1
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Kalita M, Yadav K, Archana A, Gopakumar TG, Vasudev PG, Ramapanicker R. Incorporation of phenylcarbonyl groups in the sidechain: A tool to induce ordered assembly of peptides on surfaces. J Pept Sci 2024; 30:e3629. [PMID: 38898708 DOI: 10.1002/psc.3629] [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: 04/04/2024] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024]
Abstract
The possibility of introducing various functionalities on peptides with relative ease allows them to be used for molecular applications. However, oligopeptides prepared entirely from proteinogenic amino acids seldom assemble as ordered structures on surfaces. Therefore, sidechain modifications of peptides that can increase the intermolecular interactions without altering the constitution of a given peptide become an attractive route to self-assembling them on surfaces. We find that replacing phenylalanine residues with unusual amino acids that have phenylcarbonyl sidechains in oligopeptides increases the formation of ordered self-assembly on a highly ordered pyrolytic graphite surface. Peptides containing the modified amino acids provided extended long-range ordered assemblies, while the analogous peptides containing phenylalanine residues failed to form long-range assemblies. X-ray crystallographic analysis of the bulk structures of these peptides and the analogous peptides containing phenylalanine residues reveal that such modifications do not alter the secondary structure in crystals. It also reveals that the secondary hydrogen bonding interaction through phenylcarbonyl sidechains facilitates extended growth of the peptides on graphite.
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Affiliation(s)
- Mrinal Kalita
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Khushboo Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Archana Archana
- Molecular and Structural Biology Department, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | | | - Prema G Vasudev
- Molecular and Structural Biology Department, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Ramesh Ramapanicker
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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2
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van Trijp JP, Hribernik N, Lim JH, Dal Colle MCS, Mena YV, Ogawa Y, Delbianco M. Enzyme-Triggered Assembly of Glycan Nanomaterials. Angew Chem Int Ed Engl 2024; 63:e202410634. [PMID: 39008635 DOI: 10.1002/anie.202410634] [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: 06/05/2024] [Revised: 07/05/2024] [Accepted: 07/15/2024] [Indexed: 07/17/2024]
Abstract
A comprehensive molecular understanding of carbohydrate aggregation is key to optimize carbohydrate utilization and to engineer bioinspired analogues with tailored shapes and properties. However, the lack of well-defined synthetic standards has substantially hampered advances in this field. Herein, we employ a phosphorylation-assisted strategy to synthesize previously inaccessible long oligomers of cellulose, chitin, and xylan. These oligomers were subjected to enzyme-triggered assembly (ETA) for the on-demand formation of well-defined carbohydrate nanomaterials, including elongated platelets, helical bundles, and hexagonal particles. Cryo-electron microscopy and electron diffraction analysis provided molecular insights into the aggregation behavior of these oligosaccharides, establishing a direct connection between the resulting morphologies and the oligosaccharide primary sequence. Our findings demonstrate that ETA is a powerful approach to elucidate the intrinsic aggregation behavior of carbohydrates in nature. Moreover, the ability to access a diverse array of morphologies, expanded with a non-natural sequence, underscores the potential of ETA, coupled with sequence design, as a robust tool for accessing programmable glycan architectures.
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Affiliation(s)
- Jacobus P van Trijp
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Nives Hribernik
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Jia Hui Lim
- Jia Hui Lim, Yadiel Vázquez Mena, Yu Ogawa, Univ. Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Marlene C S Dal Colle
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Yadiel Vázquez Mena
- Jia Hui Lim, Yadiel Vázquez Mena, Yu Ogawa, Univ. Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Yu Ogawa
- Jia Hui Lim, Yadiel Vázquez Mena, Yu Ogawa, Univ. Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
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3
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Mallada B, Villalobos F, Donoso B, Casares R, Longhi G, Mendieta-Moreno JI, Jiménez-Martín A, Haïdour A, Seepersaud R, Rajagopal L, de la Torre B, Millán A, Cuerva JM. Single-Molecule Identification of the Isomers of a Lipidic Antibody Activator. J Phys Chem Lett 2024; 15:6935-6942. [PMID: 38935930 PMCID: PMC11247479 DOI: 10.1021/acs.jpclett.4c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/29/2024] [Accepted: 05/03/2024] [Indexed: 06/29/2024]
Abstract
Molecular structural elucidation can be accomplished by different techniques, such as nuclear magnetic resonance or X-ray diffraction. However, the former does not give information about the three-dimensional atomic arrangement, and the latter needs crystallizable solid samples. An alternative is direct, real-space visualization of the molecules by cryogenic scanning tunneling microscopy (STM). This technique is usually limited to thermally robust molecules because an annealing step is required for sample deposition. A landmark development has been the coupling of STM with electrospray deposition (ESD), which smooths the process and widens the scope of the visualization technique. In this work, we present the on-surface characterization of air-, light-, and temperature-sensitive rhamnopolyene with relevance in molecular biology. Supported by theoretical calculations, we characterize two isomers of this flexible molecule, confirming the potential of the technique to inspect labile, non-crystallizable compounds.
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Affiliation(s)
- Benjamin Mallada
- Institute
of Physics, Czech Academy of Sciences, 16200 Prague, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, 78371 Olomouc, Czech Republic
| | - Federico Villalobos
- Departamento
de Química Orgánica, Unidad de Excelencia de Química
Aplicada a la Biomedicina y Medioambiente, C. U. Fuentenueva, Universidad de Granada, 18071 Granada, Spain
| | - Beatriz Donoso
- Departamento
de Química Orgánica, Unidad de Excelencia de Química
Aplicada a la Biomedicina y Medioambiente, C. U. Fuentenueva, Universidad de Granada, 18071 Granada, Spain
| | - Raquel Casares
- Departamento
de Química Orgánica, Unidad de Excelencia de Química
Aplicada a la Biomedicina y Medioambiente, C. U. Fuentenueva, Universidad de Granada, 18071 Granada, Spain
| | - Giovanna Longhi
- Dipartimento
di Medicina Molecolare e Traslazionale, Universitá di Brescia, Viale Europa 11, 25121 Brescia, Italy
| | - Jesús I. Mendieta-Moreno
- Instituto
de Ciencia de Materiales de Madrid (ICMM), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Alejandro Jiménez-Martín
- Institute
of Physics, Czech Academy of Sciences, 16200 Prague, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, 78371 Olomouc, Czech Republic
- Faculty
of Nuclear Sciences and Physical Engineering, Czech Technical University, 11519 Prague, Czech
Republic
| | - Ali Haïdour
- Unidad
de Resonancia Magnética Nuclear, Centro de Instrumentación
Científica, Universidad de Granada, Paseo Juan Osorio s/n, 18071 Granada, Spain
| | - Ravin Seepersaud
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Lakshmi Rajagopal
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98105, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98105, United States
| | - Bruno de la Torre
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, 78371 Olomouc, Czech Republic
| | - Alba Millán
- Departamento
de Química Orgánica, Unidad de Excelencia de Química
Aplicada a la Biomedicina y Medioambiente, C. U. Fuentenueva, Universidad de Granada, 18071 Granada, Spain
| | - Juan M. Cuerva
- Departamento
de Química Orgánica, Unidad de Excelencia de Química
Aplicada a la Biomedicina y Medioambiente, C. U. Fuentenueva, Universidad de Granada, 18071 Granada, Spain
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4
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Kojima T, Xie C, Sakaguchi H. On-Surface Fabrication toward Polar 2D Macromolecular Crystals. Chempluschem 2024; 89:e202300775. [PMID: 38439510 DOI: 10.1002/cplu.202300775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/16/2024] [Accepted: 03/04/2024] [Indexed: 03/06/2024]
Abstract
Polar 2D macromolecular structures have attracted significant attention because of their ferroelectricity and ferro-magnetism. However, it is challenging to synthesize them experimentally because dipoles or spins of these macromolecules tend to cancel each other. So far, there has been no successful strategy for assembling macromolecules in a unidirectional manner, achieving stereoregular polymerization on metal surfaces, and creating polar 2D polymer crystals. Recent progress in molecular assembly, on-surface polymer synthesis, and direct control of molecules using electric field applications provides an opportunity to develop such strategies. In this regard, we first review past studies on chiral and achiral molecular assembly, on-surface polymer synthesis, and orientation control of polar molecules. Then, we discuss our newly developed approach called "vectorial on-surface synthesis", which is based on "dynamic chirality" of compass precursors, stereoselective polymerization, and favorable interchain interactions originating from CH-π interactions. Finally, we conclude with a prospective outlook.
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Affiliation(s)
- Takahiro Kojima
- Institute of Advanced Energy, Kyoto University, Gokasyo, Uji, Kyoto, 611-0011, Japan
| | - Cong Xie
- Institute of Advanced Energy, Kyoto University, Gokasyo, Uji, Kyoto, 611-0011, Japan
| | - Hiroshi Sakaguchi
- Institute of Advanced Energy, Kyoto University, Gokasyo, Uji, Kyoto, 611-0011, Japan
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5
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Lu X, Zhang K, Niu X, Ren DD, Zhou Z, Dang LL, Fu HR, Tan C, Ma L, Zang SQ. Encapsulation engineering of porous crystalline frameworks for delayed luminescence and circularly polarized luminescence. Chem Soc Rev 2024; 53:6694-6734. [PMID: 38747082 DOI: 10.1039/d3cs01026k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Delayed luminescence (DF), including phosphorescence and thermally activated delayed fluorescence (TADF), and circularly polarized luminescence (CPL) exhibit common and broad application prospects in optoelectronic displays, biological imaging, and encryption. Thus, the combination of delayed luminescence and circularly polarized luminescence is attracting increasing attention. The encapsulation of guest emitters in various host matrices to form host-guest systems has been demonstrated to be an appealing strategy to further enhance and/or modulate their delayed luminescence and circularly polarized luminescence. Compared with conventional liquid crystals, polymers, and supramolecular matrices, porous crystalline frameworks (PCFs) including metal-organic frameworks (MOFs), covalent-organic frameworks (COFs), zeolites and hydrogen-bonded organic frameworks (HOFs) can not only overcome shortcomings such as flexibility and disorder but also achieve the ordered encapsulation of guests and long-term stability of chiral structures, providing new promising host platforms for the development of DF and CPL. In this review, we provide a comprehensive and critical summary of the recent progress in host-guest photochemistry via the encapsulation engineering of guest emitters in PCFs, particularly focusing on delayed luminescence and circularly polarized luminescence. Initially, the general principle of phosphorescence, TADF and CPL, the combination of DF and CPL, and energy transfer processes between host and guests are introduced. Subsequently, we comprehensively discuss the critical factors affecting the encapsulation engineering of guest emitters in PCFs, such as pore structures, the confinement effect, charge and energy transfer between the host and guest, conformational dynamics, and aggregation model of guest emitters. Thereafter, we summarize the effective methods for the preparation of host-guest systems, especially single-crystal-to-single-crystal (SC-SC) transformation and epitaxial growth, which are distinct from conventional methods based on amorphous materials. Then, the recent advancements in host-guest systems based on PCFs for delayed luminescence and circularly polarized luminescence are highlighted. Finally, we present our personal insights into the challenges and future opportunities in this promising field.
