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Peng X, Zhang Y, Liu X, Qian Y, Ouyang Z, Kong H. From Short- to Long-Range Chiral Recognition on Surfaces: Chiral Assembly and Synthesis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307171. [PMID: 38054810 DOI: 10.1002/smll.202307171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/13/2023] [Indexed: 12/07/2023]
Abstract
Research on chiral behaviors of small organic molecules at solid surfaces, including chiral assembly and synthesis, can not only help unravel the origin of the chiral phenomenon in biological/chemical systems but also provide promising strategies to build up unprecedented chiral surfaces or nanoarchitectures with advanced applications in novel nanomaterials/nanodevices. Understanding how molecular chirality is recognized is considered to be a mandatory basis for such studies. In this review, a series of recent studies in chiral assembly and synthesis at well-defined metal surfaces under ultra-high vacuum conditions are outlined. More importantly, the intrinsic mechanisms of chiral recognition are highlighted, including short/long-range chiral recognition in chiral assembly and two main strategies to steer the reaction pathways and modulate selective synthesis of specific chiral products on surfaces.
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Affiliation(s)
- Xinchen Peng
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Yinhui Zhang
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Xinbang Liu
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Yinyue Qian
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Zuoling Ouyang
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Huihui Kong
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
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2
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Yi Z, Guo Y, Hou R, Zhang Z, Gao Y, Zhang C, Xu W. Revealing the Orientation Selectivity of Tetrapyridyl-Substituted Porphyrins Constrained in Molecular "Klotski Puzzles". J Am Chem Soc 2023; 145:22366-22373. [PMID: 37769215 DOI: 10.1021/jacs.3c03777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Understanding and controlling molecular orientations in self-assembled organic nanostructures are crucial to the development of advanced functional nanodevices. Scanning tunneling microscopy (STM) provides a powerful toolbox to recognize molecular orientations and to induce orientation changes on surfaces at the single-molecule level. Enormous effort has been devoted to directly controlling the molecular orientations of isolated single molecules in free space. However, revealing and further controlling molecular orientation selectivity in constrained environments remain elusive. In this study, by a combination of STM imaging/manipulations and density functional theory calculations, we report the orientation selectivity of tetrapyridyl-substituted porphyrins in response to various local molecular environments in artificially constructed molecular "Klotski puzzles" on Au(111). With the assistance of STM lateral manipulations, "sliding-block" molecules were able to enter predefined positions, and specific molecular orientations were adopted to fit the local molecular environments, in which the intermolecular interaction was revealed to be the key to achieving the eventual molecular orientation selectivity. Our results demonstrate the essential role of local molecular environments in directing single-molecule orientations, which would shed light on the design of molecular structures to control preferred orientations for further applications in molecular nanodevices.
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Affiliation(s)
- Zewei Yi
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Yuan Guo
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Rujia Hou
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Zhaoyu Zhang
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Yuhong Gao
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Chi Zhang
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Wei Xu
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
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3
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Hu H, Xue R, Chen F. Biomineralization and Properties of Guanine Crystals. Molecules 2023; 28:6138. [PMID: 37630390 PMCID: PMC10459440 DOI: 10.3390/molecules28166138] [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: 06/20/2023] [Revised: 08/12/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Guanine crystals with unique optical properties in organisms have been extensively studied and the biomineralization principles of guanine are being established. This review summarizes the fundamental physicochemical properties (solubility, tautomers, bands, and refractivity), polymorphs, morphology of biological and synthetic forms, and the reported biomineralization principles of guanine (selective recrystallization of amorphous precursor, preassembled scaffolds, additives, twinning, hypoxanthine doping, fluorescence, and assembly). The biomineralization principles of guanine will be helpful for the synthesis of guanine crystals with excellent properties and the design of functional organic materials for drugs, dyes, organic semiconductors, etc.
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Affiliation(s)
- Haoxin Hu
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, China;
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China
| | - Rongrong Xue
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China
| | - Fenghua Chen
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China
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4
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Hou R, Guo Y, Yi Z, Zhang Z, Zhang C, Xu W. Construction and Structural Transformation of Metal-Organic Nanostructures Induced by Alkali Metals and Alkali Metal Salts. J Phys Chem Lett 2023; 14:3636-3642. [PMID: 37026779 DOI: 10.1021/acs.jpclett.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Metal-organic nanostructures are attractive in a variety of scientific fields, such as biomedicine, energy harvesting, and catalysis. Alkali-based metal-organic nanostructures have been extensively fabricated on surfaces based on pure alkali metals and alkali metal salts. However, their differences in the construction of alkali-based metal-organic nanostructures have been less discussed, and the influence on structural diversity remains elusive. In this work, from the interplay of scanning tunneling microscopy imaging and density functional theory calculations, we constructed Na-based metal-organic nanostructures by applying Na and NaCl as sources of alkali metals and visualized the structural transformations in real space. Moreover, a reverse structural transformation was achieved by dosing iodine into the Na-based metal-organic nanostructures, revealing the connections and differences between NaCl and Na in the structural evolutions, which provided fundamental insights into the evolution of electrostatic ionic interactions and the precise fabrication of alkali-based metal-organic nanostructures.
