1
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Portela PC, Shipps CC, Shen C, Srikanth V, Salgueiro CA, Malvankar NS. Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE. Nat Commun 2024; 15:2434. [PMID: 38509081 PMCID: PMC10954620 DOI: 10.1038/s41467-024-46192-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
Extracellular electron transfer (EET) via microbial nanowires drives globally-important environmental processes and biotechnological applications for bioenergy, bioremediation, and bioelectronics. Due to highly-redundant and complex EET pathways, it is unclear how microbes wire electrons rapidly (>106 s-1) from the inner-membrane through outer-surface nanowires directly to an external environment despite a crowded periplasm and slow (<105 s-1) electron diffusion among periplasmic cytochromes. Here, we show that Geobacter sulfurreducens periplasmic cytochromes PpcABCDE inject electrons directly into OmcS nanowires by binding transiently with differing efficiencies, with the least-abundant cytochrome (PpcC) showing the highest efficiency. Remarkably, this defined nanowire-charging pathway is evolutionarily conserved in phylogenetically-diverse bacteria capable of EET. OmcS heme reduction potentials are within 200 mV of each other, with a midpoint 82 mV-higher than reported previously. This could explain efficient EET over micrometres at ultrafast (<200 fs) rates with negligible energy loss. Engineering this minimal nanowire-charging pathway may yield microbial chassis with improved performance.
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Affiliation(s)
- Pilar C Portela
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Catharine C Shipps
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Carlos A Salgueiro
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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2
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Marongiu M, Ha T, Gil-Guerrero S, Garg K, Mandado M, Melle-Franco M, Diez-Perez I, Mateo-Alonso A. Molecular Graphene Nanoribbon Junctions. J Am Chem Soc 2024; 146:3963-3973. [PMID: 38305745 PMCID: PMC10870704 DOI: 10.1021/jacs.3c11340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/20/2023] [Accepted: 01/12/2024] [Indexed: 02/03/2024]
Abstract
One of the challenges for the realization of molecular electronics is the design of nanoscale molecular wires displaying long-range charge transport. Graphene nanoribbons are an attractive platform for the development of molecular wires with long-range conductance owing to their unique electrical properties. Despite their potential, the charge transport properties of single nanoribbons remain underexplored. Herein, we report a synthetic approach to prepare N-doped pyrene-pyrazinoquinoxaline molecular graphene nanoribbons terminated with diamino anchoring groups at each end. These terminal groups allow for the formation of stable molecular graphene nanoribbon junctions between two metal electrodes that were investigated by scanning tunneling microscope-based break-junction measurements. The experimental and computational results provide evidence of long-range tunneling charge transport in these systems characterized by a shallow conductance length dependence and electron tunneling through >6 nm molecular backbone.
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Affiliation(s)
- Mauro Marongiu
- POLYMAT, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 Donostia-San Sebastian, Spain
| | - Tracy Ha
- Department
of Chemistry, Faculty of Natural & Mathematical Sciences, King’s College London, Britannia House, 7 Trinity Street, SE1 1DB London, United Kingdom
| | - Sara Gil-Guerrero
- CICECO—Aveiro
Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Kavita Garg
- Department
of Chemistry, Faculty of Natural & Mathematical Sciences, King’s College London, Britannia House, 7 Trinity Street, SE1 1DB London, United Kingdom
| | - Marcos Mandado
- Department
of Physical Chemistry, University of Vigo, Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Manuel Melle-Franco
- CICECO—Aveiro
Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ismael Diez-Perez
- Department
of Chemistry, Faculty of Natural & Mathematical Sciences, King’s College London, Britannia House, 7 Trinity Street, SE1 1DB London, United Kingdom
| | - Aurelio Mateo-Alonso
- POLYMAT, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 Donostia-San Sebastian, Spain
- Ikerbasque, Basque
Foundation for Science, 48009 Bilbao, Spain
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3
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Scarpetta-Pizo L, Venegas R, Barrías P, Muñoz-Becerra K, Vilches-Labbé N, Mura F, Méndez-Torres AM, Ramírez-Tagle R, Toro-Labbé A, Hevia S, Zagal JH, Oñate R, Aspée A, Ponce I. Electron Spin-Dependent Electrocatalysis for the Oxygen Reduction Reaction in a Chiro-Self-Assembled Iron Phthalocyanine Device. Angew Chem Int Ed Engl 2024; 63:e202315146. [PMID: 37953459 DOI: 10.1002/anie.202315146] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/14/2023]
Abstract
The chiral-induced spin selectivity effect (CISS) is a breakthrough phenomenon that has revolutionized the field of electrocatalysis. We report the first study on the electron spin-dependent electrocatalysis for the oxygen reduction reaction, ORR, using iron phthalocyanine, FePc, a well-known molecular catalyst for this reaction. The FePc complex belongs to the non-precious catalysts group, whose active site, FeN4, emulates catalytic centers of biocatalysts such as Cytochrome c. This study presents an experimental platform involving FePc self-assembled to a gold electrode surface using chiral peptides (L and D enantiomers), i.e., chiro-self-assembled FePc systems (CSAFePc). The chiral peptides behave as spin filters axial ligands of the FePc. One of the main findings is that the peptides' handedness and length in CSAFePc can optimize the kinetics and thermodynamic factors governing ORR. Moreover, the D-enantiomer promotes the highest electrocatalytic activity of FePc for ORR, shifting the onset potential up to 1.01 V vs. RHE in an alkaline medium, a potential close to the reversible potential of the O2 /H2 O couple. Therefore, this work has exciting implications for developing highly efficient and bioinspired catalysts, considering that, in biological organisms, biocatalysts that promote O2 reduction to water comprise L-enantiomers.
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Affiliation(s)
- Laura Scarpetta-Pizo
- Departamento de Ciencias del Ambiente, Departamento Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estación Central, Santiago, Chile
| | - Ricardo Venegas
- Departamento de Ciencias del Ambiente, Departamento Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estación Central, Santiago, Chile
| | - Pablo Barrías
- Departamento de Ciencias del Ambiente, Departamento Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estación Central, Santiago, Chile
| | - Karina Muñoz-Becerra
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O'Higgins, General Gana 1702, Santiago, 8370854, Chile
| | - Nayareth Vilches-Labbé
- Departamento de Ciencias del Ambiente, Departamento Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estación Central, Santiago, Chile
| | - Francisco Mura
- Departamento de Ciencias del Ambiente, Departamento Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estación Central, Santiago, Chile
| | - Ana María Méndez-Torres
- Departamento de Ciencias del Ambiente, Departamento Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estación Central, Santiago, Chile
| | - Rodrigo Ramírez-Tagle
- Facultad de Ingeniería y Arquitectura Universidad Central de Chile, Av. Sta. Isabel 1186, Santiago, 8330563, Chile
| | - Alejandro Toro-Labbé
- Departamento de Química-Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Región Metropolitana, Santiago, Chile
| | - Samuel Hevia
- Instituto de Física, Centro de Investigación en Nanotecnología y Materiales Avanzados (CIEN-UC), Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago, 6904411, Chile
| | - José H Zagal
- Departamento de Ciencias del Ambiente, Departamento Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estación Central, Santiago, Chile
| | - Rubén Oñate
- Departamento de Ciencias del Ambiente, Departamento Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estación Central, Santiago, Chile
| | - Alexis Aspée
- Departamento de Ciencias del Ambiente, Departamento Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estación Central, Santiago, Chile
| | - Ingrid Ponce
- Departamento de Ciencias del Ambiente, Departamento Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estación Central, Santiago, Chile
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4
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Jena MK, Mittal S, Manna SS, Pathak B. Deciphering DNA nucleotide sequences and their rotation dynamics with interpretable machine learning integrated C 3N nanopores. NANOSCALE 2023; 15:18080-18092. [PMID: 37916991 DOI: 10.1039/d3nr03771a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
A solid-state nanopore combined with the quantum transport method has garnered substantial attention and intrigue for DNA sequencing due to its potential for providing rapid and accurate sequencing results, which could have numerous applications in disease diagnosis and personalized medicine. However, the intricate and multifaceted nature of the experimental protocol poses a formidable challenge in attaining precise single nucleotide analysis. Here, we report a machine learning (ML) framework combined with the quantum transport method to accelerate high-throughput single nucleotide recognition with C3N nanopores. The optimized eXtreme Gradient Boosting Regression (XGBR) algorithm has predicted the fingerprint transmission of each unknown nucleotide and their rotation dynamics with root mean square error scores as low as 0.07. Interpretability of ML black box models with the game theory-based SHapley Additive exPlanation method has provided a quasi-explanation for the model working principle and the complex relationship between electrode-nucleotide coupling and transmission. Moreover, a comprehensive ML classification of nucleotides based on binary, ternary, and quaternary combinations shows maximum accuracy and F1 scores of 100%. The results suggest that ML in tandem with a nanopore device can potentially alleviate the experimental hurdles associated with quantum tunneling and facilitate fast and high-precision DNA sequencing.
