1
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Heiner BR, Handy KM, Devlin AM, Soucek JL, Pittsford AM, Turner DA, Petersen JP, Oliver AG, Corcelli SA, Kandel SA. Enantiopure molecules form apparently racemic monolayers of chiral cyclic pentamers. Phys Chem Chem Phys 2024. [PMID: 39319688 DOI: 10.1039/d4cp02094d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Ultra-high vacuum scanning tunneling microscopy (UHV-STM) was used to investigate two related molecules pulse-deposited onto Au(111) surfaces: indoline-2-carboxylic acid and proline (pyrrolidine-2-carboxylic acid). Indoline-2-carboxylic acid and proline form both dimers and C5-symmetric "pinwheel" pentamers. Enantiomerically pure S-(-)-indoline-2-carboxylic acid and S-proline were used, and the pentamer structures observed for both were chiral. However, the presence of apparently equal numbers of 'right-' and 'left-handed' pinwheels is contrary to the general understanding that the chirality of the molecule dictates supramolecular chirality. A variety of computational methods were used to elucidate pentamer geometry for S-proline. Straightforward geometry optimization proved difficult, as the size of the cluster and the number of possible intermolecular interactions produced an interaction potential with multiple local minima. Instead, the Amber force field was used to exhaustively search all of phase space for chemically reasonable pentamer structures, producing a limited number of candidate structures that were then optimized as gas-phase clusters using density functional theory (DFT). The binding energies of the two lowest-energy pentamers on the Au(111) surface were then calculated by plane-wave DFT using the VASP software, and STM images predicted. These calculations indicate that the right- and left-handed pentamers are instead two different polymorphs.
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Affiliation(s)
- Benjamin R Heiner
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Kaitlyn M Handy
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Angela M Devlin
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE 68179, USA
| | - Jewel L Soucek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Alexander M Pittsford
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | | | | | - Allen G Oliver
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - S Alex Kandel
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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2
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Li X, Cazade PA, Qi P, Thompson D, Guo C. The role of externally-modulated electrostatic interactions in amplifying charge transport across lysine-doped peptide junctions. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.04.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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3
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Wang X, Liu X, Ma Z, Mu C, Li W. Photochromic and photothermal hydrogels derived from natural amino acids and heteropoly acids. SOFT MATTER 2021; 17:10140-10148. [PMID: 34730172 DOI: 10.1039/d1sm01272j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A new class of supramolecular hydrogels have been designed and synthesized via the co-assembly of basic amino acids (AAs) and heteropoly acids (HPAs) under acidic conditions. The formation of gel-like samples is identified using an inverted tube method, rheology, and scanning and transmission electron microscopy. Fourier transform infrared spectroscopy reveals that the structural integrity of the HPAs is maintained during the gelation process. X-ray photoelectron spectroscopy (XPS) and proton nuclear magnetic resonance spectroscopy demonstrate that the anionic HPAs interact with both the protonated α-NH2 and the protonated side groups of the basic amino acids, initiating the preferential growth of one-dimensional nanofibers. These nanofibers bundle and entangle with each other to form extended three-dimensional network structures. The resulting AA/HPA supramolecular hydrogels show clear stereoselectivity of the basic amino acids. With the decreasing enantiomeric excess of the basic amino acids, the gelation propensity of the AA/HPA complexes is found to be depressed. The co-assembled hydrogels show the UV-responsive photochromic behaviour because of the presence of HPAs. The corresponding XPS data confirm that the photochromism of the hydrogels is attributed to the intervalence charge-transfer transition resulting from the reduction of HPAs. Interestingly, the reduced HPAs within the hydrogel matrix can absorb the near-infrared (NIR) light and exhibit photo-thermal conversion properties, which elevates the bulk temperature of the AA/HPA hydrogels and induces the gel-to-sol transition. This study unveils that HPAs have unique capacity to promote the gelation of basic amino acids for the construction of supramolecular soft materials with functional features.