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Affiliation(s)
- Rujia Hou
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Yuan Guo
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Zewei Yi
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Zhaoyu Zhang
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Chi Zhang
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Wei Xu
- Interdisciplinary Materials Research Center, School of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
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5
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Liu X, Matej A, Kratky T, Mendieta‐Moreno JI, Günther S, Mutombo P, Decurtins S, Aschauer U, Repp J, Jelinek P, Liu S, Patera LL. Exploiting Cooperative Catalysis for the On-Surface Synthesis of Linear Heteroaromatic Polymers via Selective C-H Activation. Angew Chem Int Ed Engl 2022; 61:e202112798. [PMID: 34788494 PMCID: PMC9299585 DOI: 10.1002/anie.202112798] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Indexed: 11/17/2022]
Abstract
Regiospecific C-H activation is a promising approach to achieve extended polymers with tailored structures. While a recent on-surface synthetic approach has enabled regioselective homocoupling of heteroaromatic molecules, only small oligomers have been achieved. Herein, selective C-H activation for dehydrogenative C-C couplings of hexaazatriphenylene by Scholl reaction is reported for the first time. By combining low-temperature scanning tunneling microscopy (STM) and atomic force microscopy (AFM), we revealed the formation of one-dimensional polymers with a double-chain structure. The details of the growth process are rationalized by density functional theory (DFT) calculations, pointing out a cooperative catalytic action of Na and Ag adatoms in steering the C-H selectivity for the polymerization.
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Affiliation(s)
- Xunshan Liu
- Department of Chemistry, Biochemistry and Pharmaceutical SciencesUniversity of Bern3012BernSwitzerland
- Department of ChemistryZhejiang Sci-Tech UniversityHangzhouChina
| | - Adam Matej
- Institute of Physics of Czech Academy of Sciences16200PragueCzech Republic
- Regional Centre of Advanced Technologies and MaterialsCzech Advanced Technology and Research Institute (CATRIN)Palacký University Olomouc78371OlomoucCzech Republic
| | - Tim Kratky
- Department of Chemistry and Catalysis Research CenterTechnical University of Munich85748GarchingGermany
| | | | - Sebastian Günther
- Department of Chemistry and Catalysis Research CenterTechnical University of Munich85748GarchingGermany
| | - Pingo Mutombo
- Institute of Physics of Czech Academy of Sciences16200PragueCzech Republic
| | - Silvio Decurtins
- Department of Chemistry, Biochemistry and Pharmaceutical SciencesUniversity of Bern3012BernSwitzerland
| | - Ulrich Aschauer
- Department of Chemistry, Biochemistry and Pharmaceutical SciencesUniversity of Bern3012BernSwitzerland
| | - Jascha Repp
- Institute of Experimental and Applied PhysicsUniversity of Regensburg93053RegensburgGermany
| | - Pavel Jelinek
- Institute of Physics of Czech Academy of Sciences16200PragueCzech Republic
- Regional Centre of Advanced Technologies and MaterialsCzech Advanced Technology and Research Institute (CATRIN)Palacký University Olomouc78371OlomoucCzech Republic
| | - Shi‐Xia Liu
- Department of Chemistry, Biochemistry and Pharmaceutical SciencesUniversity of Bern3012BernSwitzerland
| | - Laerte L. Patera
- Department of Chemistry and Catalysis Research CenterTechnical University of Munich85748GarchingGermany
- Institute of Experimental and Applied PhysicsUniversity of Regensburg93053RegensburgGermany
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6
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Liu X, Matej A, Kratky T, Mendieta‐Moreno JI, Günther S, Mutombo P, Decurtins S, Aschauer U, Repp J, Jelinek P, Liu S, Patera LL. Einsatz der kooperativen Katalyse für die Oberflächensynthese linearer heteroaromatischer Polymere durch selektive C‐H‐Aktivierung. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xunshan Liu
- Departement für Chemie und Biochemie Universität Bern 3012 Bern Schweiz
- Department of Chemistry Zhejiang Sci-Tech University Hangzhou China
| | - Adam Matej
- Institute of Physics of Czech Academy of Sciences 16200 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Czech Advanced Technology and Research Institute (CATRIN) Palacký University Olomouc 78371 Olomouc Czech Republic
| | - Tim Kratky
- Chemie Department und Zentralinstitut für Katalyseforschung Technische Universität München 85748 Garching Deutschland
| | | | - Sebastian Günther
- Chemie Department und Zentralinstitut für Katalyseforschung Technische Universität München 85748 Garching Deutschland
| | - Pingo Mutombo
- Institute of Physics of Czech Academy of Sciences 16200 Prague Czech Republic
| | - Silvio Decurtins
- Departement für Chemie und Biochemie Universität Bern 3012 Bern Schweiz
| | - Ulrich Aschauer
- Departement für Chemie und Biochemie Universität Bern 3012 Bern Schweiz
| | - Jascha Repp
- Institut für Experimentelle und Angewandte Physik Universität Regensburg 93053 Regensburg Deutschland
| | - Pavel Jelinek
- Institute of Physics of Czech Academy of Sciences 16200 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Czech Advanced Technology and Research Institute (CATRIN) Palacký University Olomouc 78371 Olomouc Czech Republic
| | - Shi‐Xia Liu
- Departement für Chemie und Biochemie Universität Bern 3012 Bern Schweiz
| | - Laerte L. Patera
- Chemie Department und Zentralinstitut für Katalyseforschung Technische Universität München 85748 Garching Deutschland
- Institut für Experimentelle und Angewandte Physik Universität Regensburg 93053 Regensburg Deutschland
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7
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Chen F, Ma Y, Qi L. Synthesis of Porous Microplatelets of α Form Anhydrous Guanine in DMSO/Water Mixed Solvents REMINDER: CrystEngComm - Invitation to submit an article. CrystEngComm 2022. [DOI: 10.1039/d1ce01709h] [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
Guanine crystals have been utilized as optical systems such as tunable structural colors, diffusive light scatters, broad-band and narrow-band reflectors, imaging mirrors, and polarization sensitive reflectors in many organisms. It...
