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Sreelakshmi PA, Mahashaya R, Leitherer S, Rashid U, Hamill JM, Nair M, Rajamalli P, Kaliginedi V. Electric Field-Induced Sequential Prototropic Tautomerism in Enzyme-like Nanopocket Created by Single Molecular Break Junction. J Am Chem Soc 2024; 146:35242-35251. [PMID: 39496492 DOI: 10.1021/jacs.4c12423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2024]
Abstract
Mastering the control of external stimuli-induced chemical transformations with detailed insights into the mechanistic pathway is the key for developing efficient synthetic strategies and designing functional molecular systems. Enzymes, the most potent biological catalysts, efficiently utilize their built-in electric field to catalyze and control complex chemical reactions within the active site. Herein, we have demonstrated the interfacial electric field-induced prototropic tautomerization reaction in acylhydrazone entities by creating an enzymatic-like nanopocket within the atomically sharp gold electrodes using a mechanically controlled break junction (MCBJ) technique. In addition to that, the molecular system used here contains two coupled acylhydrazone reaction centers, hence demonstrating a cooperative stepwise electric field-induced reaction realized at the single molecular level. Furthermore, the mechanistic studies revealed a proton relay-assisted tautomerization showing the importance of external factors such as solvent in such electric field-driven reactions. Finally, single-molecule charge transport and energetics calculations of different molecular species at various applied electric fields using a polarizable continuum solvent model confirm and support our experimental findings. Thus, this study demonstrates that mimicking an enzymatic pocket using a single molecular junction's interfacial electric field as a trigger for chemical reactions can open new avenues to the field of synthetic chemistry.
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Affiliation(s)
- P A Sreelakshmi
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Rahul Mahashaya
- Materials Research Centre, Indian Institute of Science, Bangalore 560012, India
| | - Susanne Leitherer
- Department of Chemistry and Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK- 2100 Copenhagen Ø, Denmark
| | - Umar Rashid
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Joseph M Hamill
- Department of Chemistry and Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK- 2100 Copenhagen Ø, Denmark
| | - Manivarna Nair
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | | | - Veerabhadrarao Kaliginedi
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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2
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Bro-Jørgensen W, Hamill JM, Mezei G, Lawson B, Rashid U, Halbritter A, Kamenetska M, Kaliginedi V, Solomon GC. Making the Most of Nothing: One-Class Classification for Single-Molecule Transport Studies. ACS NANOSCIENCE AU 2024; 4:250-262. [PMID: 39184833 PMCID: PMC11342344 DOI: 10.1021/acsnanoscienceau.4c00015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 08/27/2024]
Abstract
Single-molecule experiments offer a unique means to probe molecular properties of individual molecules-yet they rest upon the successful control of background noise and irrelevant signals. In single-molecule transport studies, large amounts of data that probe a wide range of physical and chemical behaviors are often generated. However, due to the stochasticity of these experiments, a substantial fraction of the data may consist of blank traces where no molecular signal is evident. One-class (OC) classification is a machine learning technique to identify a specific class in a data set that potentially consists of a wide variety of classes. Here, we examine the utility of two different types of OC classification models on four diverse data sets from three different laboratories. Two of these data sets were measured at cryogenic temperatures and two at room temperature. By training the models solely on traces from a blank experiment, we demonstrate the efficacy of OC classification as a powerful and reliable method for filtering out blank traces from a molecular experiment in all four data sets. On a labeled 4,4'-bipyridine data set measured at 4.2 K, we achieve an accuracy of 96.9 ± 0.3 and an area under the receiver operating characteristic curve of 99.5 ± 0.3 as validated over a fivefold cross-validation. Given the wide range of physical and chemical properties that can be probed in single-molecule experiments, the successful application of OC classification to filter out blank traces is a major step forward in our ability to understand and manipulate molecular properties.
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Affiliation(s)
- William Bro-Jørgensen
- Department
of Chemistry and Nano-Science Center, University
of Copenhagen, Universitetsparken
5, Copenhagen Ø DK-2100, Denmark
| | - Joseph M. Hamill
- Department
of Chemistry and Nano-Science Center, University
of Copenhagen, Universitetsparken
5, Copenhagen Ø DK-2100, Denmark
| | - Gréta Mezei
- Department
of Physics, Institute of Physics, Budapest
University of Technology and Economics, Műegyetem rkp. 3., Budapest H-1111, Hungary
- ELKH-BME
Condensed Matter Research Group, Műegyetem rkp. 3., Budapest H-1111, Hungary
| | - Brent Lawson
- Department
of Physics, Chemistry and Division of Material Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Umar Rashid
- Department
of Inorganic and Physical Chemistry, Indian
Institute of Science, Bangalore 560012, India
| | - András Halbritter
- Department
of Physics, Institute of Physics, Budapest
University of Technology and Economics, Műegyetem rkp. 3., Budapest H-1111, Hungary
- ELKH-BME
Condensed Matter Research Group, Műegyetem rkp. 3., Budapest H-1111, Hungary
| | - Maria Kamenetska
- Department
of Physics, Chemistry and Division of Material Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Veerabhadrarao Kaliginedi
- Department
of Inorganic and Physical Chemistry, Indian
Institute of Science, Bangalore 560012, India
| | - Gemma C. Solomon
- Department
of Chemistry and Nano-Science Center, University
of Copenhagen, Universitetsparken
5, Copenhagen Ø DK-2100, Denmark
- NNF
Quantum
Computing Programme, Niels Bohr Institute, University of Copenhagen, Jagtvej 155 A, Copenhagen N DK-2200, Denmark
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3
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Gao C, Gao Q, Zhao C, Huo Y, Zhang Z, Yang J, Jia C, Guo X. Technologies for investigating single-molecule chemical reactions. Natl Sci Rev 2024; 11:nwae236. [PMID: 39224448 PMCID: PMC11367963 DOI: 10.1093/nsr/nwae236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 09/04/2024] Open
Abstract
Single molecules, the smallest independently stable units in the material world, serve as the fundamental building blocks of matter. Among different branches of single-molecule sciences, single-molecule chemical reactions, by revealing the behavior and properties of individual molecules at the molecular scale, are particularly attractive because they can advance the understanding of chemical reaction mechanisms and help to address key scientific problems in broad fields such as physics, chemistry, biology and materials science. This review provides a timely, comprehensive overview of single-molecule chemical reactions based on various technical platforms such as scanning probe microscopy, single-molecule junction, single-molecule nanostructure, single-molecule fluorescence detection and crossed molecular beam. We present multidimensional analyses of single-molecule chemical reactions, offering new perspectives for research in different areas, such as photocatalysis/electrocatalysis, organic reactions, surface reactions and biological reactions. Finally, we discuss the opportunities and challenges in this thriving field of single-molecule chemical reactions.