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Affiliation(s)
- Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| | - Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| | - Surya Sekhar Manna
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
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5
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Tiwari SK, Pandey SK, Pandey R, Wang N, Bystrzejewski M, Mishra YK, Zhu Y. Stone-Wales Defect in Graphene. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303340. [PMID: 37386778 DOI: 10.1002/smll.202303340] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Indexed: 07/01/2023]
Abstract
2D graphene the most investigated structures from nanocarbon family studied in the last three decades. It is projected as an excellent material useful for quantum computing, artificial intelligence, and next generation advanced technologies. Graphene exists in several forms and its extraordinary thermal, mechanical, and electronic properties, principally depend on the kind of perfection of the hexagonal atomic lattice. Defects are always considered as undesired components but certain defects in graphene could be an asset for electrochemistry and quantum electronics due to the engineered electronclouds and quantum tunnelling. The authors carefully discuss the Stone-Wales imperfections in graphene and its derivatives comprehensively. A specific emphasis is focused on the experimental and theoretical aspects of the Stone-Wales defects in graphene with respect to structure-property relationships. The corroboration of extrinsic defects like external atomic doping, functionalization, edge distortion in the graphene consisting of Stone-Wales imperfections, which are very significant in designing graphene-based electronic devices, are summarized.
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Affiliation(s)
- Santosh K Tiwari
- Key Laboratory of New Processing Technology for Nonferrous Metals and Materials, Ministry of Education, School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China
- Department of Chemistry, NMAM Institute of Technology, Nitte (Deemed to be University), Mangaluru, Karnataka, 547110, India
| | - Sarvesh Kumar Pandey
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, Rajasthan, 303007, India
| | - Raunak Pandey
- Department of Chemical Science and Engineering, Kathmandu University, Dhulikhel, 44600, Nepal
| | - Nannan Wang
- Key Laboratory of New Processing Technology for Nonferrous Metals and Materials, Ministry of Education, School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China
| | | | - Yogendra Kumar Mishra
- Smart Materials, NanoSYD, Mads Clausen Institute, University of Southern Denmark, Alsion 2, Sønderborg, 6400, Denmark
| | - Yanqiu Zhu
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, EX4 4QF, UK
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6
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Dumont R, Dowdell J, Song J, Li J, Wang S, Kang W, Li B. Control of charge transport in electronically active systems towards integrated biomolecular circuits (IbC). J Mater Chem B 2023; 11:8302-8314. [PMID: 37464922 DOI: 10.1039/d3tb00701d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The miniaturization of traditional silicon-based electronics will soon reach its limitation as quantum tunneling and heat become serious problems at the several-nanometer scale. Crafting integrated circuits via self-assembly of electronically active molecules using a "bottom-up" paradigm provides a potential solution to these technological challenges. In particular, integrated biomolecular circuits (IbC) offer promising advantages to achieve this goal, as nature offers countless examples of functionalities entailed by self-assembly and examples of controlling charge transport at the molecular level within the self-assembled structures. To this end, the review summarizes the progress in understanding how charge transport is regulated in biosystems and the key redox-active amino acids that enable the charge transport. In addition, charge transport mechanisms at different length scales are also reviewed, offering key insights for controlling charge transport in IbC in the future.
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Affiliation(s)
- Ryan Dumont
- Department of Mechanical Engineering, Kennesaw State University, Marietta, GA, USA.
| | - Juwaan Dowdell
- Department of Mechanical Engineering, Kennesaw State University, Marietta, GA, USA.
| | - Jisoo Song
- Department of Mechanical Engineering, Kennesaw State University, Marietta, GA, USA.
| | - Jiani Li
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, China.
| | - Suwan Wang
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, China.
| | - Wei Kang
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, China.
- Ningbo Institute of Dalian University of Technology, Ningbo, China
| | - Bo Li
- Department of Mechanical Engineering, Kennesaw State University, Marietta, GA, USA.
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7
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Azami SM, Kheirmand M. Evaluation of Charge and Energy Storage in Molecular Nanocapacitors. J Phys Chem A 2023. [PMID: 37319433 DOI: 10.1021/acs.jpca.3c02025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
A model is presented herein for the evaluation of stored charge and energy in molecular-scale capacitors composed of parallel nanosheets. In this model, the nanocapacitor is exposed to an external electric field, and the charging process is considered as a three-stage mechanism, including isolated, exposed, and frozen stages, where each stage possesses its own Hamiltonian and wavefunction. In this way, the third stage's Hamiltonian is the same as that of the first stage, while its wavefunction is frozen to that of the second stage, and consequently, stored energy can be calculated as the expectation value of second stage's wavefunction with respect to the first stage's Hamiltonian. Electron density is then integrated over half-space, i.e., the space separated by a virtual plane located at the middle and parallel to electrodes, to reveal stored charge on nanosheets. The formalism is applied to two parallel hexagonal graphene flakes as nanocapacitor's electrodes, and results are compared with experimental values of similar systems.
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Affiliation(s)
- S M Azami
- Chemistry Department, College of Sciences, Yasouj University, Yasouj 75918-74934, Iran
| | - M Kheirmand
- Chemistry Department, College of Sciences, Yasouj University, Yasouj 75918-74934, Iran
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8
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Jena MK, Pathak B. Development of an Artificially Intelligent Nanopore for High-Throughput DNA Sequencing with a Machine-Learning-Aided Quantum-Tunneling Approach. NANO LETTERS 2023; 23:2511-2521. [PMID: 36799480 DOI: 10.1021/acs.nanolett.2c04062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Solid-state nanopore-based single-molecule DNA sequencing with quantum tunneling technology poses formidable challenges to achieve long-read sequencing and high-throughput analysis. Here, we propose a method for developing an artificially intelligent (AI) nanopore that does not require extraction of the signature transmission function for each nucleotide of the whole DNA strand by integrating supervised machine learning (ML) and transverse quantum transport technology with a graphene nanopore. The optimized ML model can predict the transmission function of all other nucleotides after training with data sets of all the orientations of any nucleotide inside the nanopore with a root-mean-square error (RMSE) of as low as 0.062. Further, up to 96.01% accuracy is achieved in classifying the unlabeled nucleotides with their transmission readouts. We envision that an AI nanopore can alleviate the experimental challenges of the quantum-tunneling method and pave the way for rapid and high-precision DNA sequencing by predicting their signature transmission functions.
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Affiliation(s)
- Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh 453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh 453552, India
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9
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Sun F, Tan S, Cao HJ, Lu CS, Tu D, Poater J, Solà M, Yan H. Facile Construction of New Hybrid Conjugation via Boron Cage Extension. J Am Chem Soc 2023; 145:3577-3587. [PMID: 36744315 DOI: 10.1021/jacs.2c12526] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aromatic polycyclic systems have been extensively utilized as structural subunits for the preparation of various functional molecules. Currently, aromatics-based polycyclic systems are predominantly generated from the extension of two-dimensional (2D) aromatic rings. In contrast, polycyclic compounds based on the extension of three-dimensional (3D) aromatics such as boron clusters are less studied. Here, we report three types of boron cluster-cored tricyclic molecular systems, which are constructed from a 2D aromatic ring, a 3D aromatic nido-carborane, and an alkyne. These new tricyclic compounds can be facilely accessed by Pd-catalyzed B-H activation and the subsequent cascade heteroannulation of carborane and pyridine with an alkyne in an isolated yield of up to 85% under mild conditions without any additives. Computational results indicate that the newly generated ring from the fusion of the 3D carborane, the 2D pyridyl ring, and an alkyne is non-aromatic. However, such fusion not only leads to a 1H chemical shift considerably downfield shifted owing to the strong diatropic ring current of the embedded carborane but also devotes to new/improved physicochemical properties including increased thermal stability, the emergence of a new absorption band, and a largely red-shifted emission band and enhanced emission efficiency. Besides, a number of bright, color-tunable solid emitters spanning over all visible light are obtained with absolute luminescence efficiency of up to 61%, in contrast to aggregation-caused emission quenching of, e.g., Rhodamine B containing a 2D-aromatics-fused structure. This work demonstrates that the new hybrid conjugated tricyclic systems might be promising structural scaffolds for the construction of functional molecules.
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Affiliation(s)
- Fangxiang Sun
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuaimin Tan
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hou-Ji Cao
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Chang-Sheng Lu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Deshuang Tu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jordi Poater
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, Barcelona 08028, Spain.,ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany, 69, Girona 17003, Catalonia, Spain
| | - Hong Yan
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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10
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Takashima Y, Komoto Y, Ohshiro T, Nakatani K, Taniguchi M. Quantitative Microscopic Observation of Base-Ligand Interactions via Hydrogen Bonds by Single-Molecule Counting. J Am Chem Soc 2023; 145:1310-1318. [PMID: 36597667 DOI: 10.1021/jacs.2c11260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chemical properties have been based on statistical averages since the introduction of Avogadro's number. The lack of suitable methods for counting identified single molecules has posed challenges to counting statistics. The selectivity, affinity, and mode of hydrogen bonding between base and small molecules that make up DNA, which is vital for living organisms, have not yet been revealed at the single molecule level. Here, we show the quantitation of the above-mentioned parameters via single-molecule counting based on the combination of single-molecule electrical measurements and AI. The binding selectivity values of five ligands to four different base molecules were evaluated quantitatively by determining the ratio of the number of aggregates in a solution mixture of base molecules and a ligand. In addition, we show the ligand dependence of the mode and number of microscopic hydrogen bonds via single-molecule counting and quantum chemical calculations.