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8
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Ghassami A, Oleiki E, Kim DY, Shin HJ, Lee G, Kim KS. Facile room-temperature self-assembly of extended cation-free guanine-quartet network on Mo-doped Au(111) surface. NANOSCALE ADVANCES 2021; 3:3867-3874. [PMID: 36133009 PMCID: PMC9418868 DOI: 10.1039/d1na00235j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/05/2021] [Indexed: 06/16/2023]
Abstract
Guanine-quadruplex, consisting of several stacked guanine-quartets (GQs), has emerged as an important category of novel molecular targets with applications from nanoelectronic devices to anticancer drugs. Incorporation of metal cations into a GQ structure is utilized to form stable G-quadruplexes, while formation of a cation-free GQ network has been challenging. Here we report the room temperature (RT) molecular self-assembly of extended pristine GQ networks on an Au(111) surface. An implanted molybdenum atom within the Au(111) surface is used to nucleate and stabilize the cation-free GQ network. Additionally, decoration of the Au(111) surface with 7-armchair graphene nanoribbons (7-AGNRs) enhances the GQ domain size by suppressing the influence of the disordered phase nucleated from Au step edges. Scanning tunneling microscopy/spectroscopy (STM/STS) and density functional theory (DFT) calculations confirm the formation of GQ networks and unravel the nucleation and growth mechanism. Our work, utilizing a hetero-atom doped substrate, provides a facile approach to enhance the stability and domain size of the GQ self-assembly, which would be applicable for other molecular structures.
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Affiliation(s)
- Amirreza Ghassami
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
| | - Elham Oleiki
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
| | - Dong Yeon Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
| | - Hyung-Joon Shin
- Department of Materials Science and Engineering, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
| | - Geunsik Lee
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
| | - Kwang S Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
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9
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Xie L, Jiang H, Li D, Liu M, Ding Y, Liu Y, Li X, Li X, Zhang H, Hou Z, Luo Y, Chi L, Qiu X, Xu W. Selectively Scissoring Hydrogen-Bonded Cytosine Dimer Structures Catalyzed by Water Molecules. ACS NANO 2020; 14:10680-10687. [PMID: 32687310 DOI: 10.1021/acsnano.0c05227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A single-molecule-level understanding of the activity of solvating water molecules in hydrogen-bonded assemblies would provide insights into the properties of the first hydration shells. Herein, we investigate the solvation of one of the DNA bases, cytosine, whose glassy-state network formed on Au(111) contains diverse types of hydrogen-bonded dimer configurations with hierarchical strengths. Upon water exposure, a global structural transformation from interwoven chain segments to extended chains was identified by scanning tunneling microscopy and atomic force microscopy. Density functional theory calculation and coarse-grained molecular dynamics simulation indicate that water molecules selectively break the weak-hydrogen-bonded dimers at T-junctions, while the stable ones within chains remain intact. The resulting hydrated chain segments further self-assemble into molecular chains by forming strong hydrogen bonds and spontaneously releasing water molecules. Such an intriguing transformation cannot be realized by thermal annealing, indicating the dynamic nature of water molecules in the regulation of hydrogen bonds in a catalytic manner.
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Affiliation(s)
- Lei Xie
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Huijun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale & Department of Chemical Physics, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Donglin Li
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Mengxi Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yuanqi Ding
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Yufang Liu
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China
| | - Xin Li
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuechao Li
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, China
| | - Haiming Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, China
| | - Zhonghuai Hou
- Hefei National Laboratory for Physical Sciences at the Microscale & Department of Chemical Physics, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale & Department of Chemical Physics, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lifeng Chi
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, China
| | - Xiaohui Qiu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Xu
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, China
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10
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Chen Z, Lin T, Li H, Cheng F, Su C, Loh KP. Hydrogen bond guided synthesis of close-packed one-dimensional graphdiyne on the Ag(111) surface. Chem Sci 2019; 10:10849-10852. [PMID: 32055387 PMCID: PMC7003942 DOI: 10.1039/c9sc04530a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/27/2019] [Indexed: 11/21/2022] Open
Abstract
Aided by hydrogen bonding, alkyne and oxazole functionalized precursors undergo uniform self-assembly, which serves as a template for the fabrication of one-dimensional graphdiyne-like wires on the Ag(111) surface.
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Affiliation(s)
- Zhi Chen
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology , International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education , Institute of Microscale Optoelectronics , Shenzhen University , Shenzhen , 518060 , China . .,Department of Chemistry , Centre for Advanced 2D Materials (CA2DM) , National University of Singapore , 3 Science Drive 3 , Singapore 117543 , Singapore .
| | - Tao Lin
- College of New Materials and New Energies , Shenzhen Technology University , Shenzhen 518118 , China
| | - Haohan Li
- Department of Chemistry , Centre for Advanced 2D Materials (CA2DM) , National University of Singapore , 3 Science Drive 3 , Singapore 117543 , Singapore .
| | - Fang Cheng
- Department of Chemistry , Centre for Advanced 2D Materials (CA2DM) , National University of Singapore , 3 Science Drive 3 , Singapore 117543 , Singapore .
| | - Chenliang Su
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology , International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education , Institute of Microscale Optoelectronics , Shenzhen University , Shenzhen , 518060 , China .
| | - Kian Ping Loh
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology , International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education , Institute of Microscale Optoelectronics , Shenzhen University , Shenzhen , 518060 , China . .,Department of Chemistry , Centre for Advanced 2D Materials (CA2DM) , National University of Singapore , 3 Science Drive 3 , Singapore 117543 , Singapore .