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Affiliation(s)
- Xue Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Xiaohuan Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Zhiyuan Ma
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Chuanling Mu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
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4
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Chen Z, Chi Z, Sun Y, Lv Z. Chirality in peptide-based materials: From chirality effects to potential applications. Chirality 2021; 33:618-642. [PMID: 34342057 DOI: 10.1002/chir.23344] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/24/2021] [Accepted: 07/13/2021] [Indexed: 12/23/2022]
Abstract
Chirality is ubiquitous in nature with primary cellular functions that include construction of right-/left-handed helix and selective communications among diverse biomolecules. Of particularly intriguing are the chiral peptide-based materials that can be deliberately designed to change physicochemistry properties via tuning peptide sequences. Critically, understanding their chiral effects are fundamental for the development of novel materials in chemistry and biomedicine fields. Here, we review recent researches on chirality in peptide-based materials, summarizing relevant typical chiral effects towards recognition, amplification, and induction. Driven forces for the chiral discrimination in affinity interaction as well as the handedness preferences in supramolecular structure formation at both the macroscale and microscale are illustrated. The implementation of such chirality effects of artificial copolymers, assembled aggregates and their composites in the fields of bioseparation and bioenrichment, cell incubation, protein aggregation inhibitors, chiral smart gels, and bionic electro devices are also presented. At last, the challenges in these areas and possible directions are pointed out. The diversity of chiral roles in the origin of life and chirality design in different organic or composite systems as well as their applications in drug development and chirality detection in environmental protection are discussed.
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Affiliation(s)
- Zhonghui Chen
- Guangdong Engineering Technology Research Center for High performance Organic and Polymer Photoelectric Functional Films, State Key Laboratory of OEMT, School of Chemistry, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, China
| | - Zhenguo Chi
- Guangdong Engineering Technology Research Center for High performance Organic and Polymer Photoelectric Functional Films, State Key Laboratory of OEMT, School of Chemistry, Sun Yat-sen University, Guangzhou, China
| | - Yifeng Sun
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, China
| | - Ziyu Lv
- Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, China
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5
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Azizi D, Larachi F, Garnier A, Lagüe P, Levasseur B. Sorption of aqueous amino acid species on sulphidic mineral surfaces—DFT study and insights on biosourced‐reagent mineral flotation. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23841] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Dariush Azizi
- Department of Chemical Engineering Université Laval Québec Québec Canada
| | - Faïçal Larachi
- Department of Chemical Engineering Université Laval Québec Québec Canada
| | - Alain Garnier
- Department of Chemical Engineering Université Laval Québec Québec Canada
| | - Patrick Lagüe
- Department of Biochemistry, Microbiology & Bioinformatics Université Laval Québec Québec Canada
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6
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El Merhie A, Salerno M, Heredia-Guerrero JA, Dante S. Graphene-enhanced differentiation of neuroblastoma mouse cells mediated by poly-D-lysine. Colloids Surf B Biointerfaces 2020; 191:110991. [PMID: 32408266 DOI: 10.1016/j.colsurfb.2020.110991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 12/19/2022]
Abstract
We compared the proliferation and differentiation of mouse neuroblastoma Neuro 2A cell line on single layer graphene and glass substrates. Quantitative and qualitative analysis of the cell proliferation and differentiation were performed, considering also the effect of a common adhesion factor, namely polylysine. We observed that on graphene substrates the cells proliferate faster with respect to glass; additionally, the presence of the adhesion factor enhances the difference and, remarkably, boosts the cell differentiation on the graphene-based interface. To understand the mechanism underlying a different cell behavior on the same adhesion coating, we carried out a physicochemical investigation of the studied interfaces (glass and graphene, bare and polylysine coated) by several techniques. In particular, we employed infrared spectroscopy to gain information on polylysine conformation, and atomic force microscopy force-distance curves to study adhesion properties at the surface. The results indicate that polylysine has an enhanced binding affinity for graphene, as well as a different molecular arrangement on graphene with respect to glass. These properties act as surface cues to trigger the cell response.
