1
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Zhang X, Ding H, Yang S, Yang H, Yang X, Li B, Xing X, Sun Y, Gu G, Chen X, Gao J, Pan M, Chi L, Guo Q. Kinetic Controlled Chirality Transfer and Induction in 2D Hydrogen-Bonding Assemblies of Glycylglycine on Au(111). SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207111. [PMID: 36599616 DOI: 10.1002/smll.202207111] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Chirality transfer is of vital importance that dominates the structure and functionality of biological systems and living matters. External physical stimulations, e.g. polarized light and mechanical forces, can trigger the chirality symmetry breaking, leading to the appearance of the enantiomeric entities created from a chiral self-assembly of achiral molecule. Here, several 2D assemblies with different chirality, synthesized on Au(111) surface by using achiral building blocks - glycylglycine (digly), the simplest polypeptide are reported. By delicately tuning the kinetic factors, i.e., one-step slow/rapid deposition, or stepwise slow deposition with mild annealing, achiral square hydrogen-bond organic frameworks (HOF), homochiral rhombic HOF and racemic rectangular assembly are achieved, respectively. Chirality induction and related symmetry broken in assemblies are introduced by the handedness (H-bond configurations in principle) of the assembled motifs and then amplified to the entire assemblies via the interaction between motifs. The results show that the chirality transfer and induction of biological assemblies can be tuned by altering the kinetic factors instead of applying external forces, which may offer an in-depth understanding and practical approach to peptide chiral assembly on the surfaces and can further facilitate the design of desired complex biomolecular superstructures.
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Affiliation(s)
- Xin Zhang
- School of Physics, Northwest University, Xi'an, 710069, China
| | - Haoxuan Ding
- Physics and Astronomy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Shu Yang
- School of Information Science and Engineering, Fudan University, Shanghai, 200433, China
- Zhuhai Fudan Innovation Institute, Zhuhai, 519000, China
| | - Hualin Yang
- Physics and Astronomy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Xiaoqing Yang
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an, 710119, China
| | - Bosheng Li
- Physics and Astronomy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Xueting Xing
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an, 710119, China
| | - Yaojie Sun
- School of Information Science and Engineering, Fudan University, Shanghai, 200433, China
| | - Guangxin Gu
- Zhuhai Fudan Innovation Institute, Zhuhai, 519000, China
| | - Xiaorui Chen
- School of Mechanical and Material Engineering, Xi'an University, Xi'an, 710065, China
| | - Jianzhi Gao
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an, 710119, China
| | - Minghu Pan
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an, 710119, China
| | - Lifeng Chi
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, 215123, China
| | - Quanmin Guo
- Physics and Astronomy, University of Birmingham, Birmingham, B15 2TT, UK
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2
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Shen H, Ding Y, Li D, Xu W. Self-Assembly of Glutamic Acid and Serine on Au(111). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:3168-3172. [PMID: 36796033 DOI: 10.1021/acs.langmuir.3c00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Amino acids provide novel and superior performance for two-dimensional materials and bio-based devices. The interaction and adsorption of amino acid molecules on substrates have thus attracted extensive research for exploring the driving forces involved in the formation of nanostructures. Nevertheless, the interactions within amino acid molecules on inert surfaces have not been fully understood. Herein, from the interplay of high-resolution scanning tunneling microscopy imaging and density functional theory calculations, we show the self-assembled structures of Glu and Ser molecules on Au(111), which are dominated by intermolecular hydrogen bonds, and further investigate their most stable structural models at the atomic scale. This study would be of fundamental importance in understanding the formation processes of biologically relevant nanostructures and provide possibilities for chemical modification.