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11
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Zhang C, Kazuma E, Kim Y. Atomic‐Scale Visualization of the Stepwise Metal‐Mediated Dehalogenative Cycloaddition Reaction Pathways: Competition between Radicals and Organometallic Intermediates. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Chi Zhang
- Surface and Interface Science Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Emiko Kazuma
- Surface and Interface Science Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Yousoo Kim
- Surface and Interface Science Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
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12
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Zhang C, Kazuma E, Kim Y. Atomic‐Scale Visualization of the Stepwise Metal‐Mediated Dehalogenative Cycloaddition Reaction Pathways: Competition between Radicals and Organometallic Intermediates. Angew Chem Int Ed Engl 2019; 58:17736-17744. [DOI: 10.1002/anie.201909111] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/16/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Chi Zhang
- Surface and Interface Science Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Emiko Kazuma
- Surface and Interface Science Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Yousoo Kim
- Surface and Interface Science Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
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13
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Ding Y, Wang X, Li D, Xie L, Xu W. Dissolution of Sodium Halides by Confined Water on Au(111) via Langmuir-Hinshelwood Process. ACS NANO 2019; 13:6025-6032. [PMID: 31050883 DOI: 10.1021/acsnano.9b02259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Salt dissolution is generally encountered in widespread phenomena in nature. As a typical case, the dissolution of NaCl has been widely investigated in aqueous environment, while the process and mechanism of the on-surface dissolution may differ from that in solution and remain to be explored. Herein, we model a NaCl dissolution process on the Au(111) surface with confined water at room temperature (RT) and above. With the assistance of adenine molecules as water reservoir and carrier, the dissolution of NaCl is achieved above RT via the Langmuir-Hinshelwood mechanism rather than the Eley-Rideal one, along with the selective formation of stable Cl- hydrates, which desorb from the surface in the next step. To explore the generality, such a strategy has been extended to other sodium halide systems ( e. g., NaBr and NaI), and expectedly, the dissolution of sodium halides is also achieved by forming stable Br- and I- hydrates via the Langmuir-Hinshelwood process.
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Affiliation(s)
- Yuanqi Ding
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , People's Republic of China
| | - Xinyi Wang
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , People's Republic of China
| | - Donglin Li
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , People's Republic of China
| | - Lei Xie
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , People's Republic of China
| | - Wei Xu
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , People's Republic of China
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14
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Ma Y, Chen F, Hu Y, Liu Y, Qi L. Controlled crystallization of twinned crystalline guanine microplatelets. CrystEngComm 2019. [DOI: 10.1039/c9ce00920e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this work, twinned anhydrous guanine β microplatelets were synthesized for the first time in the presence of a polyvinylpyrrolidone. The twinning angle of the two c axes for the synthetic and biogenic twinned guanine crystals is 84°, very similar to each other.
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Affiliation(s)
- Yurong Ma
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Fenghua Chen
- Beijing National Laboratory for Molecular Sciences
- College of Chemistry
- Peking University
- Beijing 100871
- China
| | - Yiran Hu
- Beijing National Laboratory for Molecular Sciences
- College of Chemistry
- Peking University
- Beijing 100871
- China
| | - Yanan Liu
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Limin Qi
- Beijing National Laboratory for Molecular Sciences
- College of Chemistry
- Peking University
- Beijing 100871
- China
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15
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Wang X, Ding Y, Li D, Xie L, Xu W. Linear array of cesium atoms assisted by uracil molecules on Au(111). Chem Commun (Camb) 2019; 55:12064-12067. [DOI: 10.1039/c9cc05709a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of metal–organic U + Cs structures are achieved in which the Cs cations tend to form linear arrays.
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Affiliation(s)
- Xinyi Wang
- Interdisciplinary Materials Research Center
- College of Materials Science and Engineering
- Tongji University
- Shanghai 201804
- P. R. China
| | - Yuanqi Ding
- Interdisciplinary Materials Research Center
- College of Materials Science and Engineering
- Tongji University
- Shanghai 201804
- P. R. China
| | - Donglin Li
- Interdisciplinary Materials Research Center
- College of Materials Science and Engineering
- Tongji University
- Shanghai 201804
- P. R. China
| | - Lei Xie
- Interdisciplinary Materials Research Center
- College of Materials Science and Engineering
- Tongji University
- Shanghai 201804
- P. R. China
| | - Wei Xu
- Interdisciplinary Materials Research Center
- College of Materials Science and Engineering
- Tongji University
- Shanghai 201804
- P. R. China
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16
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Chen C, Ding P, Mura M, Chen Y, Sun Y, Kantorovich LN, Gersen H, Besenbacher F, Yu M. Formation of Hypoxanthine Tetrad by Reaction with Sodium Chloride: From Planar to Stereo. Angew Chem Int Ed Engl 2018; 57:16015-16019. [DOI: 10.1002/anie.201808613] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Chong Chen
- State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of Technology Harbin 150001 China
| | - Pengcheng Ding
- State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of Technology Harbin 150001 China