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Affiliation(s)
- Yusuke Takashima
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan
| | - Yuki Komoto
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan.,Artificial Intelligence Research Center, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), OsakaUniversity, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan
| | - Takahito Ohshiro
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan
| | - Kazuhiko Nakatani
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan
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11
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Jena MK, Roy D, Pathak B. Machine Learning Aided Interpretable Approach for Single Nucleotide-Based DNA Sequencing using a Model Nanopore. J Phys Chem Lett 2022; 13:11818-11830. [PMID: 36520020 DOI: 10.1021/acs.jpclett.2c02824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Solid-state nanopore-based electrical detection of DNA nucleotides with the quantum tunneling technique has emerged as a powerful strategy to be the next-generation sequencing technology. However, experimental complexity has been a foremost obstacle in achieving a more accurate high-throughput analysis with industrial scalability. Here, with one of the nucleotide training data sets of a model monolayer gold nanopore, we have predicted the transmission function for all other nucleotides with root-mean-square error scores as low as 0.12 using the optimized eXtreme Gradient Boosting Regression (XGBR) model. Further, the SHapley Additive exPlanations (SHAP) analysis helped in exploring the interpretability of the XGBR model prediction and revealed the complex relationship between the molecular properties of nucleotides and their transmission functions by both global and local interpretable explanations. Hence, experimental integration of our proposed machine-learning-assisted transmission function prediction method can offer a new direction for the realization of cheap, accurate, and ultrafast DNA sequencing.
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Affiliation(s)
- Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh453552, India
| | - Diptendu Roy
- Department of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh453552, India
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12
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Peng HH, Chen C. Charge transport in molecular junctions: General physical pictures, electrical measurement techniques, and their challenges. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hao Howard Peng
- Department of Chemistry and Center for Emerging Material and Advanced Devices National Taiwan University Taipei Taiwan
| | - Chun‐hsien Chen
- Department of Chemistry and Center for Emerging Material and Advanced Devices National Taiwan University Taipei Taiwan
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13
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14
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Gupta R, Jash P, Sachan P, Bayat A, Singh V, Mondal PC. Electrochemical Potential‐Driven High‐Throughput Molecular Electronic and Spintronic Devices: From Molecules to Applications. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ritu Gupta
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh 208016 India
| | - Priyajit Jash
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh 208016 India
| | - Pradeep Sachan
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh 208016 India
| | - Akhtar Bayat
- Laboratoire Photonique Numérique et Nanosciences, UMR 5298 Université de Bordeaux 33400 Talence France
| | - Vikram Singh
- Department of Chemistry and National Science Research Institute Korea Advanced Institute of Science and Technology 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Prakash Chandra Mondal
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh 208016 India
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15
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Liu C, Yang W, Wang J, Ding X, Ren H, Chen Y, Xie Z, Sun T, Jiang J. A sextuple-decker heteroleptic phthalocyanine heterometallic samarium-cadmium complex with crystal structure and nonlinear optical properties in solution and gel glass. Dalton Trans 2021; 50:13661-13665. [PMID: 34591058 DOI: 10.1039/d1dt02963k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A sextuple-decker heteroleptic phthalocyanine heterometallic compound (1) with a subunit arrangement of {(Pc)Sm(Pc)Cd(Pc*)Cd(Pc*)Cd(Pc)Sm(Pc)} has been prepared and analyzed using various spectroscopic instruments, in which four unsubstituted phthalocyanine anions (Pc) and two substituted analogues (Pc*) with n-pentoxyl substituents at eight peripheral positions are connected through the complexation of two Sm(III) and three Cd(II) ions. In particular, its sextuple-decker structure has been disclosed by the single-crystal X-ray diffraction technique. The solution and gel glass forms of this compound display third-order nonlinear optical properties due to the intrinsic conjugated nature over the sextuple-decker sandwich complex.
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Affiliation(s)
- Chao Liu
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Wei Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Jingjing Wang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Science, Beijing 100190, China.
| | - Xu Ding
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Huimin Ren
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Yuxiang Chen
- Department of Chemistry School of Pharmaceutical and Chemical Engineering, Taizhou University, Taizhou 318000, China
| | - Zheng Xie
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Science, Beijing 100190, China.
| | - Tingting Sun
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Jianzhuang Jiang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
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16
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Weliwatte NS, Grattieri M, Minteer SD. Rational design of artificial redox-mediating systems toward upgrading photobioelectrocatalysis. Photochem Photobiol Sci 2021; 20:1333-1356. [PMID: 34550560 PMCID: PMC8455808 DOI: 10.1007/s43630-021-00099-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/03/2021] [Indexed: 12/23/2022]
Abstract
Photobioelectrocatalysis has recently attracted particular research interest owing to the possibility to achieve sunlight-driven biosynthesis, biosensing, power generation, and other niche applications. However, physiological incompatibilities between biohybrid components lead to poor electrical contact at the biotic-biotic and biotic-abiotic interfaces. Establishing an electrochemical communication between these different interfaces, particularly the biocatalyst-electrode interface, is critical for the performance of the photobioelectrocatalytic system. While different artificial redox mediating approaches spanning across interdisciplinary research fields have been developed in order to electrically wire biohybrid components during bioelectrocatalysis, a systematic understanding on physicochemical modulation of artificial redox mediators is further required. Herein, we review and discuss the use of diffusible redox mediators and redox polymer-based approaches in artificial redox-mediating systems, with a focus on photobioelectrocatalysis. The future possibilities of artificial redox mediator system designs are also discussed within the purview of present needs and existing research breadth.
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Affiliation(s)
- N Samali Weliwatte
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Matteo Grattieri
- Dipartimento Di Chimica, Università Degli Studi Di Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy.
- IPCF-CNR Istituto Per I Processi Chimico Fisici, Consiglio Nazionale Delle Ricerche, Via E. Orabona 4, 70125, Bari, Italy.
| | - Shelley D Minteer
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA.
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17
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Gupta R, Jash P, Sachan P, Bayat A, Singh V, Mondal PC. Electrochemical Potential-Driven High-Throughput Molecular Electronic and Spintronic Devices: From Molecules to Applications. Angew Chem Int Ed Engl 2021; 60:26904-26921. [PMID: 34313372 DOI: 10.1002/anie.202104724] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 01/25/2023]
Abstract
Molecules are fascinating candidates for constructing tunable and electrically conducting devices by the assembly of either a single molecule or an ensemble of molecules between two electrical contacts followed by current-voltage (I-V) analysis, which is often termed "molecular electronics". Recently, there has been also an upsurge of interest in spin-based electronics or spintronics across the molecules, which offer additional scope to create ultrafast responsive devices with less power consumption and lower heat generation using the intrinsic spin property rather than electronic charge. Researchers have been exploring this idea of utilizing organic molecules, organometallics, coordination complexes, polymers, and biomolecules (proteins, enzymes, oligopeptides, DNA) in integrating molecular electronics and spintronics devices. Although several methods exist to prepare molecular thin-films on suitable electrodes, the electrochemical potential-driven technique has emerged as highly efficient. In this Review we describe recent advances in the electrochemical potential driven growth of nanometric various molecular films on technologically relevant substrates, including non-magnetic and magnetic electrodes to investigate the stimuli-responsive charge and spin transport phenomena.
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Affiliation(s)
- Ritu Gupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, 208016, India
| | - Priyajit Jash
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, 208016, India
| | - Pradeep Sachan
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, 208016, India
| | - Akhtar Bayat
- Laboratoire Photonique Numérique et Nanosciences, UMR 5298, Université de Bordeaux, 33400, Talence, France
| | - Vikram Singh
- Department of Chemistry and National Science Research Institute, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Prakash Chandra Mondal
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, 208016, India
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18
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Kokabi A, Touski SB, Mamdouh A. Negative differential resistance, rectification, tunable peak-current position and switching effects in an alanine-based molecular device. J Med Eng Technol 2021; 45:505-510. [PMID: 34184593 DOI: 10.1080/03091902.2020.1775904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The transport properties of a molecular bio-electronic device based on the alanine amino-acid are investigated. The considered device consists of an alanine molecule as the central potential-dot coupled to two zigzag graphene nanoribbon (ZGNR) conducting electrodes. The current-voltage characteristics of this dual tunnelling molecular junction are studied at two different optimised compositions of the central molecule. The proposed amino-acid based structure utilises the tunnelling coupling similar to that of semiconducting single-electron transistors (SETs) to avoid complications due to the atomic interfaces. The current-voltage characteristics show polarity-dependent behaviour making the device feasible of being applied as a molecular rectifier. Negative differential resistance (NDR) along with tuneable peak-current position has been also observed in the current-voltage characteristics. The device is also capable of being applied as a switch controllable by the central molecule orientation.