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Affiliation(s)
- Hanlin Shen
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China
| | - Yuanqi Ding
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China
| | - Donglin Li
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China
| | - Wei Xu
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China
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3
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Zhang L, Farkhondeh H, Rahsepar FR, Chatterjee A, Leung KT. Covalent and Hydrogen Bonding in Adsorption of Alanine Molecules on Si(111)7×7. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5540-5547. [PMID: 33881889 DOI: 10.1021/acs.langmuir.1c00283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Molecular adsorption bonding configurations and specific interfacial chemistry of alanine on Si(111)7×7 have been determined by combining the results from scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) with ab initio calculations based on the density functional theory (DFT). XPS spectra of the N 1s region show that alanine molecules bind to the 7×7 surface by N-Si covalent bonding, while STM imaging reveals that such N-H dissociative adsorption of alanine occurs on an adjacent Si adatom-restatom pair, with the dehydrogenated alanine moiety and dissociated H atom occupying the Si adatom and restatom sites, respectively. At a sample bias above +2 V, the dehydrogenated alanine appears as a bright round protrusion, slightly off-center from a Si adatom site and leaning toward the opposite Si adatom across the dimer wall. The off-center character can be attributed to an electrostatic attraction between the electron-rich carbonyl O of the dehydrogenated alanine and electron-deficient nearest Si adatom across the dimer wall. Our DFT calculation also shows that the monodentate O-Si bonding configuration resulting from O-H dissociative adsorption is more thermodynamically favorable than the experimentally observed N-Si bonding configuration, suggesting that the interfacial dissociative adsorption reaction is a kinetically controlled rather than a thermodynamically driven process. Alanine molecules in the second adlayer (transitional layer) are found to attach to those in the first adlayer (interfacial layer) by N···HO hydrogen bonding, as supported by the presence of the N 1s feature at 401.0 eV. An alanine molecule H-bonded to a dehydrogenated alanine in the first adlayer has also been observed in STM as a brighter and larger protrusion close to the expected location of the free OH group in the dehydrogenated first-adlayer alanine. No thick zwitterionic alanine film can be obtained at room temperature possibly due to steric constraint caused by the methyl group.
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Affiliation(s)
- L Zhang
- WATLab, and Department of Chemistry University of Waterloo Waterloo, Ontario Canada N2L 3G1
| | - H Farkhondeh
- WATLab, and Department of Chemistry University of Waterloo Waterloo, Ontario Canada N2L 3G1
| | - F R Rahsepar
- WATLab, and Department of Chemistry University of Waterloo Waterloo, Ontario Canada N2L 3G1
| | - A Chatterjee
- WATLab, and Department of Chemistry University of Waterloo Waterloo, Ontario Canada N2L 3G1
| | - K T Leung
- WATLab, and Department of Chemistry University of Waterloo Waterloo, Ontario Canada N2L 3G1
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4
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Futera Z. Amino-acid interactions with the Au(111) surface: adsorption, band alignment, and interfacial electronic coupling. Phys Chem Chem Phys 2021; 23:10257-10266. [PMID: 33899874 DOI: 10.1039/d1cp00218j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The charge transport properties of biological molecules like peptides and proteins are intensively studied for the great flexibility, redox-state variability, long-range efficiency, and biocompatibility of potential bioelectronic applications. Yet, the electronic interactions of biomolecules with solid metal surfaces, determining the conductivities of the biomolecular junctions, are hard to predict and usually unavailable. Here, we present accurate adsorption structures and energies, electronic band alignment, and interfacial electronic coupling data for all 20 natural amino acids computed using the DFT+Σ scheme based on the vdW-DF and OT-RSH functionals. For comparison, data obtained using the popular PBE functional are provided as well. Tryptophan, compared to other amino acids, is shown to be distinctly exceptional in terms of the electronic properties related to charge transport. Its high adsorption energy, frontier-orbital levels aligned relatively close to the Fermi energy of gold and strong interfacial electronic coupling make it an ideal candidate for facilitating charge transfer on such heterogeneous interfaces. Although the amino acids in peptides and proteins are affected by the structural interactions hindering their contact with the surface, knowledge of the single-molecule surface interactions is necessary for a detailed understanding of such structural effects and tuning of potential applications.