- Condensed Matter Science and Technology InstituteHarbin Institute of Technology Harbin 150001 China
| | - Manuela Mura
- School of Mathematics and PhysicsUniversity of Lincoln Brayford Pool LN6 7TS UK
| | - Yanghan Chen
- State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of Technology Harbin 150001 China
- Condensed Matter Science and Technology InstituteHarbin Institute of Technology Harbin 150001 China
| | - Ye Sun
- Condensed Matter Science and Technology InstituteHarbin Institute of Technology Harbin 150001 China
| | - Lev N. Kantorovich
- Department of PhysicsKing's College London The Strand London WC2R 2LS UK
| | - Henkjan Gersen
- H. H. Wills Physics LaboratoryUniversity of Bristol Bristol BS8 1TL UK
| | - Flemming Besenbacher
- Interdisciplinary Nanoscience Center (iNANO) and Department of Physics and AstronomyAarhus University Aarhus 8000 Denmark
| | - Miao Yu
- State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of Technology Harbin 150001 China
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17
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Chen C, Ding P, Mura M, Chen Y, Sun Y, Kantorovich LN, Gersen H, Besenbacher F, Yu M. Formation of Hypoxanthine Tetrad by Reaction with Sodium Chloride: From Planar to Stereo. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808613] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chong Chen
- State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of Technology Harbin 150001 China
| | - Pengcheng Ding
- State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of Technology Harbin 150001 China
- Condensed Matter Science and Technology InstituteHarbin Institute of Technology Harbin 150001 China
| | - Manuela Mura
- School of Mathematics and PhysicsUniversity of Lincoln Brayford Pool LN6 7TS UK
| | - Yanghan Chen
- State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of Technology Harbin 150001 China
- Condensed Matter Science and Technology InstituteHarbin Institute of Technology Harbin 150001 China
| | - Ye Sun
- Condensed Matter Science and Technology InstituteHarbin Institute of Technology Harbin 150001 China
| | - Lev N. Kantorovich
- Department of PhysicsKing's College London The Strand London WC2R 2LS UK
| | - Henkjan Gersen
- H. H. Wills Physics LaboratoryUniversity of Bristol Bristol BS8 1TL UK
| | - Flemming Besenbacher
- Interdisciplinary Nanoscience Center (iNANO) and Department of Physics and AstronomyAarhus University Aarhus 8000 Denmark
| | - Miao Yu
- State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of Technology Harbin 150001 China
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18
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Zhang L, Ulstrup J, Zhang J. Voltammetry and molecular assembly of G-quadruplex DNAzyme on single-crystal Au(111)-electrode surfaces - hemin as an electrochemical intercalator. Faraday Discuss 2018; 193:99-112. [PMID: 27722546 DOI: 10.1039/c6fd00091f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
DNA quadruplexes (qs) are a class of "non-canonical" oligonucleotides (OGNs) composed of stacked guanine (G) quartets stabilized by specific cations. Metal porphyrins selectively bind to G-qs complexes to form what is known as DNAzyme, which can exhibit peroxidase and other catalytic activity similar to heme group metalloenzymes. In the present study we investigate the electrochemical properties and the structure of DNAzyme monolayers on single-crystal Au(111)-electrode surfaces using cyclic voltammetry and scanning tunnelling microscopy under electrochemical potential control (in situ STM). The target DNAzyme is formed from a single-strand OGN with 12 guanines and iron(iii) porphyrin IX (hemin), and assembles on Au(111) through a mercapto alkyl linker. The DNAzyme monolayers exhibit a strong pair of redox peaks at 0.0 V (NHE) at pH 7 in acetate buffer, shifted positively by about 50 mV compared to free hemin weakly physisorbed on the Au(111)-electrode surface. The voltammetric hemin signal of DNAzyme is enhanced 15 times compared with that of hemin adsorbed directly on the Au(111)-electrode surface. This is indicative of both the formation of a close to dense DNAzyme monolayer and that hemin is strongly bound to the immobilized 12G-qs in well-defined orientation favorable for interfacial ET with a rate constant of 6.0 ± 0.4 s-1. This is supported by in situ STM which discloses single-molecule G-quartet structures with a size of 1.6 ± 0.2 nm.
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Affiliation(s)
- Ling Zhang
- Department of Chemistry, Technical University of Denmark, Building 207, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark.
| | - Jens Ulstrup
- Department of Chemistry, Technical University of Denmark, Building 207, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark.
| | - Jingdong Zhang
- Department of Chemistry, Technical University of Denmark, Building 207, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark.
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19
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Kong H, Zhang C, Sun Q, Yu X, Xie L, Wang L, Li L, Hu S, Ju H, He Y, Zhu J, Xu W. Nickel Adatoms Induced Tautomeric Dehydrogenation of Thymine Molecules on Au(111). ACS NANO 2018; 12:9033-9039. [PMID: 30130397 DOI: 10.1021/acsnano.8b02821] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tautomerization of nucleobases may induce base mismatches resulting in the abnormal disturbance of gene replication and expression, which has therefore attracted widespread interests in many disciplines. Metal atoms participating in a variety of important biological processes are found to be able to affect the nucleobase tautomerization as evidenced by many theoretical and spectroscopic studies. To get the real-space evidence and to unravel the underlying mechanism for the metal-induced tautomerization, especially from the keto form to the enol one, the interplay of high-resolution scanning tunneling microscopy imaging/manipulation and density functional theory (DFT) calculations has been employed. We present a process showing the Ni adatom-induced keto-enol tautomeric dehydrogenation of thymine molecules on Au(111). The key to making such a process feasible is the Ni atoms which greatly lower the energy barrier for the tautomerization from keto to enol form, which is rationalized by extensive DFT-based transition-state search calculations.