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Affiliation(s)
- Alireza Kokabi
- Department of Electrical Engineering, Hamedan University of Technology, Hamedan, Iran
| | - Shoeib Babaee Touski
- Department of Electrical Engineering, Hamedan University of Technology, Hamedan, Iran
| | - Amir Mamdouh
- Department of Electrical Engineering, Hamedan University of Technology, Hamedan, Iran
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19
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Schmiel S, Butenschön H. New π‐Extended 1,1′‐Disubstituted Ferrocenes with Thioate and Dithioate End Groups. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sinem‐Fatma Schmiel
- Institut für Organische Chemie Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Germany
| | - Holger Butenschön
- Institut für Organische Chemie Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Germany
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20
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Tian J, Xing F, Gao Q. Graphene-Based Nanomaterials as the Cathode for Lithium-Sulfur Batteries. Molecules 2021; 26:2507. [PMID: 33923027 PMCID: PMC8123287 DOI: 10.3390/molecules26092507] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/25/2022] Open
Abstract
The global energy crisis and environmental problems are becoming increasingly serious. It is now urgent to vigorously develop an efficient energy storage system. Lithium-sulfur batteries (LSBs) are considered to be one of the most promising candidates for next-generation energy storage systems due to their high energy density. Sulfur is abundant on Earth, low-cost, and environmentally friendly, which is consistent with the characteristics of new clean energy. Although LSBs possess numerous advantages, they still suffer from numerous problems such as the dissolution and diffusion of sulfur intermediate products during the discharge process, the expansion of the electrode volume, and so on, which severely limit their further development. Graphene is a two-dimensional crystal material with a single atomic layer thickness and honeycomb bonding structure formed by sp2 hybridization of carbon atoms. Since its discovery in 2004, graphene has attracted worldwide attention due to its excellent physical and chemical properties. Herein, this review summarizes the latest developments in graphene frameworks, heteroatom-modified graphene, and graphene composite frameworks in sulfur cathodes. Moreover, the challenges and future development of graphene-based sulfur cathodes are also discussed.
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Affiliation(s)
| | - Fei Xing
- School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255049, China;
| | - Qiqian Gao
- School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255049, China;
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21
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Tuning Single-Molecule Conductance by Controlled Electric Field-Induced trans-to-cis Isomerisation. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11083317] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
External electric fields (EEFs) have proven to be very efficient in catalysing chemical reactions, even those inaccessible via wet-chemical synthesis. At the single-molecule level, oriented EEFs have been successfully used to promote in situ single-molecule reactions in the absence of chemical catalysts. Here, we elucidate the effect of an EEFs on the structure and conductance of a molecular junction. Employing scanning tunnelling microscopy break junction (STM-BJ) experiments, we form and electrically characterize single-molecule junctions of two tetramethyl carotene isomers. Two discrete conductance signatures show up more prominently at low and high applied voltages which are univocally ascribed to the trans and cis isomers of the carotenoid, respectively. The difference in conductance between both cis-/trans- isomers is in concordance with previous predictions considering π-quantum interference due to the presence of a single gauche defect in the trans isomer. Electronic structure calculations suggest that the electric field polarizes the molecule and mixes the excited states. The mixed states have a (spectroscopically) allowed transition and, therefore, can both promote the cis-isomerization of the molecule and participate in electron transport. Our work opens new routes for the in situ control of isomerisation reactions in single-molecule contacts.
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22
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Harris AW, Roy S, Ganguly S, Parameswar AV, Lucas FWS, Holewinski A, Goodwin AP, Cha JN. Investigating the use of conducting oligomers and redox molecules in CdS-MoFeP biohybrids. NANOSCALE ADVANCES 2021; 3:1392-1396. [PMID: 36132854 PMCID: PMC9418983 DOI: 10.1039/d0na00678e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/18/2020] [Indexed: 05/11/2023]
Abstract
In this work we report the effect of incorporating conducting oligophenylenes and a cobaltocene-based redox mediator on photodriven electron transfer between thioglycolic acid (TGA) capped CdS nanorods (NR) and the native nitrogenase MoFe protein (MoFeP) by following the reduction of H+ to H2. First, we demonstrate that the addition of benzidine-a conductive diphenylene- to TGA-CdS and MoFeP increased catalytic activity by up to 3-fold as compared to CdS-MoFeP alone. In addition, in comparing the use of oligophenylenes composed of one (p-phenylenediamine), two (benzidine) or three (4,4''-diamino-p-terphenyl)phenylene groups, the largest gain in H2 was observed with the addition of benzidine and the lowest with phenylenediamine. As a comparison to the conductive oligophenylenes, a cobaltocene-based redox mediator was also tested with the TGA-CdS NRs and MoFeP. However, adding either cobaltocene diacid or diamine caused negligible gains in H2 production and at higher concentrations, caused a significant decrease. Agarose gel electrophoresis revealed little to no detectable interaction between benzidine and TGA-CdS but strong binding between cobaltocene and TGA-CdS. These results suggest that the tight binding of the cobaltocene mediator to CdS may hinder electron transfer between CdS and MoFe and cause the mediator to undergo continuous reduction/oxidation events at the surface of CdS.
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Affiliation(s)
- Alexander W Harris
- Department of Chemical and Biological Engineering, University of Colorado Boulder 3415 Colorado Avenue Boulder CO 80303 USA
| | - Shambojit Roy
- Department of Chemical and Biological Engineering, University of Colorado Boulder 3415 Colorado Avenue Boulder CO 80303 USA
| | - Saheli Ganguly
- Department of Chemical and Biological Engineering, University of Colorado Boulder 3415 Colorado Avenue Boulder CO 80303 USA
| | - Ashray V Parameswar
- Materials Science and Engineering Program, University of Colorado Boulder 3415 Colorado Avenue Boulder CO 80303 USA
| | - Francisco W S Lucas
- Department of Chemical and Biological Engineering, University of Colorado Boulder 3415 Colorado Avenue Boulder CO 80303 USA
| | - Adam Holewinski
- Department of Chemical and Biological Engineering, University of Colorado Boulder 3415 Colorado Avenue Boulder CO 80303 USA
- Renewable and Sustainable Energy Institute, University of Colorado Boulder CO 80303 USA
| | - Andrew P Goodwin
- Department of Chemical and Biological Engineering, University of Colorado Boulder 3415 Colorado Avenue Boulder CO 80303 USA
- Materials Science and Engineering Program, University of Colorado Boulder 3415 Colorado Avenue Boulder CO 80303 USA
| | - Jennifer N Cha
- Department of Chemical and Biological Engineering, University of Colorado Boulder 3415 Colorado Avenue Boulder CO 80303 USA
- Materials Science and Engineering Program, University of Colorado Boulder 3415 Colorado Avenue Boulder CO 80303 USA
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23
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Furuhata T, Komoto Y, Ohshiro T, Taniguchi M, Ueki R, Sando S. Key aurophilic motif for robust quantum-tunneling-based characterization of a nucleoside analogue marker. Chem Sci 2020; 11:10135-10142. [PMID: 34094276 PMCID: PMC8162310 DOI: 10.1039/d0sc03946b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A quantum sequencer offers a scalable electrical platform for single-molecule analysis of genomic events. A thymidine (dT) analog exhibiting uniquely high single-molecule conductance is a key element in capturing DNA synthesis dynamics by serving as a decodable marker for enzymatic labeling of nascent strands. However, the current design strategies of dT analogs that focus on their molecular orbital energy levels require bulky chemical modifications to extend the π-conjugation, which hinders polymerase recognition. We report herein a polymerase-compatible dT analog that is highly identifiable in quantum sequencing. An ethynyl group is introduced as a small gold-binding motif to differentiate the nucleobase-gold electronic coupling, which has been an overlooked factor in modifying nucleobase conductance. The resulting C5-ethynyl-2'-deoxyuridine exhibits characteristic signal profiles that allowed its correct identification at a 93% rate while maintaining polymerase compatibility. This study would expand the applicability of quantum sequencing by demonstrating a robust nucleoside marker with high identifiability.
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Affiliation(s)
- Takafumi Furuhata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Yuki Komoto
- The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Takahito Ohshiro
- The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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24
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Zhao S, Wu Q, Pi J, Liu J, Zheng J, Hou S, Wei J, Li R, Sadeghi H, Yang Y, Shi J, Chen Z, Xiao Z, Lambert C, Hong W. Cross-plane transport in a single-molecule two-dimensional van der Waals heterojunction. SCIENCE ADVANCES 2020; 6:eaba6714. [PMID: 32524003 PMCID: PMC7259930 DOI: 10.1126/sciadv.aba6714] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 03/31/2020] [Indexed: 06/01/2023]
Abstract
Two-dimensional van der Waals heterojunctions (2D-vdWHs) stacked from atomically thick 2D materials are predicted to be a diverse class of electronic materials with unique electronic properties. These properties can be further tuned by sandwiching monolayers of planar organic molecules between 2D materials to form molecular 2D-vdWHs (M-2D-vdWHs), in which electricity flows in a cross-plane way from one 2D layer to the other via a single molecular layer. Using a newly developed cross-plane break junction technique, combined with density functional theory calculations, we show that M-2D-vdWHs can be created and that cross-plane charge transport can be tuned by incorporating guest molecules. The M-2D-vdWHs exhibit distinct cross-plane charge transport signatures, which differ from those of molecules undergoing in-plane charge transport.