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Affiliation(s)
- Amira El Merhie
- Nanoscopy & NIC@IIT, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Marco Salerno
- Materials Characterization Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - José Alejandro Heredia-Guerrero
- Smart Materials, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy; IHSM La Mayora, Departamento de Mejora Genética y Biotecnología, Consejo Superior de Investigaciones Científicas, E-29750 Algarrobo-Costa, Málaga, Spain
| | - Silvia Dante
- Materials Characterization Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
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7
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Antosova A, Bednarikova Z, Koneracka M, Antal I, Marek J, Kubovcikova M, Zavisova V, Jurikova A, Gazova Z. Amino Acid Functionalized Superparamagnetic Nanoparticles Inhibit Lysozyme Amyloid Fibrillization. Chemistry 2019; 25:7501-7514. [DOI: 10.1002/chem.201806262] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Andrea Antosova
- Institute of Experimental Physics Slovak Academy Science Watsonova 47 040 01 Kosice Slovakia
| | - Zuzana Bednarikova
- Institute of Experimental Physics Slovak Academy Science Watsonova 47 040 01 Kosice Slovakia
| | - Martina Koneracka
- Institute of Experimental Physics Slovak Academy Science Watsonova 47 040 01 Kosice Slovakia
| | - Iryna Antal
- Institute of Experimental Physics Slovak Academy Science Watsonova 47 040 01 Kosice Slovakia
| | - Jozef Marek
- Institute of Experimental Physics Slovak Academy Science Watsonova 47 040 01 Kosice Slovakia
| | - Martina Kubovcikova
- Institute of Experimental Physics Slovak Academy Science Watsonova 47 040 01 Kosice Slovakia
| | - Vlasta Zavisova
- Institute of Experimental Physics Slovak Academy Science Watsonova 47 040 01 Kosice Slovakia
| | - Alena Jurikova
- Institute of Experimental Physics Slovak Academy Science Watsonova 47 040 01 Kosice Slovakia
| | - Zuzana Gazova
- Institute of Experimental Physics Slovak Academy Science Watsonova 47 040 01 Kosice Slovakia
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8
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Kojima S, Nagata F, Inagaki M, Kugimiya S, Kato K. Enzyme immobilisation on poly-l-lysine-containing calcium phosphate particles for highly sensitive glucose detection. RSC Adv 2019; 9:10832-10841. [PMID: 35515311 PMCID: PMC9062467 DOI: 10.1039/c9ra01764j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/01/2019] [Indexed: 01/01/2023] Open
Abstract
High catalytic activities of enzymes are necessary for enzyme immobilising technology for the development of glucose sensors. The aim of this study is to synthesise two types of poly(l-lysine)-containing calcium phosphate particles (pLys-HAp) and to achieve the immobilisation of glucose oxidase (GOX) on them. The oxidation activity of GOX immobilised on these particles was more than 80% compared to that of native GOX (considered to be 100%). Additionally, the relative activity of GOX immobilised on poly-ε-lysine-containing HAp (ε-pLys-HAp) remained approximately 70% after ten cycles. Moreover, glucose detection was able to be performed in the linear range of 4–400 μM using GOX immobilised on pLys-HAp composites. In the direct electrochemistry measurement using the cyclic voltammetry (CV) method, a glassy carbon electrode (GCE) modified by ε-pLys-HAp was a good enzyme electrode and can be used for glucose detection with high sensitivity. From these results, poly(l-lysine)-containing HAp composites can be expected to be enzyme immobilisation agents with high stability and biosensors with high sensitivity. The as-synthesised poly-l-lysine-containing HAp with high enzyme stability could be a candidate for a glucose sensor with high sensitivity.![]()
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Affiliation(s)
- Suzuka Kojima
- National Institute of Advanced Industrial Science and Technology
- Nagoya
- Japan
- Materials Chemistry Course
- Graduate School of Engineering
| | - Fukue Nagata
- National Institute of Advanced Industrial Science and Technology
- Nagoya
- Japan
| | - Masahiko Inagaki
- National Institute of Advanced Industrial Science and Technology
- Nagoya
- Japan
- Materials Chemistry Course
- Graduate School of Engineering
| | - Shinichi Kugimiya
- Materials Chemistry Course
- Graduate School of Engineering
- Aichi Institute of Technology
- Toyota
- Japan
| | - Katsuya Kato
- National Institute of Advanced Industrial Science and Technology
- Nagoya
- Japan
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9
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Antal I, Koneracka M, Kubovcikova M, Zavisova V, Khmara I, Lucanska D, Jelenska L, Vidlickova I, Zatovicova M, Pastorekova S, Bugarova N, Micusik M, Omastova M, Kopcansky P. d,l-lysine functionalized Fe3O4 nanoparticles for detection of cancer cells. Colloids Surf B Biointerfaces 2018; 163:236-245. [DOI: 10.1016/j.colsurfb.2017.12.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/29/2017] [Accepted: 12/11/2017] [Indexed: 11/17/2022]
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10
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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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11
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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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12
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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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13
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Raouafi F, Seydou M, Lassoued K, Taleb A, Diawara B. First-principles investigation of methanethiol adsorption and dissociation mechanisms on the high-Miller-index vicinal surface Cu(4 1 0). JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:175001. [PMID: 27028163 DOI: 10.1088/0953-8984/28/17/175001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this work, we present detailed investigations of methanethiol adsorption on a Cu(4 1 0) surface within the framework of the self-consistent first-principles calculations as implemented in the Vienna ab initio simulation package (VASP). In particular, the adsorption sites, the surface coverage rate and electronic properties have been determined and compared to experimental values. The results indicate that the favorable adsorption site in the case of low coverage rate is a bridge on the step followed by the hollow site on the terrace. The adsorption significantly affects the outermost layer of the surface mainly for a higher coverage rate in a (2 × 2) supercell. The nature of the chemisorption process on the surface is analyzed by means of the density of states which, combined with charge density difference and atomic charge calculations, confirms the ionic character of the S-Cu bond. The specific effect of the presence of steps is highlighted by comparing the adsorption on the (1 0 0) terrace to the adsorption on the extended Cu(1 0 0) surface. Compared to the flat Cu(1 0 0), it is found here that while the stability is almost the same at p(2 × 2) coverage, the CH3S/Cu(4 1 0) becomes more stable than CH3S/Cu(1 0 0) at c(2 × 2) coverage with 0.30 eV per molecule. The mechanism of methanethiol dissociation is explored by the nudged elastic band method and demonstrates that the most favorable path is dissociation followed by migration of hydrogen from the step to its most stable position (hollow on the terrace) with energy barriers less than 0.5 eV.