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Affiliation(s)
- Xiaoyan Lu
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, P. R. China.
| | - Kun Zhang
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, P. R. China.
- College of Materials and Chemical Engineering, China Three Gorges University, Yichang 443002, P. R. China
| | - Xinkai Niu
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, P. R. China.
- Xinjiang Production & Construction Corps Key Laboratory of Advanced Energy Storage Materials and Technology, College of Science, Shihezi University, Shihezi 832003, P. R. China
| | - Dan-Dan Ren
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, P. R. China.
- College of Materials and Chemical Engineering, China Three Gorges University, Yichang 443002, P. R. China
| | - Zhan Zhou
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, P. R. China.
| | - Li-Long Dang
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, P. R. China.
| | - Hong-Ru Fu
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, P. R. China.
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, China
| | - Chaoliang Tan
- Department Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, SAR 999077, P. R. China.
| | - Lufang Ma
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, P. R. China.
| | - Shuang-Quan Zang
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China.
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6
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Seibel J, Anggara K, Delbianco M, Rauschenbach S. Scanning Probe Microscopy Characterization of Biomolecules enabled by Mass-Selective, Soft-landing Electrospray Ion Beam Deposition. Chemphyschem 2024:e202400419. [PMID: 38945838 DOI: 10.1002/cphc.202400419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
Scanning probe microscopy (SPM), in particular at low temperature (LT) under ultra-high vacuum (UHV) conditions, offers the possibility of real-space imaging with resolution reaching the atomic level. However, its potential for the analysis of complex biological molecules has been hampered by requirements imposed by sample preparation. Transferring molecules onto surfaces in UHV is typically accomplished by thermal sublimation in vacuum. This approach however is limited by the thermal stability of the molecules, i. e. not possible for biological molecules with low vapour pressure. Bypassing this limitation, electrospray ionisation offers an alternative method to transfer molecules from solution to the gas-phase as intact molecular ions. In soft-landing electrospray ion beam deposition (ESIBD), these molecular ions are subsequently mass-selected and gently landed on surfaces which permits large and thermally fragile molecules to be analyzed by LT-UHV SPM. In this concept, we discuss how ESIBD+SPM prepares samples of complex biological molecules at a surface, offering controls of the molecular structural integrity, three-dimensional shape, and purity. These achievements unlock the analytical potential of SPM which is showcased by imaging proteins, peptides, DNA, glycans, and conjugates of these molecules, revealing details of their connectivity, conformation, and interaction that could not be accessed by any other technique.
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Affiliation(s)
- Johannes Seibel
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber Weg 2, D-76131, Karlsruhe, Germany
| | - Kelvin Anggara
- Nanoscale Science Department, Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569, Stuttgart, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, D-14476, Potsdam, Germany
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7
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Peng X, Zhang Y, Liu X, Qian Y, Ouyang Z, Kong H. From Short- to Long-Range Chiral Recognition on Surfaces: Chiral Assembly and Synthesis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307171. [PMID: 38054810 DOI: 10.1002/smll.202307171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/13/2023] [Indexed: 12/07/2023]
Abstract
Research on chiral behaviors of small organic molecules at solid surfaces, including chiral assembly and synthesis, can not only help unravel the origin of the chiral phenomenon in biological/chemical systems but also provide promising strategies to build up unprecedented chiral surfaces or nanoarchitectures with advanced applications in novel nanomaterials/nanodevices. Understanding how molecular chirality is recognized is considered to be a mandatory basis for such studies. In this review, a series of recent studies in chiral assembly and synthesis at well-defined metal surfaces under ultra-high vacuum conditions are outlined. More importantly, the intrinsic mechanisms of chiral recognition are highlighted, including short/long-range chiral recognition in chiral assembly and two main strategies to steer the reaction pathways and modulate selective synthesis of specific chiral products on surfaces.
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Affiliation(s)
- Xinchen Peng
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Yinhui Zhang
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Xinbang Liu
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Yinyue Qian
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Zuoling Ouyang
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Huihui Kong
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
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8
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Wu X, Borca B, Sen S, Koslowski S, Abb S, Rosenblatt DP, Gallardo A, Mendieta-Moreno JI, Nachtigall M, Jelinek P, Rauschenbach S, Kern K, Schlickum U. Molecular sensitised probe for amino acid recognition within peptide sequences. Nat Commun 2023; 14:8335. [PMID: 38097575 PMCID: PMC10721870 DOI: 10.1038/s41467-023-43844-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
The combination of low-temperature scanning tunnelling microscopy with a mass-selective electro-spray ion-beam deposition established the investigation of large biomolecules at nanometer and sub-nanometer scale. Due to complex architecture and conformational freedom, however, the chemical identification of building blocks of these biopolymers often relies on the presence of markers, extensive simulations, or is not possible at all. Here, we present a molecular probe-sensitisation approach addressing the identification of a specific amino acid within different peptides. A selective intermolecular interaction between the sensitiser attached at the tip-apex and the target amino acid on the surface induces an enhanced tunnelling conductance of one specific spectral feature, which can be mapped in spectroscopic imaging. Density functional theory calculations suggest a mechanism that relies on conformational changes of the sensitiser that are accompanied by local charge redistributions in the tunnelling junction, which, in turn, lower the tunnelling barrier at that specific part of the peptide.
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Affiliation(s)
- Xu Wu
- Max Planck Institute for Solid State Research, Stuttgart, Germany
- School of Integrated Circuits and Electronics, Beijing Institute of Technology, Beijing, 100081, China
| | - Bogdana Borca
- Institute of Applied Physics and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, 38104, Braunschweig, Germany
- National Institute of Materials Physics, 077125, Magurele, Romania
| | - Suman Sen
- Max Planck Institute for Solid State Research, Stuttgart, Germany
| | | | - Sabine Abb
- Max Planck Institute for Solid State Research, Stuttgart, Germany
| | | | - Aurelio Gallardo
- Institute of Physics of the Czech Academy of Science, Prague, Czech Republic
- Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | | | - Matyas Nachtigall
- Institute of Physics of the Czech Academy of Science, Prague, Czech Republic
| | - Pavel Jelinek
- Institute of Physics of the Czech Academy of Science, Prague, Czech Republic.
| | - Stephan Rauschenbach
- Max Planck Institute for Solid State Research, Stuttgart, Germany.
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Klaus Kern
- Max Planck Institute for Solid State Research, Stuttgart, Germany
- Institut de Physique, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Uta Schlickum
- Max Planck Institute for Solid State Research, Stuttgart, Germany.
- Institute of Applied Physics and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, 38104, Braunschweig, Germany.
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9
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Liu X, Qian B, Zhang D, Yu M, Chang Z, Bu X. Recent progress in host–guest metal–organic frameworks: Construction and emergent properties. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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10
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Dai X, Chen Y. Computational Biomaterials: Computational Simulations for Biomedicine. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2204798. [PMID: 35916024 DOI: 10.1002/adma.202204798] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/23/2022] [Indexed: 05/14/2023]
Abstract
With the flourishing development of material simulation methods (quantum chemistry methods, molecular dynamics, Monte Carlo, phase field, etc.), extensive adoption of computing technologies (high-throughput, artificial intelligence, machine learning, etc.), and the invention of high-performance computing equipment, computational simulation tools have sparked the fundamental mechanism-level explorations to predict the diverse physicochemical properties and biological effects of biomaterials and investigate their enormous application potential for disease prevention, diagnostics, and therapeutics. Herein, the term "computational biomaterials" is proposed and the computational methods currently used to explore the inherent properties of biomaterials, such as optical, magnetic, electronic, and acoustic properties, and the elucidation of corresponding biological behaviors/effects in the biomedical field are summarized/discussed. The theoretical calculation of the physiochemical properties/biological performance of biomaterials applied in disease diagnosis, drug delivery, disease therapeutics, and specific paradigms such as biomimetic biomaterials is discussed. Additionally, the biosafety evaluation applications of theoretical simulations of biomaterials are presented. Finally, the challenges and future prospects of such computational simulations for biomaterials development are clarified. It is anticipated that these simulations would offer various methodologies for facilitating the development and future clinical translations/utilization of versatile biomaterials.
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Affiliation(s)
- Xinyue Dai
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Yu Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
- School of Medicine, Shanghai University, Shanghai, 200444, P. R. China
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11
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Esser TK, Böhning J, Fremdling P, Bharat T, Gault J, Rauschenbach S. Cryo-EM samples of gas-phase purified protein assemblies using native electrospray ion-beam deposition. Faraday Discuss 2022; 240:67-80. [PMID: 36065984 PMCID: PMC9641999 DOI: 10.1039/d2fd00065b] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
An increasing number of studies on biomolecular function indirectly combine mass spectrometry (MS) with imaging techniques such as cryo electron microscopy (cryo-EM). This approach allows information on the homogeneity, stoichiometry, shape, and interactions of native protein complexes to be obtained, complementary to high-resolution protein structures. We have recently demonstrated TEM sample preparation via native electrospray ion-beam deposition (ES-IBD) as a direct link between native MS and cryo-EM. This workflow forms a potential new route to the reliable preparation of homogeneous cryo-EM samples and a better understanding of the relation between native solution-phase and native-like gas-phase structures. However, many aspects of the workflow need to be understood and optimized to obtain performance comparable to that of state-of-the-art cryo-EM. Here, we expand on the previous discussion of key factors by probing the effects of substrate type and deposition energy. We present and discuss micrographs from native ES-IBD samples with amorphous carbon, graphene, and graphene oxide, as well as landing energies in the range between 2 and 150 eV per charge.