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Affiliation(s)
- Shiqiang Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Qingqing Wu
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK
| | - Jiuchan Pi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Junyang Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Jueting Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Songjun Hou
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK
| | - Junying Wei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Ruihao Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Hatef Sadeghi
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Jia Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Zhaobin Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Zongyuan Xiao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Colin Lambert
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
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25
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Yu H, Li S, Schwieter KE, Liu Y, Sun B, Moore JS, Schroeder CM. Charge Transport in Sequence-Defined Conjugated Oligomers. J Am Chem Soc 2020; 142:4852-4861. [PMID: 32069403 DOI: 10.1021/jacs.0c00043] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A major challenge in synthetic polymers lies in understanding how primary monomer sequence affects materials properties. In this work, we show that charge transport in single molecule junctions of conjugated oligomers critically depends on the primary sequence of monomers. A series of sequence-defined oligomers ranging from two to seven units was synthesized by an iterative approach based on the van Leusen reaction, providing conjugated oligomers with backbones consisting of para-linked phenylenes connected to oxazole, imidazole, or nitro-substituted pyrrole. The charge transport properties of these materials were characterized using a scanning tunneling microscope-break junction (STM-BJ) technique, thereby enabling direct measurement of molecular conductance for sequence-defined dimers, trimers, pentamers, and a heptamer. Our results show that oligomers with specific monomer sequences exhibit unexpected and distinct charge transport pathways that enhance molecular conductance more than 10-fold. A systematic analysis using monomer substitution patterns established that sequence-defined pentamers containing imidazole or pyrrole groups in specific locations provide molecular attachment points on the backbone to the gold electrodes, thereby giving rise to multiple conductance pathways. These findings reveal the subtle but important role of molecular structure including steric hindrance and directionality of heterocycles in determining charge transport in these molecular junctions. This work brings new understanding for designing molecular electronic components.
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Affiliation(s)
- Hao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Songsong Li
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kenneth E Schwieter
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yun Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Boran Sun
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jeffrey S Moore
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Charles M Schroeder
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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26
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Baghel AS, Jaiswal Y, Kumar A. Pd(II)-Catalyzed One-Pot Multiple C-C Bond Formation: En Route Synthesis of Succinimide-Fused Unsymmetrical 9,10-Dihydrophenanthrenes from Aryl Iodides and Maleimides. Org Lett 2020; 22:1908-1913. [PMID: 32065754 DOI: 10.1021/acs.orglett.0c00255] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An expeditious approach has been developed for the synthesis of succinimide-fused unsymmetrical 9,10-dihydrophenanthrenes from simple aryl iodides and maleimides. The developed transformation, overall proceeding with high regioselectivity via a cascade approach through palladium(II)-catalyzed Micheal-type addition/C-H activation/intramolecular cross-dehydrogenative coupling (ICDC)/C-H activation, allows formation of four fundamental carbon-carbon bonds in one-pot fashion. The reactions tolerate broad functional groups and satisfy the parameters of atom and step economy. Detailed mechanistic studies were carried out to support the proposed synthetic pathway.
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Affiliation(s)
- Akanksha Singh Baghel
- Department of Chemistry, Indian Institute of Technology Patna, Bihta 801106, Bihar, India
| | - Yogesh Jaiswal
- Department of Chemistry, Indian Institute of Technology Patna, Bihta 801106, Bihar, India
| | - Amit Kumar
- Department of Chemistry, Indian Institute of Technology Patna, Bihta 801106, Bihar, India
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27
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Chen X, Qi D, Liu C, Wang H, Xie Z, Chen TW, Chen SM, Tseng TW, Jiang J. Elucidating π–π interaction-induced extension effect in sandwich phthalocyaninato compounds. RSC Adv 2020; 10:317-322. [PMID: 35558861 PMCID: PMC9092954 DOI: 10.1039/c9ra07847a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/18/2019] [Indexed: 12/24/2022] Open
Abstract
π–π interaction-linked extension in the perpendicular direction to the monomers and corresponding effect on nonlinear optic properties have been clearly disclosed over the multiple-decker sandwich-type phthalocyaninato metal compounds.
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Affiliation(s)
- Xin Chen
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials
- Department of Chemistry
- University of Science and Technology Beijing
- Beijing 100083
- China
| | - Dongdong Qi
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials
- Department of Chemistry
- University of Science and Technology Beijing
- Beijing 100083
- China
| | - Chao Liu
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials
- Department of Chemistry
- University of Science and Technology Beijing
- Beijing 100083
- China
| | - Hailong Wang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials
- Department of Chemistry
- University of Science and Technology Beijing
- Beijing 100083
- China
| | - Zheng Xie
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials
- Technical Institute of Physics and Chemistry
- Chinese Academy of Science
- Beijing 100190
- China
| | - Tse-Wei Chen
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei 10608
- Taiwan
| | - Shen-Ming Chen
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei 10608
- Taiwan
| | - Tien-Wen Tseng
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei 10608
- Taiwan
| | - Jianzhuang Jiang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials
- Department of Chemistry
- University of Science and Technology Beijing
- Beijing 100083
- China
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28
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Limberti S, Emmett L, Trandafir A, Kociok-Köhn G, Pantoş GD. Borazatruxenes. Chem Sci 2019; 10:9565-9570. [PMID: 32055329 PMCID: PMC6979502 DOI: 10.1039/c9sc02489a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/27/2019] [Indexed: 01/01/2023] Open
Abstract
We report the synthesis and characterization of a series of arene-borazine hybrids called borazatruxenes. These molecules are BN-isosteres of truxene whereby the central benzene core has been replaced by a borazine ring. The straightforward three step synthesis, stability and their chiroptical and electronic properties recommend them as new scaffolds for BN-carbon hybrid materials. Computational studies at DFT level, closely matching the experimental data, provided insights in the electronic structure of these molecules.
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Affiliation(s)
- Simone Limberti
- Department of Chemistry , University of Bath , Bath , BA2 7AY , UK .
| | - Liam Emmett
- Department of Chemistry , University of Bath , Bath , BA2 7AY , UK .
| | | | | | - G Dan Pantoş
- Department of Chemistry , University of Bath , Bath , BA2 7AY , UK .
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29
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Ohto T, Inoue T, Stewart H, Numai Y, Aso Y, Ie Y, Yamada R, Tada H. Effects of cis- trans Conformation between Thiophene Rings on Conductance of Oligothiophenes. J Phys Chem Lett 2019; 10:5292-5296. [PMID: 31436425 DOI: 10.1021/acs.jpclett.9b02059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oligothiophenes have been established as important π-conjugated frameworks in organic electronics and molecular electronics. Although oligothiophenes possess the rotational flexibility of thiophene rings, the effects of cis-trans conformations on their electrical conductance have not been investigated yet. To investigate the effects of cis-trans conformations between thiophene rings on the conductance of oligothiophenes, we performed first-principles transport calculations. The conductance of the cis-oligothiophene was calculated to be higher than that of trans-oligothiophene, because the highest occupied molecular orbital was closer to the Fermi level of the gold electrode in the cis isomer than the trans isomer. This prediction was confirmed through mechanically controllable break junction measurements and fitting of the current-voltage characteristics for the newly synthesized, insulated oligothiophenes with controlled cis-trans conformations. This study demonstrates that cis- and trans-conformations can affect the electrical properties of oligothiophene frameworks and can potentially be used to control the electronic structure of long oligothiophene molecular wires.
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Affiliation(s)
- Tatsuhiko Ohto
- Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka , Osaka 560-8531 , Japan
| | - Takuya Inoue
- The Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka , Ibaraki , Osaka 567-0047 , Japan
| | - Helen Stewart
- Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka , Osaka 560-8531 , Japan
| | - Yuichi Numai
- Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka , Osaka 560-8531 , Japan
| | - Yoshio Aso
- The Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka , Ibaraki , Osaka 567-0047 , Japan
| | - Yutaka Ie
- The Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka , Ibaraki , Osaka 567-0047 , Japan
| | - Ryo Yamada
- Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka , Osaka 560-8531 , Japan
| | - Hirokazu Tada
- Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka , Osaka 560-8531 , Japan
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30
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Wang X, Cheng L. Multifunctional two-dimensional nanocomposites for photothermal-based combined cancer therapy. NANOSCALE 2019; 11:15685-15708. [PMID: 31355405 DOI: 10.1039/c9nr04044g] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Two-dimensional (2D) nanocomposites have been widely used in biomedical applications during the past few years due to their extraordinary physicochemical properties, which has proved their importance in the field of nanomedicine. Benefiting from the excellent optical absorption in the near-infrared window and large specific surface area, many efforts have been devoted to fabricating 2D nanomaterial-based multifunctional nanoplatforms to realize photothermal therapy (PTT)-based or chemotherapy-based synergistic treatment, which exhibits obvious anti-tumor effects and significantly enhances the therapeutic efficiency of cancer compared with monotherapy. In particular, 2D nanocomposites are usually fabricated as intelligent nanoplatforms for stimuli-responsive nanocarriers, whose therapeutic effects could be specifically activated by the tumor microenvironment (TME). In addition, different fluorescent probes and functional inorganic nanomaterials could be absorbed on the surface of 2D nanomaterials to fabricate multifunctional hybrid nanomaterials with satisfactory magnetic, optical, or other properties that are widely used for multimodal imaging-guided cancer therapy. In this review, the latest development of multifunctional 2D nanocomposites for combination therapy is systematically summarized, mainly focusing on PTT-based synergistic cancer therapy, and the other forms and potential forms of synergistic cancer therapy are also simply summarized. Furthermore, the design principles of 2D nanocomposites are particularly emphasized, and the current challenges and future prospects of 2D nanocomposites for cancer theranostics are discussed simultaneously.