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Affiliation(s)
- Zdenek Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
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5
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Simões B, Guedens WJ, Keene C, Kubiak-Ossowska K, Mulheran P, Kotowska AM, Scurr DJ, Alexander MR, Broisat A, Johnson S, Muyldermans S, Devoogdt N, Adriaensens P, Mendes PM. Direct Immobilization of Engineered Nanobodies on Gold Sensors. ACS APPLIED MATERIALS & INTERFACES 2021; 13:17353-17360. [PMID: 33845569 PMCID: PMC8153533 DOI: 10.1021/acsami.1c02280] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/25/2021] [Indexed: 05/25/2023]
Abstract
Single-domain antibodies, known as nanobodies, have great potential as biorecognition elements for sensors because of their small size, affinity, specificity, and robustness. However, facile and efficient methods of nanobody immobilization are sought that retain their maximum functionality. Herein, we describe the direct immobilization of nanobodies on gold sensors by exploiting a modified cysteine strategically positioned at the C-terminal end of the nanobody. The experimental data based on secondary ion mass spectrometry, circular dichroism, and surface plasmon resonance, taken together with a detailed computational work (molecular dynamics simulations), support the formation of stable and well-oriented nanobody monolayers. Furthermore, the nanobody structure and activity is preserved, wherein the nanobody is immobilized at a high density (approximately 1 nanobody per 13 nm2). The strategy for the spontaneous nanobody self-assembly is simple and effective and possesses exceptional potential to be used in numerous sensing platforms, ranging from clinical diagnosis to environmental monitoring.
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Affiliation(s)
- Bárbara Simões
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Wanda J. Guedens
- Institute
for Materials Research (IMO), Hasselt University, BE-3590 Diepenbeek, Belgium
| | - Charlie Keene
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | | | - Paul Mulheran
- Department
of Chemical & Process Engineering, University
of Strathclyde, Glasgow G1 1XQ, United Kingdom
| | - Anna M. Kotowska
- School
of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - David J. Scurr
- School
of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Morgan R Alexander
- School
of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Alexis Broisat
- Laboratory
of Bioclinical Radiopharmaceutics, Université
Grenoble Alpes, Inserm, CHU Grenoble Alpes, LRB, 38000 Grenoble, France
| | - Steven Johnson
- Department
of Electronic Engineering, University of
York, York YO19 5DD, United Kingdom
| | - Serge Muyldermans
- Cellular
and Molecular Immunology laboratory, Vrije
Universiteit Brussel (VUB), BE-1050 Brussels, Belgium
| | - Nick Devoogdt
- In
vivo Cellular and Molecular Imaging laboratory, Vrije Universiteit Brussel (VUB), BE-1090 Brussels, Belgium
| | - Peter Adriaensens
- Institute
for Materials Research (IMO), Hasselt University, BE-3590 Diepenbeek, Belgium
| | - Paula M. Mendes
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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6
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Awuah JB, Walsh TR. Side-chain effects on the co-existence of emergent nanopatterns in amino acid adlayers on graphene. NANOSCALE 2020; 12:13662-13673. [PMID: 32568329 DOI: 10.1039/d0nr01333a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The spontaneous tendency of amino acid adlayers to self-assemble into ordered patterns on non-reactive surfaces is thought to be chiefly influenced by amino acid termination state. Experiments have shown that different side chains can produce different patterns, with a distinction drawn between side chains that can support hydrogen bonds or electrostatic interactions, and those that are hydrophobic. However, as is demonstrated in this work, this distinction is not clear cut, implying that there is currently no way to predict in advance what type of pattern will be formed. Here, we use molecular dynamics simulations of amino acid adlayers in neutral, zwitterion, and neutral-zwitterion states for two types of amino acids, either histidine or alanine, adsorbed at the in-vacuo graphene interface. In contrast to earlier studies on adlayers of tryptophan and methionine on graphene that reveal the presence of only a single type of pattern motif, the canonical dimer row, here we find that emergent patterns of histidine and alanine adlayers supported the co-existence of several different types of motifs, influenced by the different side-chain characteristics. For alanine, the compact side-chain does not support hydrogen bonding and engages weakly with the surface, leading to the emergence of a new dimer row configuration in addition to the canonical dimer row motif. On the contrary, for histidine, the side-chain supports hydrogen bonding, leading to the emergence of a dimer row motif different from the canonical dimer row, co-existing with several different monomer row motifs. On this basis, we propose that emergent canonical dimer row patterns are more likely for amino acids with side-chains that are non-compact and that also lack extensive hydrogen bonding capacity, and that engage strongly with the underlying substrate. These findings provide a fundamental basis to rationally guide the design of desired self-assembled nanostructures on planar surfaces.
