy difference between type I and type II contacts is reversed upon adsorption due to the substrate induced mismatch energy penalty. This result provides fundamental understanding of halogen-mediated interactions in molecular recognition and crystallization on surface. Halogen-mediated interactions control molecular recognition in many chemical and biological systems. Here, the authors demonstrate two types of Br⋯Br contacts and their importance in chiral on-surface crystallization.
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7
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. The Pnictogen Bond, Together with Other Non-Covalent Interactions, in the Rational Design of One-, Two- and Three-Dimensional Organic-Inorganic Hybrid Metal Halide Perovskite Semiconducting Materials, and Beyond. Int J Mol Sci 2022; 23:ijms23158816. [PMID: 35955945 PMCID: PMC9369011 DOI: 10.3390/ijms23158816] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
The pnictogen bond, a somewhat overlooked supramolecular chemical synthon known since the middle of the last century, is one of the promising types of non-covalent interactions yet to be fully understood by recognizing and exploiting its properties for the rational design of novel functional materials. Its bonding modes, energy profiles, vibrational structures and charge density topologies, among others, have yet to be comprehensively delineated, both theoretically and experimentally. In this overview, attention is largely centered on the nature of nitrogen-centered pnictogen bonds found in organic-inorganic hybrid metal halide perovskites and closely related structures deposited in the Cambridge Structural Database (CSD) and the Inorganic Chemistry Structural Database (ICSD). Focusing on well-characterized structures, it is shown that it is not merely charge-assisted hydrogen bonds that stabilize the inorganic frameworks, as widely assumed and well-documented, but simultaneously nitrogen-centered pnictogen bonding, and, depending on the atomic constituents of the organic cation, other non-covalent interactions such as halogen bonding and/or tetrel bonding, are also contributors to the stabilizing of a variety of materials in the solid state. We have shown that competition between pnictogen bonding and other interactions plays an important role in determining the tilting of the MX6 (X = a halogen) octahedra of metal halide perovskites in one, two and three-dimensions. The pnictogen interactions are identified to be directional even in zero-dimensional crystals, a structural feature in many engineered ordered materials; hence an interplay between them and other non-covalent interactions drives the structure and the functional properties of perovskite materials and enabling their application in, for example, photovoltaics and optoelectronics. We have demonstrated that nitrogen in ammonium and its derivatives in many chemical systems acts as a pnictogen bond donor and contributes to conferring stability, and hence functionality, to crystalline perovskite systems. The significance of these non-covalent interactions should not be overlooked, especially when the focus is centered on the rationale design and discovery of such highly-valued materials.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
- Correspondence: (A.V.); (P.R.V.)
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
- Correspondence: (A.V.); (P.R.V.)
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
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8
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Tsukahara N, Yoshinobu J. Substrate-Selective Intermolecular Interaction and the Molecular Self-Assemblies: 1,3,5-Tris(4-bromophenyl)benzene Molecules on the Ag(111) and Si(111) (√3 × √3)-Ag Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8881-8889. [PMID: 35770974 DOI: 10.1021/acs.langmuir.2c00991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We report the formation processes of the self-assembled layer of 1,3,5-tris(4-bromophenyl)benzene (TBB) molecules on the Ag(111) and Si(111) (√3 × √3)-Ag surfaces by STM measurements and density functional theory (DFT) calculations. The self-assembled layers on the surfaces show characteristic structures controlled by the interplay between the intermolecular interaction and the molecule-substrate interaction. Through the cooperative interplay between the molecule-substrate interaction and the intermolecular halogen bond (XB), the periodic arrangement of TBB molecules appears on the Ag(111) surface. On the other hand, the two types of TBB arrangement appear on the Si(111) (√3 × √3)-Ag surface (phases 1 and 2). Phase 1 is the periodic arrangement of the TBB molecules and is derived from the cooperative interplay between the molecule-substrate interaction and the intermolecular van der Waals (vdW) interaction and the hydrogen bond (HB), and phase 2 is a random arrangement and is derived from the competitive interplay between the molecule-substrate interaction and the intermolecular XB and HB. Our present study specifies the role of the substrate in the molecular self-assembly of the substrate. Although the structure of the molecular self-assembly is controlled by the choice of the substrate, the cooperative interplay between the molecule-substrate interaction and the intermolecular interaction is necessary to realize the ideal periodic arrangement.