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Affiliation(s)
- Xianwen Wang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, P. R. China.
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31
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He C, Zhang Q, Fan Y, Zhao C, Zhao C, Ye J, Dappe YJ, Nichols RJ, Yang L. Effect of Asymmetric Anchoring Groups on Electronic Transport in Hybrid Metal/Molecule/Graphene Single Molecule Junctions. Chemphyschem 2019; 20:1830-1836. [PMID: 31108024 DOI: 10.1002/cphc.201900424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/17/2019] [Indexed: 11/08/2022]
Abstract
A combined experimental and theoretical study on molecular junctions with asymmetry in both the electrode type and in the anchoring group type is presented. A scanning tunnelling microscope is used to create the "asymmetric" Au-S-(CH2 )n-COOH-graphene molecular junctions and determine their conductance. The measurements are combined with electron transport calculations based on density functional theory (DFT) to analyze the electrical conductance and its length attenuation factor from a series of junctions of different molecular length (n). These results show an unexpected trend with a rather high conductance and a smaller attenuation factor for the Au-S-(CH2 )n -COOH-graphene configuration compared to the equivalent junction with the "symmetrical" COOH contacting using the HOOC-(CH2 )n -COOH series. Owing to the effect of the graphene electrode, the attenuation factor is also smaller than the one obtained for Au/Au electrodes. These results are interpreted through the relative molecule/electrode couplings and molecular level alignments as determined with DFT calculations. In an asymmetric junction, the electrical current flows through the less resistive conductance channel, similarly to what is observed in the macroscopic regime.
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Affiliation(s)
- Chunhui He
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, 215123, Suzhou, China.,Department of Chemistry, University of Liverpool, Liverpool, L697ZD, UK
| | - Qian Zhang
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, 215123, Suzhou, China.,Department of Chemistry, University of Liverpool, Liverpool, L697ZD, UK
| | - Yinqi Fan
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, 215123, Suzhou, China.,Department of Chemistry, University of Liverpool, Liverpool, L697ZD, UK
| | - Cezhou Zhao
- Department of Electrical and Electronic Engineering, Xi'an-Jiaotong Liverpool University, 215123, Suzhou, China
| | - Chun Zhao
- Department of Electrical and Electronic Engineering, Xi'an-Jiaotong Liverpool University, 215123, Suzhou, China
| | - Jingyao Ye
- Department of Inorganic Chemistry, Copenhagen University, Universitetparken 21, Copenhagen, Denmark
| | - Yannick J Dappe
- SPEC, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette, Cedex, France
| | - Richard J Nichols
- Department of Chemistry, University of Liverpool, Liverpool, L697ZD, UK
| | - Li Yang
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, 215123, Suzhou, China.,Department of Chemistry, University of Liverpool, Liverpool, L697ZD, UK
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32
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Xu W, Leary E, Hou S, Sangtarash S, González MT, Rubio‐Bollinger G, Wu Q, Sadeghi H, Tejerina L, Christensen KE, Agraït N, Higgins SJ, Lambert CJ, Nichols RJ, Anderson HL. Unusual Length Dependence of the Conductance in Cumulene Molecular Wires. Angew Chem Int Ed Engl 2019; 58:8378-8382. [PMID: 31026371 PMCID: PMC6563095 DOI: 10.1002/anie.201901228] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/22/2019] [Indexed: 01/29/2023]
Abstract
Cumulenes are sometimes described as "metallic" because an infinitely long cumulene would have the band structure of a metal. Herein, we report the single-molecule conductance of a series of cumulenes and cumulene analogues, where the number of consecutive C=C bonds in the core is n=1, 2, 3, and 5. The [n]cumulenes with n=3 and 5 have almost the same conductance, and they are both more conductive than the alkene (n=1). This is remarkable because molecular conductance normally falls exponentially with length. The conductance of the allene (n=2) is much lower, because of its twisted geometry. Computational simulations predict a similar trend to the experimental results and indicate that the low conductance of the allene is a general feature of [n]cumulenes where n is even. The lack of length dependence in the conductance of [3] and [5]cumulenes is attributed to the strong decrease in the HOMO-LUMO gap with increasing length.
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Affiliation(s)
- Wenjun Xu
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryOxfordOX1 3TAUK
| | - Edmund Leary
- Department of ChemistryDonnan and Robert Robinson LaboratoriesUniversity of LiverpoolLiverpoolL69 7ZDUK
- Surface Science Research CentreUniversity of LiverpoolOxford StreetLiverpoolL69 3BXUK
| | - Songjun Hou
- Department of PhysicsLancaster UniversityLancasterLA1 4YWUK
| | | | - M. Teresa González
- Instituto Madrileño de Estudios Avanzados (IMDEA)Calle Faraday 9, Campus Universitario de Cantoblanco28049MadridSpain
| | - Gabino Rubio‐Bollinger
- Departamento de Física de la Materia CondensadaIFIMAC and Instituto “Nicolás Cabrera”Universidad Autónoma de Madrid28049MadridSpain
| | - Qingqing Wu
- Department of PhysicsLancaster UniversityLancasterLA1 4YWUK
| | - Hatef Sadeghi
- Department of PhysicsLancaster UniversityLancasterLA1 4YWUK
| | - Lara Tejerina
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryOxfordOX1 3TAUK
| | | | - Nicolás Agraït
- Instituto Madrileño de Estudios Avanzados (IMDEA)Calle Faraday 9, Campus Universitario de Cantoblanco28049MadridSpain
- Departamento de Física de la Materia CondensadaIFIMAC and Instituto “Nicolás Cabrera”Universidad Autónoma de Madrid28049MadridSpain
| | - Simon J. Higgins
- Department of ChemistryDonnan and Robert Robinson LaboratoriesUniversity of LiverpoolLiverpoolL69 7ZDUK
| | | | - Richard J. Nichols
- Department of ChemistryDonnan and Robert Robinson LaboratoriesUniversity of LiverpoolLiverpoolL69 7ZDUK
- Surface Science Research CentreUniversity of LiverpoolOxford StreetLiverpoolL69 3BXUK
| | - Harry L. Anderson
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryOxfordOX1 3TAUK
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33
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Furuhata T, Ohshiro T, Akimoto G, Ueki R, Taniguchi M, Sando S. Highly Conductive Nucleotide Analogue Facilitates Base-Calling in Quantum-Tunneling-Based DNA Sequencing. ACS NANO 2019; 13:5028-5035. [PMID: 30888791 DOI: 10.1021/acsnano.9b01250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Quantum-tunneling-based DNA sequencing is a single molecular technology that has great potential for achieving facile and high-throughput DNA sequencing. In principle, the sequence of DNA could be read out by the time trace of the tunnel current that can be changed according to molecular conductance of nucleobases passing through nanosized gap electrodes. However, efficient base-calling of four genetic alphabets has been seriously impeded due to the similarity of molecular conductance among canonical nucleotides. In this article, we demonstrate that replacement of canonical 2'-deoxyadenosine (dA) with a highly conductive dA analogue, 7-deaza dA, could expand the difference of molecular conductance between four genetic alphabets. Additionally, systematic evaluation of molecular conductance using a series of dA and dG analogues revealed that molecular conductance of the nucleotide is highly dependent on the HOMO level. Thus, the present study demonstrating that signal characteristics of the nucleotide can be modulated based on the HOMO level provides a widely applicable chemical approach and insight for facilitation of single molecular sensing as well as DNA sequencing based on quantum tunneling.