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Affiliation(s)
- Huihui Kong
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering , Nanjing University of Science and Technology , Xiaolingwei 200 , Nanjing 210094 , Jiangsu , P. R. China
| | - Chi Zhang
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Qiang Sun
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Xin Yu
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Lei Xie
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Likun Wang
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Lei Li
- Ministry of Education Key Laboratory of Green Preparation and Application for Functional Materials, School of Materials Science and Engineering , Hubei University , Wuhan 430062 , P. R. China
| | - Shanwei Hu
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei 230029 , P. R. China
| | - Huanxin Ju
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei 230029 , P. R. China
| | - Yunbin He
- Ministry of Education Key Laboratory of Green Preparation and Application for Functional Materials, School of Materials Science and Engineering , Hubei University , Wuhan 430062 , P. R. China
| | - Junfa Zhu
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei 230029 , P. R. China
| | - Wei Xu
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
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20
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Ding Y, Wang X, Xie L, Yao X, Xu W. Two-dimensional self-assembled nanostructures of nucleobases and their related derivatives on Au(111). Chem Commun (Camb) 2018; 54:9259-9269. [PMID: 30027963 DOI: 10.1039/c8cc03585g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The construction of two-dimensional (2D) self-assembled nanostructures has been one of the considerably interesting areas of on-surface chemistry in the past few decades, and has benefited from the rapid development and improvement of scanning probe microscopy techniques. In this research field, many attempts have been made in the controllable fabrication of well-ordered and multifunctional surface nanostructures, which attracted interest because of the prospect for artificial design of functional molecular nanodevices. DNA and RNA are considered to be programmable self-assembly systems and it is possible to use their base sequences to encode instructions for assembly in a predetermined fashion at the nanometer scale. As important constituents of nucleic acids, nucleobases, with intrinsic functional groups for hydrogen bonding, coordination bonding, and electrostatic interactions, can be employed as a potential system for the versatile construction of various biomolecular nanostructures, which may be used to structure the self-assembly of DNA-based artificial molecular constructions and play an important role in novel biosensors based on surface functionalization. In this article, we will review the recent progress of on-surface self-assembly of nucleobases and their derivatives together with different reactants (e.g., metals, halogens, salts and water), and as a result, various 2D surface nanostructures are summarized.
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Affiliation(s)
- Yuanqi Ding
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China.
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21
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Li W, Jin J, Liu X, Wang L. Structural Transformation of Guanine Coordination Motifs in Water Induced by Metal Ions and Temperature. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8092-8098. [PMID: 29905486 DOI: 10.1021/acs.langmuir.8b01263] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The transformation effects of metal ions and temperature on the DNA base guanine (G) metal-organic coordination motifs in water have been investigated by scanning tunneling microcopy (STM). The G molecules form an ordered hydrogen-bonded structure at the water-highly oriented pyrolytic graphite interface. The STM observations reveal that the canonical G/9H form can be transformed into the G/(3H,7H) tautomer by increasing the temperature of the G solution to 38.6 °C. Moreover, metal ions bind with G molecules to form G4Fe13+, G3Fe32+, and the heterochiral intermixed G4Na1+ metal-organic networks after the introduction of alkali-metal ions in cellular environment.
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Affiliation(s)
- Wei Li
- Department of Physics , Nanchang University , Nanchang 330031 , P. R. China
- Department of Science , Nanchang Institute of Technology , Nanchang 330099 , P. R. China
| | - Jing Jin
- Department of Physics , Nanchang University , Nanchang 330031 , P. R. China
| | - Xiaoqing Liu
- Department of Physics , Nanchang University , Nanchang 330031 , P. R. China
| | - Li Wang
- Department of Physics , Nanchang University , Nanchang 330031 , P. R. China
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22
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Zhang Y, Ding Y, Xie L, Ma H, Yao X, Zhang C, Yuan C, Xu W. On-Surface Synthesis of Adenine Oligomers via Ullmann Reaction. Chemphyschem 2017; 18:3544-3547. [PMID: 29028154 DOI: 10.1002/cphc.201701009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/12/2017] [Indexed: 11/07/2022]
Abstract
Despite the fact that DNA bases have been well-studied on surface, the on-surface synthesis of one-dimensional DNA analogs through in situ reactions is still an interesting topic to be investigated. Herein, from the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we have delicately designed a halogenated derivative of adenine as precursor to realize the combination of DNA bases and Ullmann reaction, and then successfully synthesized adenine oligomers on Au(111) via Ullmann coupling. This model system provides a possible bottom-up strategy of fabricating adenine oligomers on surface, which may further give access to man-made DNA strands with multiple bases.
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Affiliation(s)
- Yanmin Zhang
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Caoan Road 4800, Shanghai, 201804, P. R. China
| | - Yuanqi Ding
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Caoan Road 4800, Shanghai, 201804, P. R. China
| | - Lei Xie
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Caoan Road 4800, Shanghai, 201804, P. R. China
| | - Honghong Ma
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Caoan Road 4800, Shanghai, 201804, P. R. China
| | - Xinyi Yao
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Caoan Road 4800, Shanghai, 201804, P. R. China
| | - Chi Zhang
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Caoan Road 4800, Shanghai, 201804, P. R. China
| | - Chunxue Yuan
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Caoan Road 4800, Shanghai, 201804, P. R. China
| | - Wei Xu
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Caoan Road 4800, Shanghai, 201804, P. R. China
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23
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Ding Y, Xie L, Zhang C, Xu W. Real-space evidence of the formation of the GCGC tetrad and its competition with the G-quartet on the Au(111) surface. Chem Commun (Camb) 2017; 53:9846-9849. [PMID: 28825090 DOI: 10.1039/c7cc05548j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we show the first real-space evidence of the formation of GCGC tetrad on an Au(111) surface, and further investigate its competition with the well-known G-quartet with the aid of NaCl under ultrahigh vacuum (UHV) conditions.
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Affiliation(s)
- Yuanqi Ding
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China.
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24
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Xie L, Zhang C, Ding Y, E W, Yuan C, Xu W. Structural diversity of metal-organic self-assembly assisted by chlorine. Chem Commun (Camb) 2017; 53:8767-8769. [PMID: 28730208 DOI: 10.1039/c7cc04446a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From the combination of STM imaging and DFT calculations, we show that both alkali metal and halogens interact with different sites of the target molecules resulting in structural formation in a synergistic way. The elementary metal-organic motifs are connected by Cl in a variety of fashions demonstrating structural diversity.