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Affiliation(s)
- Tim K. Esser
- Department of Chemistry, University of OxfordOxfordOX1 3TFUK
| | - Jan Böhning
- Sir William Dunn School of Pathology, University of OxfordSouth Parks RoadOxfordOX1 3REUK
| | - Paul Fremdling
- Department of Chemistry, University of OxfordOxfordOX1 3TFUK
| | - Tanmay Bharat
- Sir William Dunn School of Pathology, University of OxfordSouth Parks RoadOxfordOX1 3REUK,Structural Studies Division, MRC Laboratory of Molecular BiologyFrancis Crick AvenueCambridgeCB2 0QHUK
| | - Joseph Gault
- Department of Chemistry, University of OxfordOxfordOX1 3TFUK
| | - Stephan Rauschenbach
- Department of Chemistry, University of OxfordOxfordOX1 3TFUK,Max Planck Institute for Solid State ResearchHeisenbergstrasse 1StuttgartDE-70569Germany
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12
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Fremdling P, Esser TK, Saha B, Makarov AA, Fort KL, Reinhardt-Szyba M, Gault J, Rauschenbach S. A Preparative Mass Spectrometer to Deposit Intact Large Native Protein Complexes. ACS NANO 2022; 16:14443-14455. [PMID: 36037396 PMCID: PMC9527803 DOI: 10.1021/acsnano.2c04831] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Electrospray ion-beam deposition (ES-IBD) is a versatile tool to study the structure and reactivity of molecules from small metal clusters to large protein assemblies. It brings molecules gently into the gas phase, where they can be accurately manipulated and purified, followed by controlled deposition onto various substrates. In combination with imaging techniques, direct structural information on well-defined molecules can be obtained, which is essential to test and interpret results from indirect mass spectrometry techniques. To date, ion-beam deposition experiments are limited to a small number of custom instruments worldwide, and there are no commercial alternatives. Here we present a module that adds ion-beam deposition capabilities to a popular commercial MS platform (Thermo Scientific Q Exactive UHMR mass spectrometer). This combination significantly reduces the overhead associated with custom instruments, while benefiting from established high performance and reliability. We present current performance characteristics including beam intensity, landing-energy control, and deposition spot size for a broad range of molecules. In combination with atomic force microscopy (AFM) and transmission electron microscopy (TEM), we distinguish near-native from unfolded proteins and show retention of the native shape of protein assemblies after dehydration and deposition. Further, we use an enzymatic assay to quantify the activity of a noncovalent protein complex after deposition on a dry surface. Together, these results not only indicate a great potential of ES-IBD for applications in structural biology, but also outline the challenges that need to be solved for it to reach its full potential.
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Affiliation(s)
- Paul Fremdling
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tim K. Esser
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Bodhisattwa Saha
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Alexander A. Makarov
- Thermo
Fisher Scientific, Bremen 28199, Germany
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
| | | | | | - Joseph Gault
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Stephan Rauschenbach
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart 70569, Germany
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13
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Legleiter J, Thakkar R, Velásquez-Silva A, Miranda-Carvajal I, Whitaker S, Tomich J, Comer J. Design of Peptides that Fold and Self-Assemble on Graphite. J Chem Inf Model 2022; 62:4066-4082. [PMID: 35881533 PMCID: PMC9472279 DOI: 10.1021/acs.jcim.2c00419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 11/28/2022]
Abstract
The graphite-water interface provides a unique environment for polypeptides that generally favors ordered structures more than in solution. Therefore, systems consisting of designed peptides and graphitic carbon might serve as a convenient medium for controlled self-assembly of functional materials. Here, we computationally designed cyclic peptides that spontaneously fold into a β-sheet-like conformation at the graphite-water interface and self-assemble, and we subsequently observed evidence of such assembly by atomic force microscopy. Using a novel protocol, we screened nearly 2000 sequences, optimizing for formation of a unique folded conformation while discouraging unfolded or misfolded conformations. A head-to-tail cyclic peptide with the sequence GTGSGTGGPGGGCGTGTGSGPG showed the greatest apparent propensity to fold spontaneously, and this optimized sequence was selected for larger scale molecular dynamics simulations, rigorous free-energy calculations, and experimental validation. In simulations ranging from hundreds of nanoseconds to a few microseconds, we observed spontaneous folding of this peptide at the graphite-water interface under many different conditions, including multiple temperatures (295 and 370 K), with different initial orientations relative to the graphite surface, and using different molecular dynamics force fields (CHARMM and Amber). The thermodynamic stability of the folded conformation on graphite over a range of temperatures was verified by replica-exchange simulations and free-energy calculations. On the other hand, in free solution, the folded conformation was found to be unstable, unfolding in tens of picoseconds. Intermolecular hydrogen bonds promoted self-assembly of the folded peptides into linear arrangements where the peptide backbone exhibited a tendency to align along one of the six zigzag directions of the graphite basal plane. For the optimized peptide, atomic force microscopy revealed growth of single-molecule-thick linear patterns of 6-fold symmetry, consistent with the simulations, while no such patterns were observed for a control peptide with the same amino acid composition but a scrambled sequence.
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Affiliation(s)
- Justin Legleiter
- The
C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Ravindra Thakkar
- Nanotechnology
Innovation Center of Kansas State, Institute of Computational Comparative
Medicine, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Astrid Velásquez-Silva
- Facultad
de Ciencias de la Salud, Programa de Fisioterapia, Corporación Universitaria Iberoamericana, Calle 67 No. 5-27, 110231 Bogotá, Colombia
| | - Ingrid Miranda-Carvajal
- Centro
de Innovación y Tecnología − Instituto Colombiano
del Petróleo - Ecopetrol S.A., Km 7 vía Bucaramanga, 681011 Piedecuesta, Colombia
| | - Susan Whitaker
- Department
of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - John Tomich
- Department
of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Jeffrey Comer
- Nanotechnology
Innovation Center of Kansas State, Institute of Computational Comparative
Medicine, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
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14
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Esser TK, Böhning J, Fremdling P, Agasid MT, Costin A, Fort K, Konijnenberg A, Gilbert JD, Bahm A, Makarov A, Robinson CV, Benesch JLP, Baker L, Bharat TAM, Gault J, Rauschenbach S. Mass-selective and ice-free electron cryomicroscopy protein sample preparation via native electrospray ion-beam deposition. PNAS NEXUS 2022; 1:pgac153. [PMID: 36714824 PMCID: PMC9802471 DOI: 10.1093/pnasnexus/pgac153] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/03/2022] [Indexed: 02/01/2023]
Abstract
Despite tremendous advances in sample preparation and classification algorithms for electron cryomicroscopy (cryo-EM) and single-particle analysis (SPA), sample heterogeneity remains a major challenge and can prevent access to high-resolution structures. In addition, optimization of preparation conditions for a given sample can be time-consuming. In the current work, it is demonstrated that native electrospray ion-beam deposition (native ES-IBD) is an alternative, reliable approach for the preparation of extremely high-purity samples, based on mass selection in vacuum. Folded protein ions are generated by native electrospray ionization, separated from other proteins, contaminants, aggregates, and fragments, gently deposited on cryo-EM grids, frozen in liquid nitrogen, and subsequently imaged by cryo-EM. We demonstrate homogeneous coverage of ice-free cryo-EM grids with mass-selected protein complexes. SPA reveals that the complexes remain folded and assembled, but variations in secondary and tertiary structures are currently limiting information in 2D classes and 3D EM density maps. We identify and discuss challenges that need to be addressed to obtain a resolution comparable to that of the established cryo-EM workflow. Our results show the potential of native ES-IBD to increase the scope and throughput of cryo-EM for protein structure determination and provide an essential link between gas-phase and solution-phase protein structures.
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Affiliation(s)
- Tim K Esser
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Mark T Agasid
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Adam Costin
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Kyle Fort
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany
| | - Albert Konijnenberg
- Thermo Fisher Scientific, Zwaanstraat 31G/H, 5651 CA Eindhoven, The Netherlands
| | - Joshua D Gilbert
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alan Bahm
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alexander Makarov
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Lindsay Baker
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Stephan Rauschenbach
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, DE-70569 Stuttgart, Germany
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15
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Rodríguez-Galván A, Contreras-Torres FF. Scanning Tunneling Microscopy of Biological Structures: An Elusive Goal for Many Years. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3013. [PMID: 36080050 PMCID: PMC9457988 DOI: 10.3390/nano12173013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/29/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Scanning tunneling microscopy (STM) is a technique that can be used to directly observe individual biomolecules at near-molecular scale. Within this framework, STM is of crucial significance because of its role in the structural analysis, the understanding the imaging formation, and the development of relative techniques. Four decades after its invention, it is pertinent to ask how much of the early dream has come true. In this study, we aim to overview different analyses for DNA, lipids, proteins, and carbohydrates. The relevance of STM imaging is exhibited as an opportunity to assist measurements and biomolecular identification in nanobiotechnology, nanomedicine, biosensing, and other cutting-edge applications. We believe STM research is still an entire science research ecosystem for joining several areas of expertise towards a goal settlement that has been elusive for many years.
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Affiliation(s)
- Andrés Rodríguez-Galván
- Carrera de Biología, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edo. Mex., Mexico
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16
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Chen C, Ding PC, Li Z, Shi GQ, Sun Y, Kantorovich LN, Besenbacher F, Yu M. Super‐Robust Xanthine–Sodium Complexes on Au(111). Angew Chem Int Ed Engl 2022; 61:e202200064. [DOI: 10.1002/anie.202200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Chong Chen
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
- School of Chemistry and Chemical Engineering Suzhou University Suzhou 234000 China
- Interdisciplinary Nanoscience Center (iNANO) and Deptment of Physics and Astronomy Aarhus University Aarhus 8000 Denmark
| | - Pengcheng C. Ding
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
- School of Instrumentation Science and Engineering Harbin Institute of Technology Harbin 150001 China
| | - Zhuo Li
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Guoqiang Q. Shi
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Ye Sun
- School of Instrumentation Science and Engineering Harbin Institute of Technology Harbin 150001 China
| | - Lev N. Kantorovich
- Department of Physics King's College London The Strand London WC2R 2LS UK
| | - Flemming Besenbacher
- Interdisciplinary Nanoscience Center (iNANO) and Deptment of Physics and Astronomy Aarhus University Aarhus 8000 Denmark
| | - Miao Yu
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
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17
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Ran W, Walz A, Stoiber K, Knecht P, Xu H, Papageorgiou AC, Huettig A, Cortizo‐Lacalle D, Mora‐Fuentes JP, Mateo‐Alonso A, Schlichting H, Reichert J, Barth JV. Depositing Molecular Graphene Nanoribbons on Ag(111) by Electrospray Controlled Ion Beam Deposition: Self-Assembly and On-Surface Transformations. Angew Chem Int Ed Engl 2022; 61:e202111816. [PMID: 35077609 PMCID: PMC9305426 DOI: 10.1002/anie.202111816] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/31/2022]
Abstract
The chemical processing of low-dimensional carbon nanostructures is crucial for their integration in future devices. Here we apply a new methodology in atomically precise engineering by combining multistep solution synthesis of N-doped molecular graphene nanoribbons (GNRs) with mass-selected ultra-high vacuum electrospray controlled ion beam deposition on surfaces and real-space visualisation by scanning tunnelling microscopy. We demonstrate how this method yields solely a controllable amount of single, otherwise unsublimable, GNRs of 2.9 nm length on a planar Ag(111) surface. This methodology allows for further processing by employing on-surface synthesis protocols and exploiting the reactivity of the substrate. Following multiple chemical transformations, the GNRs provide reactive building blocks to form extended, metal-organic coordination polymers.