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Affiliation(s)
- Takafumi Furuhata
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Takahito Ohshiro
- The Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka , Ibaraki , Osaka 567-0047 , Japan
| | - Gaku Akimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka , Ibaraki , Osaka 567-0047 , Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
- Department of Bioengineering, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
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34
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Xu W, Leary E, Hou S, Sangtarash S, González MT, Rubio‐Bollinger G, Wu Q, Sadeghi H, Tejerina L, Christensen KE, Agraït N, Higgins SJ, Lambert CJ, Nichols RJ, Anderson HL. Unusual Length Dependence of the Conductance in Cumulene Molecular Wires. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wenjun Xu
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory Oxford OX1 3TA UK
| | - Edmund Leary
- Department of ChemistryDonnan and Robert Robinson LaboratoriesUniversity of Liverpool Liverpool L69 7ZD UK
- Surface Science Research CentreUniversity of Liverpool Oxford Street Liverpool L69 3BX UK
| | - Songjun Hou
- Department of PhysicsLancaster University Lancaster LA1 4YW UK
| | - Sara Sangtarash
- Department of PhysicsLancaster University Lancaster LA1 4YW UK
| | - M. Teresa González
- Instituto Madrileño de Estudios Avanzados (IMDEA) Calle Faraday 9, Campus Universitario de Cantoblanco 28049 Madrid Spain
| | - Gabino Rubio‐Bollinger
- Departamento de Física de la Materia CondensadaIFIMAC and Instituto “Nicolás Cabrera”Universidad Autónoma de Madrid 28049 Madrid Spain
| | - Qingqing Wu
- Department of PhysicsLancaster University Lancaster LA1 4YW UK
| | - Hatef Sadeghi
- Department of PhysicsLancaster University Lancaster LA1 4YW UK
| | - Lara Tejerina
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory Oxford OX1 3TA UK
| | - Kirsten E. Christensen
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory Oxford OX1 3TA UK
| | - Nicolás Agraït
- Instituto Madrileño de Estudios Avanzados (IMDEA) Calle Faraday 9, Campus Universitario de Cantoblanco 28049 Madrid Spain
- Departamento de Física de la Materia CondensadaIFIMAC and Instituto “Nicolás Cabrera”Universidad Autónoma de Madrid 28049 Madrid Spain
| | - Simon J. Higgins
- Department of ChemistryDonnan and Robert Robinson LaboratoriesUniversity of Liverpool Liverpool L69 7ZD UK
| | | | - Richard J. Nichols
- Department of ChemistryDonnan and Robert Robinson LaboratoriesUniversity of Liverpool Liverpool L69 7ZD UK
- Surface Science Research CentreUniversity of Liverpool Oxford Street Liverpool L69 3BX UK
| | - Harry L. Anderson
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory Oxford OX1 3TA UK
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35
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Watanabe H, Fujimaki Y, Hayashi K, Imai H. Enhanced Quantum Yield of Nanographenes Incorporated in Supermicroporous Silicas and the Co-Adsorption Effect of Water Molecules. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroto Watanabe
- Tokyo Metropolitan Industrial Technology Research Institute, 2-4-10 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yasuto Fujimaki
- Tokyo Metropolitan Industrial Technology Research Institute, 2-4-10 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kosei Hayashi
- Tokyo Metropolitan Industrial Technology Research Institute, 2-4-10 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hiroaki Imai
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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36
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He Y, Cheng N, Zhao J. First-principle study on the conductance of benzene-based molecules with various bonding characteristics. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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37
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Dhakal U, Rai D. Circular current and induced force in a molecular ring junction. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:125302. [PMID: 30625438 DOI: 10.1088/1361-648x/aafd09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We consider bias-induced circular current in a molecular ring junction. It is natural to define circular current as a component of ring current that acts as a sole source of magnetic flux induced in the ring. Alternatively, the bias-induced circular current can also be determined from the magnetic response of the ring junction to an external flux in the zero-flux limit. This leads to determination of bias-induced circular current without actually calculating the bond currents. We also explore the possibility of circular current-induced force rupturing the covalent bonds in the ring leading to ultimate breakdown of the ring junction. Our calculations underscore the reliability problem posed by the current magnification effect in the molecular ring structures.
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Affiliation(s)
- Umesh Dhakal
- Department of Physics, Sikkim University, Samdur, East Sikkim, 737102, India
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38
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Direct Analysis of Incorporation of an Anticancer Drug into DNA at Single-Molecule Resolution. Sci Rep 2019; 9:3886. [PMID: 30846775 PMCID: PMC6405915 DOI: 10.1038/s41598-019-40504-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/18/2019] [Indexed: 01/10/2023] Open
Abstract
Identifying positions at which anticancer drug molecules incorporate into DNA is essential to define mechanisms underlying their activity, but current methodologies cannot yet achieve this. The thymidine fluorine substitution product trifluridine (FTD) is a DNA-damaging anticancer agent thought to incorporate into thymine positions in DNA. This mechanism, however, has not been directly confirmed. Here, we report a means to detect FTD in a single-stranded oligonucleotide using a method to distinguish single molecules by differences in electrical conductance. Entire sequences of 21-base single-stranded DNAs with and without incorporated drug were determined based on single-molecule conductances of the drug and four deoxynucleosides, the first direct observation of its kind. This methodology may foster rapid development of more effective anticancer drugs.
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39
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Gu Z, Zhu S, Yan L, Zhao F, Zhao Y. Graphene-Based Smart Platforms for Combined Cancer Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1800662. [PMID: 30039878 DOI: 10.1002/adma.201800662] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/25/2018] [Indexed: 06/08/2023]
Abstract
The extensive research of graphene and its derivatives in biomedical applications during the past few years has witnessed its significance in the field of nanomedicine. Starting from simple drug delivery systems, the application of graphene and its derivatives has been extended to a versatile platform of multiple therapeutic modalities, including photothermal therapy, photodynamic therapy, magnetic hyperthermia therapy, and sonodynamic therapy. In addition to monotherapy, graphene-based materials are widely applied in combined therapies for enhanced anticancer activity and reduced side effects. In particular, graphene-based materials are often designed and fabricated as "smart" platforms for stimuli-responsive nanocarriers, whose therapeutic effects can be activated by the tumor microenvironment, such as acidic pH and elevated glutathione (termed as "endogenous stimuli"), or light, magnetic, or ultrasonic stimuli (termed as "exogenous stimuli"). Herein, the recent advances of smart graphene platforms for combined therapy applications are presented, starting with the principle for the design of graphene-based smart platforms in combined therapy applications. Next, recent advances of combined therapies contributed by graphene-based materials, including chemotherapy-based, photothermal-therapy-based, and ultrasound-therapy-based synergistic therapy, are outlined. In addition, current challenges and future prospects regarding this promising field are discussed.
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Affiliation(s)
- Zhanjun Gu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuang Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Yan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Feng Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing, 100190, China
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40
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Aragonès AC, Darwish N, Ciampi S, Jiang L, Roesch R, Ruiz E, Nijhuis CA, Díez-Pérez I. Control over Near-Ballistic Electron Transport through Formation of Parallel Pathways in a Single-Molecule Wire. J Am Chem Soc 2018; 141:240-250. [DOI: 10.1021/jacs.8b09086] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Albert C. Aragonès
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
- Institut de Química Teòrica i Computacional (IQTC), Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Nadim Darwish
- School of Molecular and Life Sciences, Curtin University, Bentley WA 6102, Australia
| | - Simone Ciampi
- School of Molecular and Life Sciences, Curtin University, Bentley WA 6102, Australia
| | - Li Jiang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Raphael Roesch
- Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Eliseo Ruiz
- Institut de Química Teòrica i Computacional (IQTC), Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Christian A. Nijhuis
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore 117546
| | - Ismael Díez-Pérez
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
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41
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Synthesis and intramolecular electronic interactions of hexaarylbenzene bearing redox-active Cp*(dppe)Fe-C≡C- termini. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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42
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Zimbovskaya NA. Thermoelectric efficiency of single-molecule junctions with long molecular linkers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:305301. [PMID: 29911988 DOI: 10.1088/1361-648x/aacd3a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We report results of theoretical studies of thermoelectric efficiency of single-molecule junctions with long molecular linkers. The linker is simulated by a chain of identical sites described using a tight-binding model. It is shown that thermoelectric figure of merit ZT strongly depends on the bridge length, being controlled by the lineshape of electron transmission function within the tunnel energy range corresponding to HOMO/LUMO transport channel. Using the adopted model we demonstrate that ZT may significantly increase as the linker lengthens, and that gateway states on the bridge (if any) may noticeably affect the length-dependent ZT. Temperature dependences of ZT for various bridge lengths are analyzed. It is shown that broad minima emerge in ZT versus temperature curves whose positions are controlled by the bridge lengths.
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Affiliation(s)
- Natalya A Zimbovskaya
- Department of Physics and Electronics, University of Puerto Rico-Humacao, CUH Station, Humacao, PR 00791, United States of America
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43
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Electronic and Magnetic Properties of Stone⁻Wales Defected Graphene Decorated with the Half-Metallocene of M ( M = Fe, Co, Ni): A First Principle Study. NANOMATERIALS 2018; 8:nano8070552. [PMID: 30037016 PMCID: PMC6071256 DOI: 10.3390/nano8070552] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 11/17/2022]
Abstract
The geometrical, electronic structure, and magnetic properties of the half-metallocene of M (M = Fe, Co, Ni) adsorbed on Stone⁻Wales defected graphene (SWG) were studied using the density functional theory (DFT), aiming to tune the band structure of SWG. The introduction of cyclopentadienyl (Cp) and half-metallocene strongly affected the band structure of SWG. The magnetic properties of the complex systems originated from the 3D orbitals of M (M = Fe, Co, Ni), the molecular orbital of Cp, and SWG. This phenomenon was different from that found in a previous study, which was due to metal ion-induced sandwich complexes. The results have potential applications in the design of electronic devices based on SWG.