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Affiliation(s)
- Chunyan Gao
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Qinghua Gao
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Cong Zhao
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Yani Huo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Zhizhuo Zhang
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Jinlong Yang
- Hefei National Research Center for Physical Sciences at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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4
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Gorenskaia E, Low PJ. Methods for the analysis, interpretation, and prediction of single-molecule junction conductance behaviour. Chem Sci 2024; 15:9510-9556. [PMID: 38939131 PMCID: PMC11206205 DOI: 10.1039/d4sc00488d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/06/2024] [Indexed: 06/29/2024] Open
Abstract
This article offers a broad overview of measurement methods in the field of molecular electronics, with a particular focus on the most common single-molecule junction fabrication techniques, the challenges in data analysis and interpretation of single-molecule junction current-distance traces, and a summary of simulations and predictive models aimed at establishing robust structure-property relationships of use in the further development of molecular electronics.
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Affiliation(s)
- Elena Gorenskaia
- School of Molecular Sciences, University of Western Australia 35 Stirling Highway Crawley Western Australia 6026 Australia
| | - Paul J Low
- School of Molecular Sciences, University of Western Australia 35 Stirling Highway Crawley Western Australia 6026 Australia
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5
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Guo J, Chen PK, Chang S. Molecular-Scale Electronics: From Individual Molecule Detection to the Application of Recognition Sensing. Anal Chem 2024; 96:9303-9316. [PMID: 38809941 DOI: 10.1021/acs.analchem.3c04656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
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6
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Wang D, Wang Y, Zimudzi TJ, Chen LQ, Yang J. Harnessing the duality of bases toward controlled color and fluorescence. SCIENCE ADVANCES 2024; 10:eadn9692. [PMID: 38758781 PMCID: PMC11100562 DOI: 10.1126/sciadv.adn9692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/12/2024] [Indexed: 05/19/2024]
Abstract
Bases can promote keto-enol tautomerism, a prevalent form of prototropic tautomerism, and facilitate the ring opening of anhydride ring structures. The intrinsic chemical distinctions between these processes provide an opportunity to modulate these seemingly parallel reactions. However, this potential remains largely unexplored. In this work, we report homophthalic anhydride, the first molecule exhibiting simultaneous halochromism, turn-on fluorescence (halofluorochromism), and subsequent self-destruction. Through comprehensive spectroscopic analysis and theoretical calculations, we unravel the mechanisms underlying these phenomena, revealing that the pivotal roles of the base's basicity and nucleophilicity specifically allow us to achieve controlled durations of color change and turn-on fluorescence. Capitalizing on these intriguing properties, we develop a highly dynamic CMY (cyan-magenta-yellow) palette ideal for entity encryption and anti-counterfeiting applications. Our work reshapes the understanding of the relationship between the basicity and nucleophilicity of bases, enriching the comprehension of keto-enol tautomerism and homophthalic anhydride chemistry, and unveils a spectrum of potential applications.
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Affiliation(s)
- Dingbowen Wang
- School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang 310030, China
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Wang
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tawanda J. Zimudzi
- Materials Research Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Long-Qing Chen
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jian Yang
- School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang 310030, China
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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7
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Chen L, Yang Z, Lin Q, Li X, Bai J, Hong W. Evolution of Single-Molecule Electronic Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1988-2004. [PMID: 38227964 DOI: 10.1021/acs.langmuir.3c03104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Single-molecule electronics can fabricate single-molecule devices via the construction of molecule-electrode interfaces and also provide a unique tool to investigate single-molecule scale physicochemical processes at these interfaces. To investigate single-molecule electronic devices with desired functionalities, an understanding of the interface evolution processes in single-molecule devices is essential. In this review, we focus on the evolution of molecule-electrode interface properties, including the background of interface evolution in single-molecule electronics, the construction of different types of single-molecule interfaces, and the regulation methods. Finally, we discuss the perspective of future characterization techniques and applications for single-molecule electronic interfaces.
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Affiliation(s)
- Lichuan Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen 361000, China
| | - Zixian Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen 361000, China
| | - Qichao Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen 361000, China
| | - Xiaohui Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen 361000, China
| | - Jie Bai
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen 361000, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen 361000, China
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