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Affiliation(s)
- Lei Xie
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China.
| | - Chi Zhang
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China.
| | - Yuanqi Ding
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China.
| | - Wenlong E
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China.
| | - Chunxue Yuan
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China.
| | - Wei Xu
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China.
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25
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Centore R, Manfredi C, Capobianco A, Volino S, Ferrara MV, Carella A, Fusco S, Peluso A. Solid State Separation and Isolation of Tautomers of Fused-Ring Triazolotriazoles. J Org Chem 2017; 82:5155-5161. [PMID: 28452478 DOI: 10.1021/acs.joc.7b00380] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fine control of the tautomeric forms of [1,2,4]triazolo[3,2-c][1,2,4]triazole derivatives in acidic conditions has been achieved by acting on the electronic character of the substituent at position 7 of the heterobicycle and on the counterion. Strong electron releasing or electron withdrawing substituents lead almost exclusively to a single tautomeric form, the 1H-3H or the 2H-3H, respectively. In the case of the phenol substituent, both tautomeric forms are present in comparable amount in solution; the two tautomers can also be selectively precipitated in different crystalline salts using suitable counterions.
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Affiliation(s)
- Roberto Centore
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Carla Manfredi
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Amedeo Capobianco
- Department of Chemistry and Biology, University of Salerno , Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Sabato Volino
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Maria Vittoria Ferrara
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Antonio Carella
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Sandra Fusco
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Andrea Peluso
- Department of Chemistry and Biology, University of Salerno , Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
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26
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Cai L, Sun Q, Bao M, Ma H, Yuan C, Xu W. Competition between Hydrogen Bonds and Coordination Bonds Steered by the Surface Molecular Coverage. ACS NANO 2017; 11:3727-3732. [PMID: 28383885 DOI: 10.1021/acsnano.6b08374] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In addition to the choices of metal atoms/molecular linkers and surfaces, several crucial parameters, including surface temperature, molecular stoichiometric ratio, electrical stimulation, concentration, and solvent effect for liquid/solid interfaces, have been demonstrated to play key roles in the formation of on-surface self-assembled supramolecular architectures. Moreover, self-assembled structural transformations frequently occur in response to a delicate control over those parameters, which, in most cases, involve either conversions from relatively weak interactions to stronger ones (e.g., hydrogen bonds to coordination bonds) or transformations between the comparable interactions (e.g., different coordination binding modes or hydrogen bonding configurations). However, intermolecular bond conversions from relatively strong coordination bonds to weak hydrogen bonds were rarely reported. Moreover, to our knowledge, a reversible conversion between hydrogen bonds and coordination bonds has not been demonstrated before. Herein, we have demonstrated a facile strategy for the regulation of stepwise intermolecular bond conversions from the metal-organic coordination bond (Cu-N) to the weak hydrogen bond (CH···N) by increasing the surface molecular coverage. From the DFT calculations we quantify that the loss in intermolecular interaction energy is compensated by the increased molecular adsorption energy at higher molecular coverage. Moreover, we achieved a reversible conversion from the weak hydrogen bond to the coordination bond by decreasing the surface molecular coverage.
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Affiliation(s)
- Liangliang Cai
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University , Shanghai 201804, P. R. China
| | - Qiang Sun
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University , Shanghai 201804, P. R. China
| | - Meiling Bao
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University , Shanghai 201804, P. R. China
| | - Honghong Ma
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University , Shanghai 201804, P. R. China
| | - Chunxue Yuan
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University , Shanghai 201804, P. R. China
| | - Wei Xu
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University , Shanghai 201804, P. R. China
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27
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Novko D, Blanco-Rey M, Tremblay JC. Intermode Coupling Drives the Irreversible Tautomerization in Porphycene on Copper(111) Induced by Scanning Tunnelling Microscopy. J Phys Chem Lett 2017; 8:1053-1059. [PMID: 28198627 DOI: 10.1021/acs.jpclett.7b00141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this contribution, we develop a nonadiabatic theory that explains, from first-principles, the recently reported irreversible trans → cis tautomerization of porphycene on Cu(111) induced by a scanning tunnelling microscope at finite bias. The inelastic contribution to the STM current is found to excite a large number of skeletal vibrational modes of the molecule, thereby inducing a deformation of the potential energy landscape along the hydrogen transfer coordinate. Above a threshold bias, the stability of the tautomers is reversed, which indirectly drives the reaction via intermode coupling. The proposed potential deformation term accounts effectively for the excitation of all internal vibrational modes without increasing the dimensionality of the problem. The model yields information about reaction rates, explains the reaction irreversibility at low temperatures, and accounts for the presence of resonant processes.