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Affiliation(s)
- Noriyuki Tsukahara
- National Institute of Technology, Gunma College, Toriba-machi 580, Maebashi-shi 370-8530, Gunma, Japan
| | - Jun Yoshinobu
- The Institute for Solid State Physics (ISSP), The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa-shi 277-8581, Chiba, Japan
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9
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Wang D, Wang Z, Liu W, Zhong S, Feng YP, Loh KP, Wee ATS. Real-Space Investigation of the Multiple Halogen Bonds by Ultrahigh-Resolution Scanning Probe Microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202368. [PMID: 35719029 DOI: 10.1002/smll.202202368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Indexed: 06/15/2023]
Abstract
The chemical bond is of central interest in chemistry, and it is of significance to study the nature of intermolecular bonds in real-space. Herein, non-contact atomic force microscopy (nc-AFM) and low-temperature scanning tunneling microscopy (LT-STM) are employed to acquire real-space atomic information of molecular clusters, i.e., monomer, dimer, trimer, tetramer, formed on Au(111). The formation of the various molecular clusters is due to the diversity of halogen bonds. DFT calculation also suggests the formation of three distinct halogen bonds among the molecular clusters, which originates from the noncovalent interactions of Br-atoms with the positive potential H-atoms, neutral potential Br-atoms, and negative potential N-atoms, respectively. This work demonstrates the real-space investigation of the multiple halogen bonds by nc-AFM/LT-STM, indicating the potential use of this technique to study other intermolecular bonds and to understand complex supramolecular assemblies at the atomic/sub-molecular level.
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Affiliation(s)
- Dingguan Wang
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore, 117551, Singapore
| | - Zishen Wang
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore, 117551, Singapore
| | - Wei Liu
- School of Physics, Southeast University, 2 Southeast University Road, Nanjing, China
| | - Siying Zhong
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore, 117551, Singapore
| | - Yuan Ping Feng
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore, 117551, Singapore
| | - Kian Ping Loh
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Andrew Thye Shen Wee
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore, 117551, Singapore
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10
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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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11
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Schunke C, Miller DP, Zurek E, Morgenstern K. Halogen and structure sensitivity of halobenzene adsorption on copper surfaces. Phys Chem Chem Phys 2022; 24:4485-4492. [PMID: 35113111 DOI: 10.1039/d1cp05660c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adsorption orientation of molecules on surfaces influences their reactivity, but it is still challenging to tailor the interactions that govern their orientation. Here, we investigate how the substituent and the surface structure alter the adsorption orientation of halogenated benzene molecules from parallel to tilted relative to the surface plane. The deviation of the parallel orientation of bromo-, chloro-, and fluorobenzene molecules adsorbed on Cu(111) and Cu(110) surfaces is determined, utilising the surface selection rule in reflection-absorption infrared spectroscopy. On Cu(111), all three halogenated molecules are adsorbed with their molecular plane almost parallel to the surface at low coverages. However, they are tilted at higher coverages; yet, the threshold coverages differ. On Cu(110), merely bromo- and chlorobenzene follow this trend, albeit with a lower threshold for both. In contrast, fluorobenzene molecules are tilted already at low coverages. The substantial influence of the halogen atom and the surface structure on the adsorption orientation, resulting from an interplay of molecule-molecule and molecule-surface interactions, is highly relevant for reactivity confined to two dimensions.
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Affiliation(s)
- Christina Schunke
- Ruhr-Universität Bochum, Lehrstuhl für Physikalische Chemie I, Universitässtraße 150, D-44803 Bochum, Germany.
| | - Daniel P Miller
- Hofstra University, Department of Chemistry, 106 Berliner Hall, Hempstead, NY 11549, USA
| | - Eva Zurek
- State University of New York at Buffalo, Department of Chemistry, 777 Natural Sciences Complex, Buffalo, NY 14260-3000, USA
| | - Karina Morgenstern
- Ruhr-Universität Bochum, Lehrstuhl für Physikalische Chemie I, Universitässtraße 150, D-44803 Bochum, Germany.
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12
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Sun S, Li B, Fu B, Ruan Z, Zhang H, Xiong W, Zhang Y, Niu G, Lu J, Zuo X, Gao L, Cai J. Chiral structures of 6,12-dibromochrysene on Au(111) and Cu(111) surfaces. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.12.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Liu GN, Li MK, Xu RD, Zhang NN, Quan XJ, Qian BJ, Lu YH, Li C. A halogen bonding assembled hybrid copper halide framework as a promising hypotoxicity photodetector. Inorg Chem Front 2022. [DOI: 10.1039/d2qi01441f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The first halogen bonding assembled three-dimensional hybrid copper iodide was obtained by a facile and sustainable “All-in-One” synthesis strategy and shows great application potential as a hypotoxicity photodetector.