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Affiliation(s)
- Joel B Awuah
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia.
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7
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Awuah JB, Walsh TR. Predictions of Pattern Formation in Amino Acid Adlayers at the In Vacuo Graphene Interface: Influence of Termination State. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1903403. [PMID: 31663292 DOI: 10.1002/smll.201903403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Controlled self-assembly of biomolecules on graphene offers a pathway for realizing its full potential in biological applications. Microscopy has revealed the self-assembly of amino acid adlayers into dimer rows on nonreactive substrates. However, neither the spontaneous formation of these patterns, nor the influence of amino acid termination state on the formation of patterns has been directly resolved to date. Molecular dynamics simulations, with the ability to reveal atomic level details and exert full control over the termination state, are used here to model initially disordered adlayers of neutral, zwitterionic, and neutral-zwitterionic mixtures for two types of amino acids, tryptophan and methionine, adsorbed on graphene in vacuo. The simulations of the zwitterion-containing adlayers exhibit the spontaneous emergence of dimer row ordering, mediated by charge-driven intermolecular interactions. In contrast, adlayers containing only neutral species do not assemble into ordered patterns. It is also found that the presence of trace amounts of water reduces the interamino acid interactions in the adlayers, but does not induce or disrupt pattern formation. Overall, the findings reveal the balance between the lateral interamino acid interactions and amino acid-graphene interactions, providing foundational insights for ultimately realizing the predictable pattern formation of biomolecules adsorbed on unreactive surfaces.
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Affiliation(s)
- Joel B Awuah
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3216, Australia
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3216, Australia
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8
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Xue Q, Zhang Y, Li R, Li C, Li N, Yuan C, Hou S, Wang Y. Self-assembly of l-tryptophan on Cu(111) studied by low-temperature scanning tunneling microscopy. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.09.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Vinoth K, Ganesh T, Senthil Kumar P, Maria Sylvester M, Anand Karunakaran D, Ramrao Deshmukh A, Kumbharkhane A. Molecular dynamics and dielectric relaxation by DRS, calorimetric analysis and spectral inferences of amino acid complexes. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Wu D, Kong Y. Dynamic Interaction between Host and Guest for Enantioselective Recognition: Application of β-Cyclodextrin-Based Charged Catenane As Electrochemical Probe. Anal Chem 2019; 91:5961-5967. [DOI: 10.1021/acs.analchem.9b00378] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Datong Wu
- Jiangsu Key Laboratory of Advanced Materials and Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
| | - Yong Kong
- Jiangsu Key Laboratory of Advanced Materials and Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
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11
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Dong L, Zhang Y, Duan X, Zhu X, Sun H, Xu J. Chiral PEDOT-Based Enantioselective Electrode Modification Material for Chiral Electrochemical Sensing: Mechanism and Model of Chiral Recognition. Anal Chem 2017; 89:9695-9702. [DOI: 10.1021/acs.analchem.7b01095] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liqi Dong
- School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Youshan Zhang
- School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Xuemin Duan
- School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Xiaofei Zhu
- School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Hui Sun
- School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Jingkun Xu
- School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, China
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12
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Méthivier C, Cruguel H, Pradier CM, Humblot V. Supramolecular chiral self-assemblies of Gly–Pro dipeptides on metallic fcc(110) surfaces. Faraday Discuss 2017; 204:69-81. [DOI: 10.1039/c7fd00116a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adsorption of the Glycine–Proline (Gly–Pro) dipeptide has been investigated using surface science complementary techniques on Au(110) and Ag(110), showing some interesting differences both in the chemical form and surface organization of the adsorbed peptide. On Au(110), Gly–Pro mainly adsorbs in neutral form (COOH/NH2), at low coverage or for a short interaction time; the surface species become zwitterionic at a higher coverage or longer interaction time. These changes are accompanied by a complete reorganization of the molecules at the surface. On Ag(110), only anionic molecules (COO−/NH2) were detected on the surface and only one type of arrangement was observed. These results will be compared to some previously obtained on Cu(110), thus providing a unique comparison of the adsorption of the same di-peptide on three different metal surfaces; the great influence of the substrate on both the chemical form and the arrangement of adsorbed di-peptides was made clear.