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Affiliation(s)
- Dino Novko
- Donostia International Physics Center (DIPC) , Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - María Blanco-Rey
- Donostia International Physics Center (DIPC) , Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
- Departamento de Fı́sica de Materiales, Facultad de Quı́micas UPV/EHU , Apartado 1072, 20018 Donostia-San Sebastián, Spain
| | - Jean Christophe Tremblay
- Institut für Chemie und Biochemie, Freie Universität Berlin , Takustrasse 3, 14195 Berlin, Germany
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28
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Novko D, Tremblay JC, Blanco-Rey M. On the tautomerisation of porphycene on copper (111): Finding the subtle balance between van der Waals interactions and hybridisation. J Chem Phys 2016; 145:244701. [DOI: 10.1063/1.4972213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Dino Novko
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Jean Christophe Tremblay
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany
| | - María Blanco-Rey
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
- Departamento de Física de Materiales, Facultad de Químicas UPV/EHU, Apartado 1072, 20018 Donostia-San Sebastián, Spain
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Kong H, Zhang C, Xie L, Wang L, Xu W. Constitutional Dynamics of Metal-Organic Motifs on a Au(111) Surface. Angew Chem Int Ed Engl 2016; 55:7157-60. [DOI: 10.1002/anie.201602572] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 04/07/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Huihui Kong
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Caoan Road 4800 Shanghai 201804 P.R. China
| | - Chi Zhang
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Caoan Road 4800 Shanghai 201804 P.R. China
| | - Lei Xie
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Caoan Road 4800 Shanghai 201804 P.R. China
| | - Likun Wang
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Caoan Road 4800 Shanghai 201804 P.R. China
| | - Wei Xu
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Caoan Road 4800 Shanghai 201804 P.R. China
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Kong H, Zhang C, Xie L, Wang L, Xu W. Constitutional Dynamics of Metal-Organic Motifs on a Au(111) Surface. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602572] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Huihui Kong
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Caoan Road 4800 Shanghai 201804 P.R. China
| | - Chi Zhang
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Caoan Road 4800 Shanghai 201804 P.R. China
| | - Lei Xie
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Caoan Road 4800 Shanghai 201804 P.R. China
| | - Likun Wang
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Caoan Road 4800 Shanghai 201804 P.R. China
| | - Wei Xu
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Caoan Road 4800 Shanghai 201804 P.R. China
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Zhang C, Xie L, Ding Y, Sun Q, Xu W. Real-Space Evidence of Rare Guanine Tautomer Induced by Water. ACS NANO 2016; 10:3776-3782. [PMID: 26876579 DOI: 10.1021/acsnano.6b00393] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Water is vital for life as a solvent. Specifically, it has been well established that DNA molecules are hydrated in vivo, and water has been found to be responsible for the presence of some noncanonical DNA base tautomers. Theoretical investigations have shown that the existence of water could significantly influence the relative stability of different DNA base tautomers, reduce the energy barrier of tautomeric conversions, and thus promote the formation of some rare base tautomers. In this work, we report the real-space experimental evidence of rare base tautomers. From the high-resolution scanning tunneling microscopy imaging, we surprisingly find the formation of the rare guanine tautomer, i.e., G/(3H,7H) form, on the Au(111) surface by delicately introducing water into the system. The key to the formation of this rare tautomer is proposed to be the "water bridge" that largely reduces the energy barriers of intramolecular proton-transfer processes as revealed by extensive density functional theory calculations. The real-space experimental evidence and the proposed mechanism make a step forward toward the fundamental understanding of water-assisted base tautomerization processes.
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Affiliation(s)
- Chi Zhang
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University , Caoan Road 4800, Shanghai 201804, People's Republic of China
| | - Lei Xie
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University , Caoan Road 4800, Shanghai 201804, People's Republic of China
| | - Yuanqi Ding
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University , Caoan Road 4800, Shanghai 201804, People's Republic of China
| | - Qiang Sun
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University , Caoan Road 4800, Shanghai 201804, People's Republic of China
| | - Wei Xu
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University , Caoan Road 4800, Shanghai 201804, People's Republic of China
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Huang H, Tan Z, He Y, Liu J, Sun J, Zhao K, Zhou Z, Tian G, Wong SL, Wee ATS. Competition between Hexagonal and Tetragonal Hexabromobenzene Packing on Au(111). ACS NANO 2016; 10:3198-3205. [PMID: 26905460 DOI: 10.1021/acsnano.5b04970] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Low-temperature scanning tunneling microscope investigations reveal that hexabromobenzene (HBB) molecules arrange in either hexagonally closely packed (hcp) [Formula: see text] or tetragonal [Formula: see text] structure on Au(111) dependent on a small substrate temperature difference around 300 K. The underlying mechanism is investigated by density functional theory calculations, which reveal that substrate-mediated intermolecular noncovalent C-Br···Br-C attractions induce hcp HBB islands, keeping the well-known Au(111)-22×√3 reconstruction intact. Upon deposition at 330 K, HBB molecules trap freely diffusing Au adatoms to form tetragonal islands. This enhances the attraction between HBB and Au(111) but partially reduces the intermolecular C-Br···Br-C attractions, altering the Au(111)-22×√3 reconstruction. In both cases, the HBB molecule adsorbs on a bridge site, forming a ∼15° angle between the C-Br direction and [112̅]Au, indicating the site-specific molecule-substrate interactions. We show that the competition between intermolecular and molecule-substrate interactions determines molecule packing at the subnanometer scale, which will be helpful for crystal engineering, functional materials, and organic electronics.
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Affiliation(s)
- Han Huang
- Department of Physics, National University of Singapore , 2 Science Drive 3, Singapore 117542, Singapore
- Centre for Advanced 2D Materials, National University of Singapore , Block S14, Level 6, 6 Science Drive 2, Singapore 117546, Singapore
| | | | | | - Jian Liu
- Institute of Physics, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
| | - Jiatao Sun
- Institute of Physics, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
| | | | | | | | - Swee Liang Wong
- Institute of Materials Research and Engineering, Agency for Science Technology and Research , 3, Research Link, Singapore 117602, Singapore
| | - Andrew Thye Shen Wee
- Department of Physics, National University of Singapore , 2 Science Drive 3, Singapore 117542, Singapore
- Centre for Advanced 2D Materials, National University of Singapore , Block S14, Level 6, 6 Science Drive 2, Singapore 117546, Singapore
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