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Affiliation(s)
- Faycal Raouafi
- Laboratoire de physico-chimie des microstructures et microsystèmes, IPEST La Marsa, Tunisia
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14
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Kitadai N. Energetics of Amino Acid Synthesis in Alkaline Hydrothermal Environments. ORIGINS LIFE EVOL B 2015; 45:377-409. [PMID: 25796392 DOI: 10.1007/s11084-015-9428-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/27/2015] [Indexed: 01/01/2023]
Abstract
Alkaline hydrothermal systems have received considerable attention as candidates for the origin and evolution of life on the primitive Earth. Nevertheless, sufficient information has not yet been obtained for the thermodynamic properties of amino acids, which are necessary components for life, at high temperatures and alkaline pH. These properties were estimated using experimental high-temperature volume and heat capacity data reported in the literature for several amino acids, together with correlation algorithms and the revised Helgeson-Kirkham-Flowers (HKF) equations of state. This approach enabled determination of a complete set of the standard molal thermodynamic data and the revised HKF parameters for the 20 protein amino acids in their zwitterionic and ionization states. The obtained dataset was then used to evaluate the energetics of amino acid syntheses from simple inorganic precursors (CO2, H2, NH3 and H2S) in a simulated alkaline hydrothermal system on the Hadean Earth. Results show that mixing between CO2-rich seawater and the H2-rich hydrothermal fluid can produce energetically favorable conditions for amino acid syntheses, particularly in the lower-temperature region of such systems. Together with data related to the pH and temperature dependences of the energetics of amino acid polymerizations presented in earlier reports, these results suggest the following. Hadean alkaline hydrothermal settings, where steep pH and temperature gradients may have existed between cool, slightly acidic Hadean ocean water and hot, alkaline hydrothermal fluids at the vent-ocean interface, may be energetically the most suitable environment for the synthesis and polymerization of amino acids.
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Affiliation(s)
- Norio Kitadai
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan,
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15
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Sebben D, Pendleton P. Infrared spectrum analysis of the dissociated states of simple amino acids. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 132:706-712. [PMID: 24910978 DOI: 10.1016/j.saa.2014.05.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/24/2014] [Accepted: 05/12/2014] [Indexed: 06/03/2023]
Abstract
In this work, we present detailed analyses of the dissociation of dilute aqueous solutions of glycine and of lysine over the range 1<pH<12. Using appropriate spectrum subtraction methods, we obtained ATR-IR spectra of the solvated species as a function of pH. Discernible changes in the ionic species were identified in the absorption region between 1800 and 1100 cm(-1). By applying peak deconvolution techniques to the spectra, we correctly interpret the apparent peak shift from 1615 to 1600 cm(-1) as being due to the receding NH3+ asymmetric deformation alongside the appearing COO- asymmetric stretching. The effect of aqueous solution environment was also investigated in terms of 10 and 100 mmol/L NaCl. Salt solution spectra at each pH were also subtracted from each solution phase spectrum. Analysis of the deconvoluted peak areas due to CO and COO- at pH ranges<4.5 and those due to NH2 and NH3+ for pH>8 resulted in consistent pKa values for the amino acids.
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Affiliation(s)
- Damien Sebben
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Phillip Pendleton
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000, Australia.