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Affiliation(s)
- C. Méthivier
- Sorbonne Universités
- UPMC Université Pierre et Marie Curie
- Univ Paris 6
- Laboratoire de Réactivité de Surface
- UMR CNRS 7197
| | - H. Cruguel
- Sorbonne Universités
- UPMC Université Pierre et Marie Curie
- Univ Paris 6
- Institut des NanoScience de Paris
- F-75005 Paris
| | - C.-M. Pradier
- Sorbonne Universités
- UPMC Université Pierre et Marie Curie
- Univ Paris 6
- Laboratoire de Réactivité de Surface
- UMR CNRS 7197
| | - V. Humblot
- Sorbonne Universités
- UPMC Université Pierre et Marie Curie
- Univ Paris 6
- Laboratoire de Réactivité de Surface
- UMR CNRS 7197
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13
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Costa D, Savio L, Pradier CM. Adsorption of Amino Acids and Peptides on Metal and Oxide Surfaces in Water Environment: A Synthetic and Prospective Review. J Phys Chem B 2016; 120:7039-52. [PMID: 27366959 DOI: 10.1021/acs.jpcb.6b05954] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acids and peptides are often used as "model" segments of proteins for studying their behavior in various types of environments, and/or elaborating functional surfaces. Indeed, though the protein behavior is much more complex than that of their isolated segments, knowledge of the binding mode as well as of the chemical structure of peptides on metal or oxide surfaces is a significant step toward the control of materials in a biological environment. Such knowledge has considerably increased in the past few years, thanks to the combination of advanced characterization techniques and of modeling methods. Investigations of biomolecule-surface interactions in water/solvent environments are quite numerous, but only in a few cases is it possible to reach an understanding of the molecule-(water)-surface interaction with a level of detail comparable to that of the UHV studies. This contribution aims at reviewing the recent data describing the amino acid and peptide interaction with metal or oxide surfaces in the presence of water.
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Affiliation(s)
- D Costa
- Institut de Recherches de Chimie de Paris UMR 8247 ENSCP Chimie Paristech , 11 Rue P. Et M. Curie, 75005 Paris, France
| | - L Savio
- Istituto dei Materiali per l'Elettronica e il Magnetismo, Consiglio Nazionale delle Ricerche, U.O.S. Genova , Via Dodecaneso 33, 16146 Genova, Italy
| | - C-M Pradier
- Laboratoire de Réactivité de Surface, Sorbonne Université, UPMC Univ Paris 06, UMR CNRS 7197 , 4 Place Jussieu, 75231 Paris Cedex 05, France
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14
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Yang S, Jeon A, Driver RW, Kim Y, Jeon EH, Kim S, Lee HS, Lee H. The formation of right-handed and left-handed chiral nanopores within a single domain during amino acid self-assembly on Au(111). Phys Chem Chem Phys 2016; 18:14172-6. [PMID: 27171609 DOI: 10.1039/c6cp01914e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the formation of both right- and left-handed chiral nanopores within a single domain during the self-assembly of an amino acid derivative on an inert Au(111) surface using STM. DFT calculations employed to rationalize this unusual result identified that intermolecular interactions between chiral, windmill-shaped tetramers are crucial for self-assembly.