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Affiliation(s)
- Wei Ran
- Physics Department E20Technical University of MunichJames Franck Straße 185748GarchingGermany
| | - Andreas Walz
- Physics Department E20Technical University of MunichJames Franck Straße 185748GarchingGermany
| | - Karolina Stoiber
- Physics Department E20Technical University of MunichJames Franck Straße 185748GarchingGermany
| | - Peter Knecht
- Physics Department E20Technical University of MunichJames Franck Straße 185748GarchingGermany
| | - Hongxiang Xu
- Physics Department E20Technical University of MunichJames Franck Straße 185748GarchingGermany
| | | | - Annette Huettig
- Physics Department E20Technical University of MunichJames Franck Straße 185748GarchingGermany
| | - Diego Cortizo‐Lacalle
- POLYMATUniversity of the Basque Country UPV/EHUAvenida de Tolosa 7220018Donostia-San SebastianSpain
| | - Juan P. Mora‐Fuentes
- POLYMATUniversity of the Basque Country UPV/EHUAvenida de Tolosa 7220018Donostia-San SebastianSpain
| | - Aurelio Mateo‐Alonso
- POLYMATUniversity of the Basque Country UPV/EHUAvenida de Tolosa 7220018Donostia-San SebastianSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
| | - Hartmut Schlichting
- Physics Department E20Technical University of MunichJames Franck Straße 185748GarchingGermany
| | - Joachim Reichert
- Physics Department E20Technical University of MunichJames Franck Straße 185748GarchingGermany
| | - Johannes V. Barth
- Physics Department E20Technical University of MunichJames Franck Straße 185748GarchingGermany
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18
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Chen C, Ding PC, Li Z, Shi GQ, Sun Y, Kantorovich LN, Besenbacher F, Yu M. Super‐Robust Xanthine–Sodium Complexes on Au(111). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chong Chen
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
- School of Chemistry and Chemical Engineering Suzhou University Suzhou 234000 China
- Interdisciplinary Nanoscience Center (iNANO) and Deptment of Physics and Astronomy Aarhus University Aarhus 8000 Denmark
| | - Pengcheng C. Ding
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
- School of Instrumentation Science and Engineering Harbin Institute of Technology Harbin 150001 China
| | - Zhuo Li
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Guoqiang Q. Shi
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Ye Sun
- School of Instrumentation Science and Engineering Harbin Institute of Technology Harbin 150001 China
| | - Lev N. Kantorovich
- Department of Physics King's College London The Strand London WC2R 2LS UK
| | - Flemming Besenbacher
- Interdisciplinary Nanoscience Center (iNANO) and Deptment of Physics and Astronomy Aarhus University Aarhus 8000 Denmark
| | - Miao Yu
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
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19
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Ran W, Walz A, Stoiber K, Knecht P, Xu H, Papageorgiou AC, Huettig A, Cortizo‐Lacalle D, Mora‐Fuentes JP, Mateo‐Alonso A, Schlichting H, Reichert J, Barth JV. Depositing Molecular Graphene Nanoribbons on Ag(111) by Electrospray Controlled Ion Beam Deposition: Self‐Assembly and On‐Surface Transformations. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wei Ran
- Physics Department E20 Technical University of Munich James Franck Straße 1 85748 Garching Germany
| | - Andreas Walz
- Physics Department E20 Technical University of Munich James Franck Straße 1 85748 Garching Germany
| | - Karolina Stoiber
- Physics Department E20 Technical University of Munich James Franck Straße 1 85748 Garching Germany
| | - Peter Knecht
- Physics Department E20 Technical University of Munich James Franck Straße 1 85748 Garching Germany
| | - Hongxiang Xu
- Physics Department E20 Technical University of Munich James Franck Straße 1 85748 Garching Germany
| | - Anthoula C. Papageorgiou
- Physics Department E20 Technical University of Munich James Franck Straße 1 85748 Garching Germany
| | - Annette Huettig
- Physics Department E20 Technical University of Munich James Franck Straße 1 85748 Garching Germany
| | - Diego Cortizo‐Lacalle
- POLYMAT University of the Basque Country UPV/EHU Avenida de Tolosa 72 20018 Donostia-San Sebastian Spain
| | - Juan P. Mora‐Fuentes
- POLYMAT University of the Basque Country UPV/EHU Avenida de Tolosa 72 20018 Donostia-San Sebastian Spain
| | - 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 Bilbao Spain
| | - Hartmut Schlichting
- Physics Department E20 Technical University of Munich James Franck Straße 1 85748 Garching Germany
| | - Joachim Reichert
- Physics Department E20 Technical University of Munich James Franck Straße 1 85748 Garching Germany
| | - Johannes V. Barth
- Physics Department E20 Technical University of Munich James Franck Straße 1 85748 Garching Germany
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20
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Ma L, Wang P, Duan W, Tu B, Zeng Q. Regulation of a Porphyrin Derivative Containing Two Symmetric Benzoic Acids by Different Pyridines. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11544-11551. [PMID: 34546063 DOI: 10.1021/acs.langmuir.1c01812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A porphyrin derivative called 5,15-di(4-carboxyphenyl)porphyrin (H2DCPp) with carboxyl groups successfully self-assembled on a highly oriented pyrolytic graphite (HOPG) surface and its co-assembly structures with three kinds of pyridine molecules were investigated by scanning tunneling microscopy (STM) with atomic resolution. H2DCPp arranged in a long-range ordered structure, and both 1,4-bis (pyridin-4-ylethynyl) benzene (BisPy), 4,4'-bipyridine (BP) and 1,3,5-tris(pyridin-4-ylethynyl) benzene (TPYB) molecules successfully regulated the host molecules as guest molecules. The well-organized model optimized by density functional theory (DFT) calculations reveals the detailed behavior of the assembly characteristics and regulation of porphyrin derivatives, which is helpful for the research and development of solar cells and nanodevices.
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Affiliation(s)
- Lin Ma
- Department of Chemistry, School of Science, Beijing Jiaotong University, Beijing 100044, China
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Peng Wang
- School of Computer Science and Engineering, Beijing Technology and Business University, Beijing 100048, China
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanophotonic Materials and Devices, CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Wubiao Duan
- Department of Chemistry, School of Science, Beijing Jiaotong University, Beijing 100044, China
| | - Bin Tu
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanophotonic Materials and Devices, CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Qingdao Zeng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
- Center of Material Science and Optoelectonics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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21
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Guo Y, Jiang L, Seitsonen AP, Zhang B, Reichert J, Papageorgiou AC, Barth JV. Interaction of cyclosporin A molecules with alkali and transition metal atoms on Cu(111). Chem Commun (Camb) 2021; 57:2923-2926. [PMID: 33620361 DOI: 10.1039/d1cc00125f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of a cyclic peptide with important biological functionalities, cyclosporin A (CsA), is investigated at the single molecule level. Its adsorption on Cu(111) under ultra-high vacuum is characterised with scanning tunnelling microscopy (STM) and density functional theory. With STM investigations, we demonstrate element specific on-surface coordination schemes of CsA with coadsorbed K, Co and Fe atoms. Thus, clear insights emerge in the behaviour of cyclic peptides at interfaces and their interactions with different metal atoms, providing control of the adsorption structure and assembly and paving the way for the integration of cyclic peptides in functional metal-organic nanostructures on surfaces.
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Affiliation(s)
- Yuanyuan Guo
- Physics Department E20, Technical University of Munich, Garching D-85748, Germany.
| | - Li Jiang
- Physics Department E20, Technical University of Munich, Garching D-85748, Germany.
| | - Ari Paavo Seitsonen
- Département de Chimie, Ecole Normale Supérieure, Paris F-75005, France and Université de recherche Paris-Sciences-et-Lettres, Sorbonne Université, Centre National de la Recherche Scientifique, Paris F-75005, France
| | - Bodong Zhang
- Physics Department E20, Technical University of Munich, Garching D-85748, Germany.
| | - Joachim Reichert
- Physics Department E20, Technical University of Munich, Garching D-85748, Germany.
| | | | - Johannes V Barth
- Physics Department E20, Technical University of Munich, Garching D-85748, Germany.
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22
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Guo Y, Nuermaimaiti A, Kjeldsen ND, Gothelf KV, Linderoth TR. Two-Dimensional Coordination Networks from Cyclic Dipeptides. J Am Chem Soc 2020; 142:19814-19818. [PMID: 33179492 DOI: 10.1021/jacs.0c08700] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide-based biomimetic nanostructures and metal-organic coordination networks on surfaces are two promising classes of hybrid materials which have been explored recently. However, despite the great versatility and structural variability of natural and synthetic peptides, the two directions have so far not been merged in fabrication of metal-organic coordination networks using peptides as building blocks. Here we demonstrate that cyclic peptides can be used as ligands to form highly ordered, two-dimensional, peptide-based metal-organic coordination networks. The networks are formed on a Au(111) surface through coadsorption of cyclic dialanine with Cu-adatoms under Ultra-High Vacuum (UHV) conditions. Scanning Tunneling Microscopy (STM) in combination with X-ray Photoelectron spectroscopy (XPS) has been utilized to characterize the network structures at submolecular resolution and expound the chemical changes involved in network coordination. The networks involve a motif of three cyclic dialanine molecules coordinating to a central Cu-adatom. Interestingly the networks expose pores functionalized by the side chain of the cyclic peptide, suggesting a general method to form functionalized porous metal-organic networks on surfaces.