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Affiliation(s)
- Guang-Ning Liu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, PR China
| | - Ming-Kun Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, PR China
| | - Rang-Dong Xu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, PR China
| | - Ning-Ning Zhang
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252059, PR China
| | - Xin-Jiao Quan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, PR China
| | - Bing-Jing Qian
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, PR China
| | - Yi-Han Lu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, PR China
| | - Cuncheng Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, PR China
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14
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Mallada B, Gallardo A, Lamanec M, de la Torre B, Špirko V, Hobza P, Jelinek P. Real-space imaging of anisotropic charge of σ-hole by means of Kelvin probe force microscopy. Science 2021; 374:863-867. [PMID: 34762455 DOI: 10.1126/science.abk1479] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- B Mallada
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371 Olomouc, Czech Republic.,Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Department of Physical Chemistry, Palacký University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - A Gallardo
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - M Lamanec
- Department of Physical Chemistry, Palacký University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic
| | - B de la Torre
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371 Olomouc, Czech Republic.,Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - V Špirko
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 12116 Prague, Czech Republic
| | - P Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,IT4Innovations, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 70800 Ostrava-Poruba, Czech Republic
| | - P Jelinek
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371 Olomouc, Czech Republic.,Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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15
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Song S, Wang L, Su J, Xu Z, Hsu CH, Hua C, Lyu P, Li J, Peng X, Kojima T, Nobusue S, Telychko M, Zheng Y, Chuang FC, Sakaguchi H, Wong MW, Lu J. Manifold dynamic non-covalent interactions for steering molecular assembly and cyclization. Chem Sci 2021; 12:11659-11667. [PMID: 34667560 PMCID: PMC8442717 DOI: 10.1039/d1sc03733a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Deciphering rich non-covalent interactions that govern many chemical and biological processes is crucial for the design of drugs and controlling molecular assemblies and their chemical transformations. However, real-space characterization of these weak interactions in complex molecular architectures at the single bond level has been a longstanding challenge. Here, we employed bond-resolved scanning probe microscopy combined with an exhaustive structural search algorithm and quantum chemistry calculations to elucidate multiple non-covalent interactions that control the cohesive molecular clustering of well-designed precursor molecules and their chemical reactions. The presence of two flexible bromo-triphenyl moieties in the precursor leads to the assembly of distinct non-planar dimer and trimer clusters by manifold non-covalent interactions, including hydrogen bonding, halogen bonding, C-H⋯π and lone pair⋯π interactions. The dynamic nature of weak interactions allows for transforming dimers into energetically more favourable trimers as molecular density increases. The formation of trimers also facilitates thermally-triggered intermolecular Ullmann coupling reactions, while the disassembly of dimers favours intramolecular cyclization, as evidenced by bond-resolved imaging of metalorganic intermediates and final products. The richness of manifold non-covalent interactions offers unprecedented opportunities for controlling the assembly of complex molecular architectures and steering on-surface synthesis of quantum nanostructures.
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Affiliation(s)
- Shaotang Song
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Lulu Wang
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Jie Su
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Zhen Xu
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Chia-Hsiu Hsu
- Department of Physics, National Sun Yat-sen University Kaohsiung 80424 Taiwan
- Physics Division, National Center for Theoretical Sciences Taipei, 10617 Taiwan
| | - Chenqiang Hua
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University Hangzhou People's Republic of China
| | - Pin Lyu
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Jing Li
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Xinnan Peng
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Takahiro Kojima
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Shunpei Nobusue
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Mykola Telychko
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Yi Zheng
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University Hangzhou People's Republic of China
| | - Feng-Chuan Chuang
- Department of Physics, National Sun Yat-sen University Kaohsiung 80424 Taiwan
- Physics Division, National Center for Theoretical Sciences Taipei, 10617 Taiwan
| | - Hiroshi Sakaguchi
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Jiong Lu
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
- Centre for Advanced 2D Materials (CA2DM), National University of Singapore 6 Science Drive 2 Singapore 117546 Singapore
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16
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Zhong Q, Ihle A, Ahles S, Wegner HA, Schirmeisen A, Ebeling D. Constructing covalent organic nanoarchitectures molecule by molecule via scanning probe manipulation. Nat Chem 2021; 13:1133-1139. [PMID: 34475530 PMCID: PMC8550974 DOI: 10.1038/s41557-021-00773-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022]
Abstract
Constructing low-dimensional covalent assemblies with tailored size and connectivity is challenging yet often key for applications in molecular electronics where optical and electronic properties of the quantum materials are highly structure dependent. We present a versatile approach for building such structures block by block on bilayer sodium chloride (NaCl) films on Cu(111) with the tip of an atomic force microscope, while tracking the structural changes with single-bond resolution. Covalent homo-dimers in cis and trans configurations and homo-/hetero-trimers were selectively synthesized by a sequence of dehalogenation, translational manipulation and intermolecular coupling of halogenated precursors. Further demonstrations of structural build-up include complex bonding motifs, like carbon–iodine–carbon bonds and fused carbon pentagons. This work paves the way for synthesizing elusive covalent nanoarchitectures, studying structural modifications and revealing pathways of intermolecular reactions. ![]()
Tailoring the size and connectivity of organic nanostructures is challenging but is often key in molecular electronics for tuning the properties of the quantum materials. Now an approach has been developed for building low-dimensional covalent architectures block by block on a surface by highly selective tip-induced intermolecular reactions.