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Tanaka Y, Kato Y, Tada T, Fujii S, Kiguchi M, Akita M. “Doping” of Polyyne with an Organometallic Fragment Leads to Highly Conductive Metallapolyyne Molecular Wire. J Am Chem Soc 2018; 140:10080-10084. [DOI: 10.1021/jacs.8b04484] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Yuya Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yuya Kato
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Tomofumi Tada
- Materials Research Center for Element Strategy, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Shintaro Fujii
- Department of Chemistry, School of Science, Tokyo Institute of Technology, Ookayama, Tokyo 152-8551, Japan
| | - Manabu Kiguchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology, Ookayama, Tokyo 152-8551, Japan
| | - Munetaka Akita
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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45
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Microbial nanowires - Electron transport and the role of synthetic analogues. Acta Biomater 2018; 69:1-30. [PMID: 29357319 DOI: 10.1016/j.actbio.2018.01.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/07/2018] [Accepted: 01/09/2018] [Indexed: 02/07/2023]
Abstract
Electron transfer is central to cellular life, from photosynthesis to respiration. In the case of anaerobic respiration, some microbes have extracellular appendages that can be utilised to transport electrons over great distances. Two model organisms heavily studied in this arena are Shewanella oneidensis and Geobacter sulfurreducens. There is some debate over how, in particular, the Geobacter sulfurreducens nanowires (formed from pilin nanofilaments) are capable of achieving the impressive feats of natural conductivity that they display. In this article, we outline the mechanisms of electron transfer through delocalised electron transport, quantum tunnelling, and hopping as they pertain to biomaterials. These are described along with existing examples of the different types of conductivity observed in natural systems such as DNA and proteins in order to provide context for understanding the complexities involved in studying the electron transport properties of these unique nanowires. We then introduce some synthetic analogues, made using peptides, which may assist in resolving this debate. Microbial nanowires and the synthetic analogues thereof are of particular interest, not just for biogeochemistry, but also for the exciting potential bioelectronic and clinical applications as covered in the final section of the review. STATEMENT OF SIGNIFICANCE Some microbes have extracellular appendages that transport electrons over vast distances in order to respire, such as the dissimilatory metal-reducing bacteria Geobacter sulfurreducens. There is significant debate over how G. sulfurreducens nanowires are capable of achieving the impressive feats of natural conductivity that they display: This mechanism is a fundamental scientific challenge, with important environmental and technological implications. Through outlining the techniques and outcomes of investigations into the mechanisms of such protein-based nanofibrils, we provide a platform for the general study of the electronic properties of biomaterials. The implications are broad-reaching, with fundamental investigations into electron transfer processes in natural and biomimetic materials underway. From these studies, applications in the medical, energy, and IT industries can be developed utilising bioelectronics.
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46
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Supur M, Van Dyck C, Bergren AJ, McCreery RL. Bottom-up, Robust Graphene Ribbon Electronics in All-Carbon Molecular Junctions. ACS APPLIED MATERIALS & INTERFACES 2018; 10:6090-6095. [PMID: 29400435 DOI: 10.1021/acsami.7b19305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Large-area molecular electronic junctions consisting of 5-carbon wide graphene ribbons (GR) with lengths of 2-12 nm between carbon electrodes were fabricated by electrochemical reduction of diazotized 1,8-diaminonaphthalene. Their conductance greatly exceeds that observed for other molecular junctions of similar thicknesses, by a factor of >1 × 104 compared to polyphenylenes and >1 × 107 compared to alkane chains. The remarkable increase of conductance of the GR nanolayer results from (i) uninterrupted planarity of fused-arene structure affording extensive π-electron delocalization and (ii) enhanced electronic coupling of molecular layer with the carbon bottom contact by two-point covalent bonding, in agreement with DFT-based simulations.
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Affiliation(s)
- Mustafa Supur
- Department of Chemistry, University of Alberta , 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada
| | - Colin Van Dyck
- National Institute for Nanotechnology (NINT), National Research Council Canada , 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Adam J Bergren
- National Institute for Nanotechnology (NINT), National Research Council Canada , 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Richard L McCreery
- Department of Chemistry, University of Alberta , 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada
- National Institute for Nanotechnology (NINT), National Research Council Canada , 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
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47
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Medvedev IG. Analytical expression for the tunnel current through the redox-mediated tunneling contact in the case of the adiabatic electron transfer at one of the working electrodes and any possible type of the electron transfer at the other electrode. J Chem Phys 2017; 147:194108. [PMID: 29166090 DOI: 10.1063/1.5011313] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We study the tunnel current through a one-level redox molecule immersed into the electrolyte solution for the case when the coupling of the molecule to one of the working electrodes is strong while it is arbitrary to the other electrode. Using the Feynman-Vernon influence functional theory and the perturbation expansion of the effective action of the classical oscillator coupled both to the valence level of the redox molecule and to the thermal bath representing the classical fluctuations of the polarization of the solvent, we obtain, following the canonical way, the Langevin equation for the oscillator. It is found that for the aqueous electrolyte solution, the damping and the stochastic forces which arise due to the tunnel current are much smaller than those due to the thermal bath and therefore can be neglected. We estimate the higher-order corrections to the effective action and show that the Langevin dynamics takes place in this case for arbitrary parameters of the tunneling junction under the condition of the strong coupling of the redox molecule to one of the working electrodes. Then the steady-state coordinate distribution function of the oscillator resulting from the corresponding Fokker-Planck equation is the Boltzmann distribution function which is determined by the adiabatic free energy surface arising from the mean current-induced force. It enables us to obtain the expression for the tunnel current in the case when the coupling of the redox molecule to one of the working electrodes is strong while it is arbitrary to the other electrode.
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Affiliation(s)
- Igor G Medvedev
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences, Leninsky Prospect 31, 119071 Moscow, Russian Federation
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48
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Medvedev IG. Exact identities between values of the tunnel current in the redox-mediated tunneling contacts and the positions of the extrema of the tunnel current/overvoltage characteristics. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.06.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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49
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Kaur RP, Sawhney RS, Engles D. Electrical characterization of C 28 fullerene junctions formed with group 1B metal electrodes. J Mol Graph Model 2017; 76:296-304. [PMID: 28750306 DOI: 10.1016/j.jmgm.2017.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/16/2017] [Accepted: 07/17/2017] [Indexed: 11/15/2022]
Abstract
We present an atomistic theory of electronic transport through single molecular junctions based on smallest stable fullerene molecule, C28. The electronic properties of single molecular junctions critically depend on the nature of electrode material. The two probe device is modeled by constraining C28 between two semi-infinite metal electrodes, from group 1B of periodic table, copper, silver and gold. We have highlighted the correlated phenomena of resonant conduction and current driven dynamics in molecular junctions using extendend Huckel theory in combination with non equilibrium Green's function framework. We conclude strong dependence of conductance on transmissions, which leads to oscillating conductance spectrum. An interesting interplay between conducting channels and different degrees of spatial localization and delocalization of molecular orbitals is evinced. The physical origin of current and conductance of so-formed C28 molecular junctions is discussed in detail by analysing their density of states, transmission spectra, molecular orbital analysis, rectification ratio and molecular projected self consistent Hamiltonian eigen states at different operating voltages ranging from -2V to +2V.
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Affiliation(s)
- Rupan Preet Kaur
- Department of Electronics Technology, Guru Nanak Dev University, Amritsar, India.
| | | | - Derick Engles
- Department of Electronics Technology, Guru Nanak Dev University, Amritsar, India.
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50
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Chen Y, Marszalek T, Fritz T, Baumgarten M, Wagner M, Pisula W, Chen L, Müllen K. Contorted polycyclic aromatic hydrocarbons with cove regions and zig-zag edges. Chem Commun (Camb) 2017; 53:8474-8477. [PMID: 28703255 DOI: 10.1039/c7cc03709k] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of tetrapyrene-fused benzocoronenes was synthesized by a "bottom-up" approach, which offers a facile access to extended polycyclic aromatic hydrocarbons with concave π-surfaces, cove regions and zig-zag edges.
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Affiliation(s)
- Yulan Chen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany. and Department of Chemistry, Tianjin University, 300072 Tianjin, P. R. China.
| | - Tomasz Marszalek
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Torsten Fritz
- Friedrich Schiller University Jena, Institute of Solid State Physics, Helmholtzweg 5, 07743 Jena, Germany
| | - Martin Baumgarten
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Wojciech Pisula
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany. and Department of Molecular Physics, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Long Chen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany. and Department of Chemistry, Tianjin University, 300072 Tianjin, P. R. China.
| | - Klaus Müllen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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