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Affiliation(s)
- Yuanyuan Guo
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Ajiguli Nuermaimaiti
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Niels Due Kjeldsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Trolle R Linderoth
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.,Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
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23
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Shen B, Kim Y, Lee M. Supramolecular Chiral 2D Materials and Emerging Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1905669. [PMID: 32009269 DOI: 10.1002/adma.201905669] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/16/2019] [Indexed: 06/10/2023]
Abstract
Chiral materials are widely applied in various fields such as enantiomeric separation, asymmetric catalysis, and chiroptical effects, providing stereospecific conditions and environments. Supramolecular concepts to create the chiral materials can provide an insight for emerging chiro-optical properties due to their well-defined scaffolds and the precise functionalization of the surfaces or skeletons. Among the various supramolecular chiral structures, 2D chiral sheet structures are particularly interesting materials because of their extremely high surface area coupled with many unique chemical and physical properties, thereby offering potential for the next generation of functional materials for optically active systems and optoelectronic devices. Nevertheless, relatively limited examples for 2D chiral materials exhibiting specific functionality have been reported because incorporation of molecular chirality into 2D architectures is difficult at the present stage. Here, a brief overview of the recent advances is provided on the construction of chiral supramolecular 2D materials and their functions. The design principles toward 2D chirality and their potential applications are also discussed.
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Affiliation(s)
- Bowen Shen
- State Key Lab of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, China
| | - Yongju Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
| | - Myongsoo Lee
- State Key Lab of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, China
- Department of Chemistry, Fudan University, Shanghai, 200438, China
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Jeong Y, Kim HW, Ku J, Seo J. Breakdown of chiral recognition of amino acids in reduced dimensions. Sci Rep 2020; 10:16166. [PMID: 32999433 PMCID: PMC7527561 DOI: 10.1038/s41598-020-73300-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/08/2020] [Indexed: 11/09/2022] Open
Abstract
The homochirality of amino acids in living organisms is one of the great mysteries in the phenomena of life. To understand the chiral recognition of amino acids, we have used scanning tunnelling microscopy to investigate the self-assembly of molecules of the amino acid tryptophan (Trp) on Au(111). Earlier experiments showed only homochiral configurations in the self-assembly of amino acids, despite using a mixture of the two opposite enantiomers. In our study, we demonstrate that heterochiral configurations can be favored energetically when L- and D-Trp molecules are mixed to form self-assembly on the Au surface. Using density functional theory calculations, we show that the indole side chain strongly interacts with the Au surface, which reduces the system effectively to two-dimension, with chiral recognition disabled. Our study provides important insight into the recognition of the chirality of amino acid molecules in life.
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Affiliation(s)
- Yongchan Jeong
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Korea.
| | - Hyo Won Kim
- Samsung Advanced Institute of Technology, Suwon, 16678, Korea
| | - JiYeon Ku
- Samsung Advanced Institute of Technology, Suwon, 16678, Korea
| | - Jungpil Seo
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Korea.
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Sršan L, Ziegler T. Nonconsensus motif directed chemical synthesis of glutamine-based glycopeptides. J Pept Sci 2020; 26:e3285. [PMID: 32902095 DOI: 10.1002/psc.3285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 11/12/2022]
Abstract
Besides the most common sequon of amino acids found in glycopeptides, namely, N-X-S/T, where X can be any amino acid except proline, a small number of nonconsensus motifs have been found in both eukaryotic and prokaryotic organisms, for example, Q-G-T. Because of the importance of glycopeptides in biotechnology and pharmacy, an adequate synthetic approach to these structures is highly important. In this manuscript, we report the efficient chemical batch synthesis of new glutamine-based glycopeptide structures, which can be used to represent cell surface elements in further biological investigations.
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Affiliation(s)
- Laura Sršan
- University of Tübingen, Institute of Organic Chemistry, Tübingen, 72076, Germany
| | - Thomas Ziegler
- University of Tübingen, Institute of Organic Chemistry, Tübingen, 72076, Germany
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26
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Wu X, Delbianco M, Anggara K, Michnowicz T, Pardo-Vargas A, Bharate P, Sen S, Pristl M, Rauschenbach S, Schlickum U, Abb S, Seeberger PH, Kern K. Imaging single glycans. Nature 2020; 582:375-378. [DOI: 10.1038/s41586-020-2362-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/27/2020] [Indexed: 11/09/2022]
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Pigliacelli C, Sánchez-Fernández R, García MD, Peinador C, Pazos E. Self-assembled peptide-inorganic nanoparticle superstructures: from component design to applications. Chem Commun (Camb) 2020; 56:8000-8014. [PMID: 32495761 DOI: 10.1039/d0cc02914a] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptides have become excellent platforms for the design of peptide-nanoparticle hybrid superstructures, owing to their self-assembly and binding/recognition capabilities. Morover, peptide sequences can be encoded and modified to finely tune the structure of the hybrid systems and pursue functionalities that hold promise in an array of high-end applications. This feature article summarizes the different methodologies that have been developed to obtain self-assembled peptide-inorganic nanoparticle hybrid architectures, and discusses how the proper encoding of the peptide sequences can be used for tailoring the architecture and/or functionality of the final systems. We also describe the applications of these hybrid superstructures in different fields, with a brief look at future possibilities towards the development of new functional hybrid materials.
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Affiliation(s)
- Claudia Pigliacelli
- Departamento de Química, Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain.
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Sršan L, Ziegler T. Synthesis of new asparagine-based glycopeptides for future scanning tunneling microscopy investigations. Beilstein J Org Chem 2020; 16:888-894. [PMID: 32461770 PMCID: PMC7214877 DOI: 10.3762/bjoc.16.80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/21/2020] [Indexed: 12/22/2022] Open
Abstract
For investigations on the biological functions of oligosaccharides and peptidomimetics, new asparagine-based mono- and disaccharides containing glycopeptides were prepared in solution. The applicability of two common peptide coupling reagents, using an orthogonal Fmoc/t-Bu strategy along with acetyl protecting groups for the carbohydrate moiety, was studied. Thus, the prepared libraries of glycopeptides were designed as model systems of cell surfaces for future investigations by combined preparative mass spectroscopy and scanning tunneling microscopy (STM) using soft-landing electrospray beam deposition (ES-IBD), on metal surfaces.
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Affiliation(s)
- Laura Sršan
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Thomas Ziegler
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
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29
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Advances in self-assembly and regulation of aromatic carboxylic acid derivatives at HOPG interface. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.04.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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30
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Carloni LE, Bezzu CG, Bonifazi D. Patterning Porous Networks through Self-Assembly of Programmed Biomacromolecules. Chemistry 2019; 25:16179-16200. [PMID: 31491049 DOI: 10.1002/chem.201902576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/11/2019] [Indexed: 11/08/2022]
Abstract
Two-dimensional (2D) porous networks are of great interest for the fabrication of complex organized functional materials for potential applications in nanotechnologies and nanoelectronics. This review aims at providing an overview of bottom-up approaches towards the engineering of 2D porous networks by using biomacromolecules, with a particular focus on nucleic acids and proteins. The first part illustrates how the advancements in DNA nanotechnology allowed for the attainment of complex ordered porous two-dimensional DNA nanostructures, thanks to a biomimetic approach based on DNA molecules self-assembly through specific hydrogen-bond base pairing. The second part focuses the attention on how polypeptides and proteins structural properties could be used to engineer organized networks templating the formation of multifunctional materials. The structural organization of all examples is discussed as revealed by scanning probe microscopy or transmission electron microscopy imaging techniques.
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Affiliation(s)
- Laure-Elie Carloni
- Department of Chemistry and Namur Research College (NARC), University of Namur, Rue de Bruxelles 61, Namur, 5000, Belgium
| | - C Grazia Bezzu
- Cardiff University, School of Chemistry, Park Place, Main Building, CF10 3AT, Cardiff, Wales, UK
| | - Davide Bonifazi
- Cardiff University, School of Chemistry, Park Place, Main Building, CF10 3AT, Cardiff, Wales, UK
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Dobscha JR, Castillo HD, Li Y, Fadler RE, Taylor RD, Brown AA, Trainor CQ, Tait SL, Flood AH. Sequence-Defined Macrocycles for Understanding and Controlling the Build-up of Hierarchical Order in Self-Assembled 2D Arrays. J Am Chem Soc 2019; 141:17588-17600. [PMID: 31503483 PMCID: PMC7461245 DOI: 10.1021/jacs.9b06410] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Anfinsen's dogma that sequence dictates structure is fundamental to understanding the activity and assembly of proteins. This idea has been applied to all manner of oligomers but not to the behavior of cyclic oligomers, aka macrocycles. We do this here by providing the first proofs that sequence controls the hierarchical assembly of nonbiological macrocycles, in this case, at graphite surfaces. To design macrocycles with one (AAA), two (AAB), or three (ABC) different carbazole units, we needed to subvert the synthetic preferences for one-pot macrocyclizations. We developed a new stepwise synthesis with sequence-defined targets made in 11, 17, and 22 steps with 25, 10, and 5% yields, respectively. The linear build up of primary sequence (1°) also enabled a thermal Huisgen cycloaddition to proceed regioselectively for the first time using geometric control. The resulting macrocycles are planar (2° structure) and form H-bonded dimers (3°) at surfaces. Primary sequences encoded into the suite of tricarb macrocycles were shown by scanning-tunneling microscopy (STM) to impact the next levels of supramolecular ordering (4°) and 2D crystalline polymorphs (5°) at solution-graphite interfaces. STM imaging of an AAB macrocycle revealed the formation of a new gap phase that was inaccessible using only C3-symmetric macrocycles. STM imaging of two additional sequence-controlled macrocycles (AAD, ABE) allowed us to identify the factors driving the formation of this new polymorph. This demonstration of how sequence controls the hierarchical patterning of macrocycles raises the importance of stepwise syntheses relative to one-pot macrocyclizations to offer new approaches for greater understanding and control of hierarchical assembly.