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Affiliation(s)
- Sena Yang
- Department of Chemistry, Molecular-Level Interface Research Center, KAIST, Daejeon 305-701, Republic of Korea.
| | - Aram Jeon
- Department of Chemistry, Molecular-Level Interface Research Center, KAIST, Daejeon 305-701, Republic of Korea.
| | - Russell W Driver
- Department of Chemistry, Molecular-Level Interface Research Center, KAIST, Daejeon 305-701, Republic of Korea.
| | - Yeonwoo Kim
- Department of Chemistry, Molecular-Level Interface Research Center, KAIST, Daejeon 305-701, Republic of Korea.
| | - Eun Hee Jeon
- Department of Chemistry, Molecular-Level Interface Research Center, KAIST, Daejeon 305-701, Republic of Korea.
| | - Sehun Kim
- Department of Chemistry, Molecular-Level Interface Research Center, KAIST, Daejeon 305-701, Republic of Korea.
| | - Hee-Seung Lee
- Department of Chemistry, Molecular-Level Interface Research Center, KAIST, Daejeon 305-701, Republic of Korea.
| | - Hangil Lee
- Department of Chemistry, Sookmyung Women's University, Seoul 140-742, Republic of Korea.
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15
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Rahsepar FR, Moghimi N, Leung KT. Surface-Mediated Hydrogen Bonding of Proteinogenic α-Amino Acids on Silicon. Acc Chem Res 2016; 49:942-51. [PMID: 27014956 DOI: 10.1021/acs.accounts.5b00534] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the adsorption, film growth mechanisms, and hydrogen bonding interactions of biological molecules on semiconductor surfaces has attracted much recent attention because of their applications in biosensors, biocompatible materials, and biomolecule-based electronic devices. One of the most challenging questions when studying the behavior of biomolecules on a metal or semiconductor surface is "What are the driving forces and film growth mechanisms for biomolecular adsorption on these surfaces?" Despite a large volume of work on self-assembly of amino acids on single-crystal metal surfaces, semiconductor surfaces offer more direct surface-mediated interactions and processes with biomolecules. This is due to their directional surface dangling bonds that could significantly perturb hydrogen bonding arrangements. For all the proteinogenic biomolecules studied to date, our group has observed that they generally follow a "universal" three-stage growth process on Si(111)7×7 surface. This is supported by corroborating data obtained from a three-pronged approach of combining chemical-state information provided by X-ray photoelectron spectroscopy (XPS) and the site-specific local density-of-state images obtained by scanning tunneling microscopy (STM) with large-scale quantum mechanical modeling based on the density functional theory with van der Waals corrections (DFT-D2). Indeed, this three-stage growth process on the 7×7 surface has been observed for small benchmark biomolecules, including glycine (the simplest nonchiral amino acid), alanine (the simplest chiral amino acid), cysteine (the smallest amino acid with a thiol group), and glycylglycine (the smallest (di)peptide of glycine). Its universality is further validated here for the other sulfur-containing proteinogenic amino acid, methionine. We use methionine as an example of prototypical proteinogenic amino acids to illustrate this surface-mediated process. This type of growth begins with the formation of a covalent-bond driven interfacial layer (first adlayer), followed by that of a transitional layer driven by interlayer and intralayer hydrogen bonding (second adlayer), and then finally the zwitterionic multilayers (with intralayer hydrogen bonding). The important role of surface-mediated hydrogen bonding as the key for this universal three-stage growth process is demonstrated. This finding provides new insight into biomolecule-semiconductor surface interactions often found in biosensors and biomolecular electronic devices. We also establish the trends in the H-bond length among different types of the hydrogen bonding for dimolecular structures in the gas phase and on the Si(111)7×7 surface, the latter of which could be validated by their STM images. Finally, five simple rules of thumb are developed to summarize the adsorption properties of these proteinogenic biomolecules as mediated by hydrogen bonding, and they are expected to provide a helpful guide to future studies of larger biomolecules and their potential applications.