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16
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Li G, Feng L, Zhao P, Xu W, Wang Y, Song A, Hao J. Lysine-based chiral vesicles. J Colloid Interface Sci 2014; 431:233-40. [DOI: 10.1016/j.jcis.2014.05.069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 05/30/2014] [Accepted: 05/31/2014] [Indexed: 10/25/2022]
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17
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Influence of mineral characteristics on the retention of low molecular weight organic compounds: A batch sorption–desorption and ATR-FTIR study. J Colloid Interface Sci 2014; 432:246-57. [DOI: 10.1016/j.jcis.2014.06.036] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 06/09/2014] [Accepted: 06/15/2014] [Indexed: 11/23/2022]
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18
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Seljamäe-Green RT, Simpson GJ, Grillo F, Greenwood J, Francis SM, Schaub R, Lacovig P, Baddeley CJ. Assembly of a chiral amino acid on an unreactive surface: (S)-proline on Au(111). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:3495-3501. [PMID: 24605884 DOI: 10.1021/la500336c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The adsorption of (S)-proline on Au(111) at 300 K was studied by low-temperature scanning tunnelling microscopy, X-ray photoelectron spectroscopy, and high resolution electron energy loss spectroscopy. (S)-proline adsorbs to produce a 2-D gas phase at 300 K, which can be condensed to form ordered molecular assemblies on cooling to 77 K. The chemical nature of the self-assembled structures is discussed in light of the information provided by photoelectron and vibrational spectroscopies.
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Affiliation(s)
- Riho T Seljamäe-Green
- EaStCHEM School of Chemistry, University of St Andrews , St Andrews, Fife, KY16 9ST, United Kingdom
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19
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Zamani F, Rezapour M, Kianpour S. Immobilization of L-Lysine on Zeolite 4A as an Organic-Inorganic Composite Basic Catalyst for Synthesis of α,β-Unsaturated Carbonyl Compounds under Mild Conditions. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.8.2367] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Tranca I, Smerieri M, Savio L, Vattuone L, Costa D, Tielens F. Unraveling the self-assembly of the (S)-glutamic acid "flower" structure on Ag(100). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7876-7884. [PMID: 23692665 DOI: 10.1021/la4012923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
(S)-Glutamic acid adsorbed on Ag(100) organizes in different self-assembled structures depending on surface temperature [Smerieri, M.; Vattuone, L.; Kravchuk, T.; Costa, D.; Savio, L. (S)-Glutamic Acid on Ag(100): Self-Assembly in the Nonzwitterionic Form. Langmuir2011, 27, 2393-2404]. In particular, two of these structures, referred to as "square" and "flower" geometries, are found to coexist on the surface upon deposition at T = 350 K. The former assembly was fully resolved at the atomic level in the work of Smerieri et al. [Smerieri, M.; Vattuone, L.; Costa, D.; Tielens, F.; Savio, L. Self-Assembly of (S)-Glutamic Acid on Ag(100): A Combined LT-STM and Ab Initio Investigation. Langmuir2010, 26, 7208-7215], in which we proved that the driving force for adsorption is the van der Waals interactions between the molecules and the Ag surface, that is, that molecules are in a physisorbed state. In this paper, we complete our work by presenting the characterization of the "flower" structure. In contrast to the case of the "square" assembly, a strong chemical bond between glutamic acid radicals and the surface is at the basis of the "flowers" geometry. Whereas the chemisorbed central GLU tetramer interacts strongly with the surface, the physisorbed surrounding GLU molecules conserve some degree of freedom in the layer which counterbalances the weak adsorption energy. The "flower" and the "square" assemblies have similar dispersion energy and H-bond interaction energy; as a consequence of the different chemical state of the GLU molecules, however, such contributions have a very different relative weight in the stabilization of the two structures.
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Affiliation(s)
- Ionut Tranca
- UPMC Univ Paris 06, Laboratoire de Réactivité de Surface, Site d'Ivry - Le Raphaël, 3 rue Galilée, F-94200 Ivry-Sur-Seine, France
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21
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Humblot V, Pradier CM. Chiral Recognition of l-Gramicidine on Chiraly Methionine-Modified Au(111). J Phys Chem Lett 2013; 4:1816-1820. [PMID: 26283114 DOI: 10.1021/jz400608n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A chiral pentadecapeptide, l-gramicidine, has been shown to undergo specific adsorption onto gold surfaces modified by chiral amino acids, d- and l-methionine, upon adsorption in the liquid phase. There is a chiral recognition only between the slightly anionic l-peptide and the l-modified surface exhibiting cationic molecules. However, whatever the probe and target molecule charges, very weak recognition was observed between molecules of opposite chirality.