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Affiliation(s)
- James R. Dobscha
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Henry D. Castillo
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Yan Li
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Rachel E. Fadler
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Rose D. Taylor
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Andrew A. Brown
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Colleen Q. Trainor
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Steven L. Tait
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Amar H. Flood
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Guo X, Wetzel KS, Solleder SC, Spann S, Meier MAR, Wilhelm M, Luy B, Guthausen G. 1
H PFG‐NMR Diffusion Study on a Sequence‐Defined Macromolecule: Confirming Monodispersity. MACROMOL CHEM PHYS 2019. [DOI: 10.1002/macp.201900155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiaoai Guo
- Institute for Chemical Technology and Polymer Chemistry Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76128 Karlsruhe Germany
| | - Katharina S. Wetzel
- Institute of Organic Chemistry (IOC) Materialwissenschaftliches Zentrum (MZE) Karlsruhe Institute of Technology (KIT) Strasse am Forum 7 76131 Karlsruhe Germany
| | - Susanne C. Solleder
- Institute of Organic Chemistry (IOC) Materialwissenschaftliches Zentrum (MZE) Karlsruhe Institute of Technology (KIT) Strasse am Forum 7 76131 Karlsruhe Germany
| | - Sebastian Spann
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 Karlsruhe Institute of Technology (KIT) Fritz‐Haber‐Weg 6 76131 Karlsruhe Germany
| | - Michael A. R. Meier
- Institute of Organic Chemistry (IOC) Materialwissenschaftliches Zentrum (MZE) Karlsruhe Institute of Technology (KIT) Strasse am Forum 7 76131 Karlsruhe Germany
| | - Manfred Wilhelm
- Institute for Chemical Technology and Polymer Chemistry Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76128 Karlsruhe Germany
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 Karlsruhe Institute of Technology (KIT) Fritz‐Haber‐Weg 6 76131 Karlsruhe Germany
| | - Gisela Guthausen
- Institute for Mechanical Process Engineering and Mechanics and Engler‐Bunte‐Institut Chair of Water Chemistry and Water Technology Karlsruhe Institute of Technology (KIT) Adenauerring 20b 76131 Karlsruhe Germany
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Abb S, Tarrat N, Cortés J, Andriyevsky B, Harnau L, Schön JC, Rauschenbach S, Kern K. Carbohydrate Self-Assembly at Surfaces: STM Imaging of Sucrose Conformation and Ordering on Cu(100). Angew Chem Int Ed Engl 2019; 58:8336-8340. [PMID: 31018027 PMCID: PMC6771801 DOI: 10.1002/anie.201901340] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/15/2019] [Indexed: 01/07/2023]
Abstract
Saccharides are ubiquitous biomolecules, but little is known about their interaction with, and assembly at, surfaces. By combining preparative mass spectrometry with scanning tunneling microscopy, we have been able to address the conformation and self‐assembly of the disaccharide sucrose on a Cu(100) surface with subunit‐level imaging. By employing a multistage modeling approach in combination with the experimental data, we can rationalize the conformation on the surface as well as the interactions between the sucrose molecules, thereby yielding models of the observed self‐assembled patterns on the surface.
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Affiliation(s)
- Sabine Abb
- Max Planck Insitute for Solid State Research, Heisenbergstrasse 1, 70569, Stuttgart, Germany
| | - Nathalie Tarrat
- CEMES, Université de Toulouse, CNRS, 29 rue Jeanne Marvig, 31055, Toulouse, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Bohdan Andriyevsky
- Koszalin University of Technology, Śniadeckich Str. 2, 75-453, Koszalin, Poland
| | - Ludger Harnau
- Bernhäuserstrasse 75, 70771, Leinfelden-Echterdingen, Germany
| | - J Christian Schön
- Max Planck Insitute for Solid State Research, Heisenbergstrasse 1, 70569, Stuttgart, Germany
| | - Stephan Rauschenbach
- Max Planck Insitute for Solid State Research, Heisenbergstrasse 1, 70569, Stuttgart, Germany.,Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Klaus Kern
- Max Planck Insitute for Solid State Research, Heisenbergstrasse 1, 70569, Stuttgart, Germany.,Institut de Physique, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
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35
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Abb S, Tarrat N, Cortés J, Andriyevsky B, Harnau L, Schön JC, Rauschenbach S, Kern K. Carbohydrate Self‐Assembly at Surfaces: STM Imaging of Sucrose Conformation and Ordering on Cu(100). Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sabine Abb
- Max Planck Insitute for Solid State Research Heisenbergstrasse 1 70569 Stuttgart Germany
| | - Nathalie Tarrat
- CEMES, Université de ToulouseCNRS 29 rue Jeanne Marvig 31055 Toulouse France
| | - Juan Cortés
- LAAS-CNRSUniversité de Toulouse, CNRS Toulouse France
| | - Bohdan Andriyevsky
- Koszalin University of Technology Śniadeckich Str. 2 75-453 Koszalin Poland
| | - Ludger Harnau
- Bernhäuserstrasse 75 70771 Leinfelden-Echterdingen Germany
| | - J. Christian Schön
- Max Planck Insitute for Solid State Research Heisenbergstrasse 1 70569 Stuttgart Germany
| | - Stephan Rauschenbach
- Max Planck Insitute for Solid State Research Heisenbergstrasse 1 70569 Stuttgart Germany
- Department of ChemistryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Klaus Kern
- Max Planck Insitute for Solid State Research Heisenbergstrasse 1 70569 Stuttgart Germany
- Institut de PhysiqueEcole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
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36
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Gong C, Sun S, Zhang Y, Sun L, Su Z, Wu A, Wei G. Hierarchical nanomaterials via biomolecular self-assembly and bioinspiration for energy and environmental applications. NANOSCALE 2019; 11:4147-4182. [PMID: 30806426 DOI: 10.1039/c9nr00218a] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bioinspired synthesis offers potential green strategies to build highly complex nanomaterials by utilizing the unique nanostructures, functions, and properties of biomolecules, in which the biomolecular recognition and self-assembly processes play important roles in tailoring the structures and functions of bioinspired materials. Further understanding of biomolecular self-assembly for inspiring the formation and assembly of nanoparticles would promote the design and fabrication of functional nanomaterials for various applications. In this review, we focus on recent advances in bioinspired synthesis and applications of hierarchical nanomaterials based on biomolecular self-assembly. We first discuss biomolecular self-assembly towards biological nanomaterials, in which the mechanisms and ways of biomolecular self-assembly as well as various self-assembled biomolecular nanostructures are demonstrated. Secondly, the bioinspired synthesis strategies including molecule-molecule interaction, molecule-material recognition, molecule-mediated nucleation and growth, and molecule-mediated reduction/oxidation are introduced and discussed. Meanwhile, typical examples and discussions on how biomolecular self-assembly inspires the formation of hierarchical hybrid nanomaterials are presented. Finally, the applications of bioinspired nanomaterials in biofuel cells, light-harvesting systems, batteries, supercapacitors, catalysis, water/air purification, and environmental monitoring are presented and discussed. We believe that this review will be very helpful for readers to understand the self-assembly of biomolecules and the biomimetic/bioinspired strategies for synthesizing hierarchical nanomaterials on the one hand, and on the other hand to design novel materials for extended applications in nanotechnology, materials science, analytical science, and biomedical engineering.
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Affiliation(s)
- Coucong Gong
- Faculty of Production Engineering and Center for Environmental Research and Sustainable technology (UFT), University of Bremen, D-28359 Bremen, Germany.
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Zhang X, Gong C, Akakuru OU, Su Z, Wu A, Wei G. The design and biomedical applications of self-assembled two-dimensional organic biomaterials. Chem Soc Rev 2019; 48:5564-5595. [DOI: 10.1039/c8cs01003j] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Self-assembling 2D organic biomaterials exhibit versatile abilities for structural and functional tailoring, as well as high potential for biomedical applications.
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Affiliation(s)
- Xiaoyuan Zhang
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- China
- Faculty of Physics and Astronomy
- University of Jena
| | - Coucong Gong
- Faculty of Production Engineering
- University of Bremen
- Bremen
- Germany
| | - Ozioma Udochukwu Akakuru
- Cixi Institute of Biomedical Engineering
- CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province
- Ningbo Institute of Materials Technology and Engineering
- Chinese Academy of Sciences
- Ningbo
| | - Zhiqiang Su
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- China
| | - Aiguo Wu
- Cixi Institute of Biomedical Engineering
- CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province
- Ningbo Institute of Materials Technology and Engineering
- Chinese Academy of Sciences
- Ningbo
| | - Gang Wei
- Faculty of Production Engineering
- University of Bremen
- Bremen
- Germany
- Cixi Institute of Biomedical Engineering
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38
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Zou Y, Tu B, Yu L, Zheng Y, Lin Y, Luo W, Yang Y, Fang Q, Wang C. Peptide conformation and oligomerization characteristics of surface-mediated assemblies revealed by molecular dynamics simulations and scanning tunneling microscopy. RSC Adv 2019; 9:41345-41350. [PMID: 35540063 PMCID: PMC9076364 DOI: 10.1039/c9ra09320f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/29/2019] [Indexed: 11/21/2022] Open
Abstract
The characteristics of peptide conformations in both solution and surface-bound states, using poly-glycine as a model structure, are analyzed by using molecular dynamics (MD) simulations and scanning tunneling microscopy (STM).
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Affiliation(s)
- Yimin Zou
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety
- CAS Key Laboratory of Standardization and Measurement for Nanotechnoloty of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- CAS Center for Excellence in Brain Science
- National Center for Nanoscience and Technology
| | - Bin Tu
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety
- CAS Key Laboratory of Standardization and Measurement for Nanotechnoloty of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- CAS Center for Excellence in Brain Science
- National Center for Nanoscience and Technology
| | - Lanlan Yu
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety
- CAS Key Laboratory of Standardization and Measurement for Nanotechnoloty of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- CAS Center for Excellence in Brain Science
- National Center for Nanoscience and Technology
| | - Yongfang Zheng
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety
- CAS Key Laboratory of Standardization and Measurement for Nanotechnoloty of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- CAS Center for Excellence in Brain Science
- National Center for Nanoscience and Technology
| | - Yuchen Lin
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety
- CAS Key Laboratory of Standardization and Measurement for Nanotechnoloty of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- CAS Center for Excellence in Brain Science
- National Center for Nanoscience and Technology
| | - Wendi Luo
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety
- CAS Key Laboratory of Standardization and Measurement for Nanotechnoloty of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- CAS Center for Excellence in Brain Science
- National Center for Nanoscience and Technology
| | - Yanlian Yang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety
- CAS Key Laboratory of Standardization and Measurement for Nanotechnoloty of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- CAS Center for Excellence in Brain Science
- National Center for Nanoscience and Technology
| | - Qiaojun Fang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety
- CAS Key Laboratory of Standardization and Measurement for Nanotechnoloty of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- CAS Center for Excellence in Brain Science
- National Center for Nanoscience and Technology
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety
- CAS Key Laboratory of Standardization and Measurement for Nanotechnoloty of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- CAS Center for Excellence in Brain Science
- National Center for Nanoscience and Technology
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39
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Qin Y, Yang Y, Wang Y, Wang X, Yao M. Theoretical study of the substrate and molecular density effects on molecular self-assembly. NEW J CHEM 2019. [DOI: 10.1039/c9nj04506f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work is aiming at theoretically exploring the substrate and molecular density effects on molecular self-assembly.