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Affiliation(s)
- Fatemeh R. Rahsepar
- WATLab
and Department of
Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Nafiseh Moghimi
- WATLab
and Department of
Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - K. T. Leung
- WATLab
and Department of
Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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16
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Youn YS, Jeon A, Kim DH, Lee HS, Kim S. Molecular tuning of amino acids to form two-dimensional molecular networks driven by conformational preorganization. Chem Commun (Camb) 2016; 52:14055-14058. [PMID: 27858018 DOI: 10.1039/c6cc05497h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated the self-assembly of rationally designed γ-Phe on Au(111) using STM with DFT calculations. In contrast to α-Phe, γ-Phe self-assembled into 2D molecular network. The better self-association was attributed to conformational preorganization through intramolecular interaction.
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Affiliation(s)
- Young-Sang Youn
- Department of Chemistry
- Molecular-Level Interface Research Center
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Aram Jeon
- Department of Chemistry
- Molecular-Level Interface Research Center
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Do Hwan Kim
- Division of Science Education and Institute of Fusion Science
- Chonbuk National University
- Jeonbuk-do 54896
- Republic of Korea
| | - Hee-Seung Lee
- Department of Chemistry
- Molecular-Level Interface Research Center
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Sehun Kim
- Department of Chemistry
- Molecular-Level Interface Research Center
- KAIST
- Daejeon 305-701
- Republic of Korea
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17
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Saavedra-Torres M, Tielens F, Santos JC. Dibenzyl disulfide adsorption on Cu(111) surface: a DFT study. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1763-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Adsorption-induced auto-amplification of enantiomeric excess on an achiral surface. Nat Chem 2015; 7:520-5. [DOI: 10.1038/nchem.2250] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/25/2015] [Indexed: 12/29/2022]
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19
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Cruguel H, Méthivier C, Pradier CM, Humblot V. Surface Chirality of Gly-Pro Dipeptide Adsorbed on a Cu(110) Surface. Chirality 2015; 27:411-6. [DOI: 10.1002/chir.22445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 03/02/2015] [Accepted: 03/02/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Hervé Cruguel
- Sorbonne Universités, UPMC Université Pierre et Marie Curie, Univ Paris 6; Paris France
- Institut des NanoScience de Paris, Université Pierre et Marie Curie, UPMC Paris 6; Paris France
| | - Christophe Méthivier
- Sorbonne Universités, UPMC Université Pierre et Marie Curie, Univ Paris 6; Paris France
- Laboratoire de Réactivité de Surface - UMR CNRS 7197; Université Pierre et Marie Curie, UPMC Paris 6; Paris France
| | - Claire-Marie Pradier
- Sorbonne Universités, UPMC Université Pierre et Marie Curie, Univ Paris 6; Paris France
- Laboratoire de Réactivité de Surface - UMR CNRS 7197; Université Pierre et Marie Curie, UPMC Paris 6; Paris France
| | - Vincent Humblot
- Sorbonne Universités, UPMC Université Pierre et Marie Curie, Univ Paris 6; Paris France
- Laboratoire de Réactivité de Surface - UMR CNRS 7197; Université Pierre et Marie Curie, UPMC Paris 6; Paris France
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20
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Feng Z, Castellarin Cudia C, Floreano L, Morgante A, Comelli G, Dri C, Cossaro A. A competitive amino-carboxylic hydrogen bond on a gold surface. Chem Commun (Camb) 2015; 51:5739-42. [DOI: 10.1039/c4cc10271a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel amino-carboxylic hetero-synthon is described, which drives the formation of a complex 2D hetero-organic architecture.
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Affiliation(s)
- Zhijing Feng
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
| | | | - Luca Floreano
- CNR-IOM Laboratorio Nazionale TASC
- I-34149 Trieste
- Italy
| | - Alberto Morgante
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
| | - Giovanni Comelli
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
| | - Carlo Dri
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
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