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Affiliation(s)
- Qigang Zhong
- Institute of Applied Physics, Justus Liebig University Giessen, Giessen, Germany. .,Center for Materials Research, Justus Liebig University Giessen, Giessen, Germany.
| | - Alexander Ihle
- Institute of Applied Physics, Justus Liebig University Giessen, Giessen, Germany.,Center for Materials Research, Justus Liebig University Giessen, Giessen, Germany
| | - Sebastian Ahles
- Center for Materials Research, Justus Liebig University Giessen, Giessen, Germany.,Institute of Organic Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Hermann A Wegner
- Center for Materials Research, Justus Liebig University Giessen, Giessen, Germany.,Institute of Organic Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Andre Schirmeisen
- Institute of Applied Physics, Justus Liebig University Giessen, Giessen, Germany. .,Center for Materials Research, Justus Liebig University Giessen, Giessen, Germany.
| | - Daniel Ebeling
- Institute of Applied Physics, Justus Liebig University Giessen, Giessen, Germany. .,Center for Materials Research, Justus Liebig University Giessen, Giessen, Germany.
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17
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Mohammed MSG, Lawrence J, García F, Brandimarte P, Berdonces-Layunta A, Pérez D, Sánchez-Portal D, Peña D, de Oteyza DG. From starphenes to non-benzenoid linear conjugated polymers by substrate templating. NANOSCALE ADVANCES 2021; 3:2351-2358. [PMID: 36133758 PMCID: PMC9419161 DOI: 10.1039/d1na00126d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/06/2021] [Indexed: 06/14/2023]
Abstract
Combining on-surface synthetic methods with the power of scanning tunneling microscopy to characterize novel materials at the single molecule level, we show how to steer the reactivity of one anthracene-based precursor towards different product nanostructures. Whereas using a Au(111) surface with three-fold symmetry results in the dominant formation of a starphene derivative, the two-fold symmetry of a reconstructed Au(110) surface allows the selective growth of non-benzenoid linear conjugated polymers. We further assess the electronic properties of each of the observed product structures via tunneling spectroscopy and DFT calculations, altogether advancing the synthesis and characterization of molecular structures of notable scientific interest that have been only scarcely investigated to date, as applies both to starphenes and to non-benzenoid conjugated polymers.
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Affiliation(s)
- Mohammed S G Mohammed
- Donostia International Physics Center (DIPC) San Sebastián Spain
- Centro de Física de Materiales (CSIC-UPV/EHU) San Sebastián Spain
| | - James Lawrence
- Donostia International Physics Center (DIPC) San Sebastián Spain
- Centro de Física de Materiales (CSIC-UPV/EHU) San Sebastián Spain
| | - Fátima García
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela Santiago de Compostela Spain
| | | | - Alejandro Berdonces-Layunta
- Donostia International Physics Center (DIPC) San Sebastián Spain
- Centro de Física de Materiales (CSIC-UPV/EHU) San Sebastián Spain
| | - Dolores Pérez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela Santiago de Compostela Spain
| | - Daniel Sánchez-Portal
- Donostia International Physics Center (DIPC) San Sebastián Spain
- Centro de Física de Materiales (CSIC-UPV/EHU) San Sebastián Spain
| | - Diego Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela Santiago de Compostela Spain
| | - Dimas G de Oteyza
- Donostia International Physics Center (DIPC) San Sebastián Spain
- Centro de Física de Materiales (CSIC-UPV/EHU) San Sebastián Spain
- Ikerbasque, Basque Foundation for Science Bilbao Spain
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