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Affiliation(s)
- Yuan Qin
- School of Materials Science and Engineering
- Dalian University of Technology
- Dalian 116024
- China
| | - Yingying Yang
- School of Materials Science and Engineering
- Dalian University of Technology
- Dalian 116024
- China
| | - Yuelin Wang
- School of Materials Science and Engineering
- Dalian University of Technology
- Dalian 116024
- China
| | - Xudong Wang
- School of Materials Science and Engineering
- Dalian University of Technology
- Dalian 116024
- China
| | - Man Yao
- School of Materials Science and Engineering
- Dalian University of Technology
- Dalian 116024
- China
- Key Laboratory of Energy Materials and Devices
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Abb S, Tarrat N, Cortés J, Andriyevsky B, Harnau L, Schön JC, Rauschenbach S, Kern K. Polymorphism in carbohydrate self-assembly at surfaces: STM imaging and theoretical modelling of trehalose on Cu(100). RSC Adv 2019; 9:35813-35819. [PMID: 35528101 PMCID: PMC9074738 DOI: 10.1039/c9ra06764g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/24/2019] [Indexed: 01/08/2023] Open
Abstract
Saccharides, also commonly known as carbohydrates, are ubiquitous biomolecules, but little is known about their interaction with surfaces. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy now provides access to the molecular details of the surface assembly of this important class of bio-molecules. Among carbohydrates, the disaccharide trehalose is outstanding as it enables strong anhydrobiotic effects in biosystems. This ability is closely related to the observed polymorphism. In this work, we explore the self-assembly of trehalose on the Cu(100) surface. Molecular imaging reveals the details of the assembly properties in this reduced symmetry environment. Already at room temperature, we observe a variety of self-assembled motifs, in contrast to other disaccharides like e.g. sucrose. Using a multistage modeling approach, we rationalize the conformation of trehalose on the copper surface as well as the intermolecular interactions and the self-assembly behavior. We rationalize the experimentally observed variety of trehalose assemblies on Cu(100) by modeling based on STM images and global optimization.![]()
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Affiliation(s)
- Sabine Abb
- Max Planck Institute for Solid State Research
- 70569 Stuttgart
- Germany
| | | | - Juan Cortés
- LAAS-CNRS, Université de Toulouse
- CNRS
- Toulouse
- France
| | | | | | | | - Stephan Rauschenbach
- Max Planck Institute for Solid State Research
- 70569 Stuttgart
- Germany
- Department of Chemistry
- University of Oxford
| | - Klaus Kern
- Max Planck Institute for Solid State Research
- 70569 Stuttgart
- Germany
- Institut de Physique
- Ecole Polytechnique Fédérale de Lausanne
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41
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Goronzy DP, Ebrahimi M, Rosei F, Fang Y, De Feyter S, Tait SL, Wang C, Beton PH, Wee ATS, Weiss PS, Perepichka DF. Supramolecular Assemblies on Surfaces: Nanopatterning, Functionality, and Reactivity. ACS NANO 2018; 12:7445-7481. [PMID: 30010321 DOI: 10.1021/acsnano.8b03513] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Understanding how molecules interact to form large-scale hierarchical structures on surfaces holds promise for building designer nanoscale constructs with defined chemical and physical properties. Here, we describe early advances in this field and highlight upcoming opportunities and challenges. Both direct intermolecular interactions and those that are mediated by coordinated metal centers or substrates are discussed. These interactions can be additive, but they can also interfere with each other, leading to new assemblies in which electrical potentials vary at distances much larger than those of typical chemical interactions. Earlier spectroscopic and surface measurements have provided partial information on such interfacial effects. In the interim, scanning probe microscopies have assumed defining roles in the field of molecular organization on surfaces, delivering deeper understanding of interactions, structures, and local potentials. Self-assembly is a key strategy to form extended structures on surfaces, advancing nanolithography into the chemical dimension and providing simultaneous control at multiple scales. In parallel, the emergence of graphene and the resulting impetus to explore 2D materials have broadened the field, as surface-confined reactions of molecular building blocks provide access to such materials as 2D polymers and graphene nanoribbons. In this Review, we describe recent advances and point out promising directions that will lead to even greater and more robust capabilities to exploit designer surfaces.
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Affiliation(s)
- Dominic P Goronzy
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Maryam Ebrahimi
- INRS Centre for Energy, Materials and Telecommunications , 1650 Boul. Lionel Boulet , Varennes , Quebec J3X 1S2 , Canada
| | - Federico Rosei
- INRS Centre for Energy, Materials and Telecommunications , 1650 Boul. Lionel Boulet , Varennes , Quebec J3X 1S2 , Canada
- Institute for Fundamental and Frontier Science , University of Electronic Science and Technology of China , Chengdu 610054 , P.R. China
| | - Yuan Fang
- Department of Chemistry , McGill University , Montreal H3A 0B8 , Canada
| | - Steven De Feyter
- Department of Chemistry , KU Leuven , Celestijnenlaan 200F , Leuven 3001 , Belgium
| | - Steven L Tait
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Chen Wang
- National Center for Nanoscience and Technology , Beijing 100190 , China
| | - Peter H Beton
- School of Physics & Astronomy , University of Nottingham , Nottingham NG7 2RD , United Kingdom
| | - Andrew T S Wee
- Department of Physics , National University of Singapore , 117542 Singapore
| | - Paul S Weiss
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Materials Science and Engineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Dmitrii F Perepichka
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Chemistry , McGill University , Montreal H3A 0B8 , Canada
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42
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Yu M, Benjalal Y, Chen C, Kalashnyk N, Xu W, Barattin R, Nagarajan S, Lægsgaard E, Stensgaard I, Hliwa M, Gourdon A, Besenbacher F, Bouju X, Linderoth TR. Three-dimensional hydrogen bonding between Landers and planar molecules facilitated by electrostatic interactions with Ni adatoms. Chem Commun (Camb) 2018; 54:8845-8848. [PMID: 30039145 DOI: 10.1039/c8cc04247k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a combination of UHV-STM and molecular mechanics calculations, we investigate the surface self-assembly of a complex multi-component metal-molecule system with synergistic non-covalent interactions. Hydrogen bonding between three-dimensional Lander-DAT molecules and planar PTCDI molecules, adsorbed closer to the surface, is found to be facilitated by electrostatic interactions between co-adsorbed Ni adatoms and the flexible molecular DAT groups.
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Affiliation(s)
- Miao Yu
- Interdisciplinary Nanoscience Center (iNANO) and Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark.
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43
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Vats N, Rauschenbach S, Sigle W, Sen S, Abb S, Portz A, Dürr M, Burghard M, van Aken PA, Kern K. Electron microscopy of polyoxometalate ions on graphene by electrospray ion beam deposition. NANOSCALE 2018; 10:4952-4961. [PMID: 29485651 DOI: 10.1039/c8nr00402a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Aberration-corrected high-resolution transmission electron microscopy (AC-HRTEM) has enabled atomically resolved imaging of molecules adsorbed on low-dimensional materials like carbon nanotubes, graphene oxide and few-layer-graphene. However, conventional methods for depositing molecules onto such supports lack selectivity and specificity. Here, we describe the chemically selective preparation and deposition of molecules-like polyoxometalate (POM) anions [PW12O40]3- using electrospray ion-beam deposition (ES-IBD) along with high-resolution TEM imaging. This approach provides access to sub-monolayer coatings of intact molecules on freestanding graphene, which enables their atomically resolved ex situ characterization by low-voltage AC-HRTEM. The capability to tune the deposition parameters in either soft or reactive landing mode, combined with the well-defined high-vacuum deposition conditions, renders the ES-IBD based method advantageous over alternative methods such as drop-casting. Furthermore, it might be expanded towards depositing and imaging large and nonvolatile molecules with complex structures.
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Affiliation(s)
- N Vats
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany.
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44
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Selivanova OM, Surin AK, Ryzhykau YL, Glyakina AV, Suvorina MY, Kuklin AI, Rogachevsky VV, Galzitskaya OV. To Be Fibrils or To Be Nanofilms? Oligomers Are Building Blocks for Fibril and Nanofilm Formation of Fragments of Aβ Peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2332-2343. [PMID: 29338255 DOI: 10.1021/acs.langmuir.7b03393] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To identify the key stages in the amyloid fibril formation we studied the aggregation of amyloidogenic fragments of Aβ peptide, Aβ(16-25), Aβ(31-40), and Aβ(33-42), using the methods of electron microscopy, X-ray analysis, mass spectrometry, and structural modeling. We have found that fragments Aβ(31-40) and Aβ(33-42) form amyloid fibrils in the shape of bundles and ribbons, while fragment Aβ(16-25) forms only nanofilms. We are the first who performed 2D reconstruction of amyloid fibrils by the Markham rotation technique on electron micrographs of negatively stained fragments of Aβ peptide. Combined analysis of the data allows us to speculate that both the fibrils and the films are formed via association of ring-shaped oligomers with the external diameter of about 6 to 7 nm, the internal diameter of 2 to 3 nm, and the height of ∼3 nm. We conclude that such oligomers are the main building blocks in fibrils of any morphology. The interaction of ring oligomers with each other in different ways makes it possible to explain their polymorphism. The new mechanism of polymerization of amyloidogenic proteins and peptides, described here, could stimulate new approaches in the development of future therapeutics for the treatment of amyloid-related diseases.
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Affiliation(s)
- Olga M Selivanova
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
- State Research Center for Applied Microbiology & Biotechnology , Obolensk 142279, Russia
| | - Yury L Ryzhykau
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russian Federation
| | - Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences , Pushchino 142290, Russia
| | - Mariya Yu Suvorina
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Alexander I Kuklin
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russian Federation
- Joint Institute for Nuclear Research , Dubna 141980, Russian Federation
| | - Vadim V Rogachevsky
- Institute of Cell Biophysics, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
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45
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Portz A, Baur M, Rinke G, Abb S, Rauschenbach S, Kern K, Dürr M. Chemical Analysis of Complex Surface-Adsorbed Molecules and Their Reactions by Means of Cluster-Induced Desorption/Ionization Mass Spectrometry. Anal Chem 2018; 90:3328-3334. [PMID: 29376333 DOI: 10.1021/acs.analchem.7b04876] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Desorption/ionization induced by neutral SO2 clusters (DINeC) is used for mass spectrometry (MS) of surface-adsorbed molecules. The method is shown to be a surface-sensitive analysis tool capable of detecting molecular adsorbates in a wide range of molecular weights as well as their reactions on surfaces, which are otherwise difficult to access. Two different surface/adsorbate systems prepared by means of electrospray ion beam deposition (ES-IBD) were investigated: For the peptide angiotensin II on gold, intact molecules were desorbed from the surface when deposited by soft landing ES-IBD. By comparison to the well-controlled amount of substance deposited by ES-IBD, the sensitivity of DINeC-MS was shown to be on the order of 0.1% of a monolayer coverage, corresponding to femtomoles of analyte. Depending on deposition and sample conditions, the original state of charge of the molecules could be retrieved. Reaction of the adsorbed molecules both with surface atoms as well as with coadsorbed D2O was monitored. Rhodamine 6G was also desorbed as an intact molecule when deposited with kinetic energies below 50 eV. For higher deposition energy, fragmentation of the dye molecules was observed by means of DINeC-MS.
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Affiliation(s)
- André Portz
- Institut für Angewandte Physik , Justus-Liebig-Universität Giessen , Heinrich-Buff-Ring 16 , D-35392 Giessen , Germany
| | - Markus Baur
- Institut für Angewandte Physik , Justus-Liebig-Universität Giessen , Heinrich-Buff-Ring 16 , D-35392 Giessen , Germany
| | - Gordon Rinke
- Max Planck Institute for Solid State Research , Heisenbergstr. 1 , D-70569 Stuttgart , Germany
| | - Sabine Abb
- Max Planck Institute for Solid State Research , Heisenbergstr. 1 , D-70569 Stuttgart , Germany
| | - Stephan Rauschenbach
- Max Planck Institute for Solid State Research , Heisenbergstr. 1 , D-70569 Stuttgart , Germany
| | - Klaus Kern
- Max Planck Institute for Solid State Research , Heisenbergstr. 1 , D-70569 Stuttgart , Germany.,Institut de Physique , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Michael Dürr
- Institut für Angewandte Physik , Justus-Liebig-Universität Giessen , Heinrich-Buff-Ring 16 , D-35392 Giessen , Germany
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46
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Cao M, Lu S, Zhao W, Deng L, Wang M, Wang J, Zhou P, Wang D, Xu H, Lu JR. Peptide Self-Assembled Nanostructures with Distinct Morphologies and Properties Fabricated by Molecular Design. ACS APPLIED MATERIALS & INTERFACES 2017; 9:39174-39184. [PMID: 29067798 DOI: 10.1021/acsami.7b11681] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Six surfactant-like peptides with the same amino acid composition but different primary sequences are designed, including G3A3V3I3K3, K3I3V3A3G3, I3V3A3G3K3, K3G3A3V3I3, V3G3I3A3K3, and K3A3I3G3V3. These peptides form antiparallel β-sheets during self-assembly. Because the constituent residues have different side chain size and hydrophobicity, sequence changes adjust group distribution and hydrophobicity on the two sides of a given β-sheet. This consequently tunes the binding energy of the side-to-side pairing conformations and leads to different self-assembled structures. G3A3V3I3K3 and K3I3V3A3G3 form short nanorods with diameters of 8.5 ± 1.0 nm and lengths <150 nm. I3V3A3G3K3 and K3G3A3V3I3 form nanosheets with heights of 4.0 ± 0.5 nm and limited lengths and widths. V3G3I3A3K3 and K3A3I3G3V3 form long fibrils with diameters of 7.0 ± 1.0 nm and lengths of micrometer scale. These nanostructures exhibit different capacity in encapsulating insoluble hydrophobic drug molecules and delivering them into the cells. The nanosheets of I3V3A3G3K3 and K3G3A3V3I3 can encapsulate both nile red and doxorubicin molecules to an extent of up to 17-23% in mole ratio. Moreover, the shape and size of the nanostructures affect the drug delivery into cells greatly, with the nanosheets and short rods exhibiting higher efficiency than the long fibrils. The study provides new insights into programmed peptide self-assembly toward specific functionalities.
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Affiliation(s)
- Meiwen Cao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Sha Lu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Wenjing Zhao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Li Deng
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Meng Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Peng Zhou
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Jian R Lu
- Biological Physics Laboratory, School of Physics and Astronomy, University of Manchester , Schuster Building, Oxford Road, Manchester M13 9PL, U.K
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47
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Seoudi RS, Mechler A. Design Principles of Peptide Based Self-Assembled Nanomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1030:51-94. [DOI: 10.1007/978-3-319-66095-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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48
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Schlipf L, Oeckinghaus T, Xu K, Dasari DBR, Zappe A, de Oliveira FF, Kern B, Azarkh M, Drescher M, Ternes M, Kern K, Wrachtrup J, Finkler A. A molecular quantum spin network controlled by a single qubit. SCIENCE ADVANCES 2017; 3:e1701116. [PMID: 28819646 PMCID: PMC5553819 DOI: 10.1126/sciadv.1701116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/12/2017] [Indexed: 05/24/2023]
Abstract
Scalable quantum technologies require an unprecedented combination of precision and complexity for designing stable structures of well-controllable quantum systems on the nanoscale. It is a challenging task to find a suitable elementary building block, of which a quantum network can be comprised in a scalable way. We present the working principle of such a basic unit, engineered using molecular chemistry, whose collective control and readout are executed using a nitrogen vacancy (NV) center in diamond. The basic unit we investigate is a synthetic polyproline with electron spins localized on attached molecular side groups separated by a few nanometers. We demonstrate the collective readout and coherent manipulation of very few (≤ 6) of these S = 1/2 electronic spin systems and access their direct dipolar coupling tensor. Our results show that it is feasible to use spin-labeled peptides as a resource for a molecular qubit-based network, while at the same time providing simple optical readout of single quantum states through NV magnetometry. This work lays the foundation for building arbitrary quantum networks using well-established chemistry methods, which has many applications ranging from mapping distances in single molecules to quantum information processing.
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Affiliation(s)
- Lukas Schlipf
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- 3. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Thomas Oeckinghaus
- 3. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Kebiao Xu
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- 3. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Chinese Academy of Sciences Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Durga Bhaktavatsala Rao Dasari
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- 3. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andrea Zappe
- 3. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | | | - Bastian Kern
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Mykhailo Azarkh
- Department of Chemistry, Zukunftskolleg, and Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry, Zukunftskolleg, and Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Markus Ternes
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Klaus Kern
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- Institut de Physique, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jörg Wrachtrup
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- 3. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Amit Finkler
- 3. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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49
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Kim J, Choi CH, Yeom SJ, Eom N, Kang KK, Lee CS. Directed Assembly of Janus Cylinders by Controlling the Solvent Polarity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:7503-7511. [PMID: 28672112 DOI: 10.1021/acs.langmuir.7b01252] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This study demonstrates the possibility of controlling the directed self-assembly of microsized Janus cylinders by changing the solvent polarity of the assembly media. Experimental results are analyzed and theoretical calculations of the free energy of adhesion (ΔGad) are performed to elucidate the underlying basic principles and investigate the effects of the solvent on the self-assembled structures. This approach will pave a predictive route for controlling the structures of assembly depending on the solvent polarity. In particular, we find that a binary solvent system with precisely controlled polarity induces directional assembly of the microsized Janus cylinders. Thus, the formation of two-dimensional (2D) and three-dimensional (3D) assembled clusters can be reliably tuned by controlling the numbers of constituent Janus cylinders in a binary solvent system. Finally, this approach is expanded to stepwise assembly, which forms unique microstructures via secondary growth of primary seed clusters formed by the Janus cylinders. We envision that this investigation is highly promising for the construction of desired superstructures using a wide variety of polymeric Janus microparticles with chemical and physical multicompartments.
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Affiliation(s)
- Jongmin Kim
- Department of Chemical Engineering, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Chang-Hyung Choi
- Department of Chemical Engineering, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Su-Jin Yeom
- Department of Chemical Engineering, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Naye Eom
- Department of Chemical Engineering, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Kyoung-Ku Kang
- Department of Chemical Engineering, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Chang-Soo Lee
- Department of Chemical Engineering, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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50
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Rauschenbach S, Rinke G, Gutzler R, Abb S, Albarghash A, Le D, Rahman TS, Dürr M, Harnau L, Kern K. Two-Dimensional Folding of Polypeptides into Molecular Nanostructures at Surfaces. ACS NANO 2017; 11:2420-2427. [PMID: 28122181 DOI: 10.1021/acsnano.6b06145] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Herein we report the fabrication of molecular nanostructures on surfaces via two-dimensional (2D) folding of the nine amino acid peptide bradykinin. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy is used to fabricate and investigate the molecular nanostructures. Subnanometer resolved images evidence the large conformational freedom of the molecules if thermal motion is inhibited and the formation of stable uniform dimers of only one specific conformation when diffusion can take place. Molecular dynamics modeling supported by density functional theory calculations give atomically precise insight into the induced-fit binding scheme when the folded dimer is formed. In the absence of solvent, we find a hierarchy of binding strength from polar to nonpolar, manifested in an inverted polar-nonpolar segregation which suppresses unspecific interactions at the rim of the nanostructure. The demonstrated 2D-folding scheme resembles many key properties of its native 3D counterpart and shows that functional, molecular nanostructures on surfaces fabricated by folding could be just as versatile and specific.
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Affiliation(s)
- Stephan Rauschenbach
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Gordon Rinke
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Rico Gutzler
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Sabine Abb
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Alyazan Albarghash
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Duy Le
- University of Central Florida , Orlando, Florida 32816, United States
| | - Talat S Rahman
- University of Central Florida , Orlando, Florida 32816, United States
| | - Michael Dürr
- Justus Liebig University Giessen, Institute of Applied Physics , Heinrich-Buff-Ring 16, Giessen DE-35392, Germany
| | - Ludger Harnau
- University of Stuttgart , Bernhäuserstr. 75, Leinfelden-Echterdingen DE-70771, Germany
| | - Klaus Kern
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
- Ecole Polytechnique Fédérale de Lausanne, Institut de Physique , Lausanne CH-1015, Switzerland
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