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Affiliation(s)
- Vincent Humblot
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Université Pierre et Marie Curie - UPMC case 178, 4 place Jussieu, 75005 Paris, France
| | - Claire-Marie Pradier
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Université Pierre et Marie Curie - UPMC case 178, 4 place Jussieu, 75005 Paris, France
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22
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Peyre J, Humblot V, Méthivier C, Berjeaud JM, Pradier CM. Co-Grafting of Amino–Poly(ethylene glycol) and Magainin I on a TiO2 Surface: Tests of Antifouling and Antibacterial Activities. J Phys Chem B 2012; 116:13839-47. [DOI: 10.1021/jp305597y] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jessie Peyre
- CNRS UMR 7197, Surface Reactivity
Laboratory, Pierre et Marie Curie University - Paris 6, 3 rue Galilée 94200 Ivry-sur-Seine, France
| | - Vincent Humblot
- CNRS UMR 7197, Surface Reactivity
Laboratory, Pierre et Marie Curie University - Paris 6, 3 rue Galilée 94200 Ivry-sur-Seine, France
| | - Christophe Méthivier
- CNRS UMR 7197, Surface Reactivity
Laboratory, Pierre et Marie Curie University - Paris 6, 3 rue Galilée 94200 Ivry-sur-Seine, France
| | - Jean-Marc Berjeaud
- Ecology & Biology Interactions - UMR 7267 CNRS, Poitiers University, IBMIG, 40 avenue du recteur Pineau, 86022 Poitiers Cedex, France
| | - Claire-Marie Pradier
- CNRS UMR 7197, Surface Reactivity
Laboratory, Pierre et Marie Curie University - Paris 6, 3 rue Galilée 94200 Ivry-sur-Seine, France
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23
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Cheong WY, Gellman AJ. Enantiospecific desorption of R- and S-propylene oxide from D- or L-lysine modified Cu(100) surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:15251-15262. [PMID: 23020648 DOI: 10.1021/la3027557] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The enantiospecific desorption kinetics of R- and S-propylene oxide (PO) from a Cu(100) surface modified by enantiomerically pure D- or L-lysine have been studied using temperature programmed desorption. These experiments have used R- or S-PO as the chiral probe for study of enantiospecific adsorption on Cu(100) surfaces modified with D- or L-lysine. This chiral probe/modifier/Cu system manifests a significant diastereomeric effect in the R- and S-PO peak desorption temperatures and, hence, true enantiospecific behavior. The enantiospecificity in the PO desorption kinetics is observed only over a narrow range of lysine modifier coverage with a maximum at a lysine coverage leaving an empty site density of θ(O) ≈ 0.25. The observation of enantiospecific behavior in the PO/lysine/Cu(100) system is in contrast with the failed results of prior attempts to observe enantiospecific desorption from chirally modified Cu surfaces. The potential for hydrogen-bonding interactions between the chiral probe and chiral modifier, which can depend on the coverage and configuration of the adsorbed modifier, may play a crucial role in enantiospecific adsorption on lysine modified Cu surfaces.
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Affiliation(s)
- Wai Yeng Cheong
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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24
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Vallée A, Humblot V, Méthivier C, Dumas P, Pradier CM. Modifying protein adsorption by layers of glutathione pre-adsorbed on Au(111). JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:484002. [PMID: 22085831 DOI: 10.1088/0953-8984/23/48/484002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Molecular interaction with metal surfaces raises fundamental questions regarding their binding tendency, their dispersion on the surface, as well as their conformation which may change their biological properties; addressing these questions, and being able to tune protein interactions, is of primary importance for the control of biointerfaces. In this study, one tripeptide, GSH (glu-cys-gly), was used to condition gold surfaces and thus influence the adsorption of bovine serum albumin (BSA). Depending on the pH value of the GSH solution, cationic, zwitterionic or anionic forms of the tripeptide could be stabilised on the surface, before interacting with BSA solutions. The amount of proteins was observed to depend both on the chemical state of the adsorbed underlying peptide and on the solvent of the protein solution, indicating an important role of electrostatic interactions upon protein adsorption. Moreover, atomic force microscopy (AFM), and synchrotron IR microscopy revealed a heterogeneous distribution of proteins on the GSH layer.
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Affiliation(s)
- Anne Vallée
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Université Pierre et Marie Curie, Paris, France
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25
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Forster M, Dyer MS, Persson M, Raval R. Tailoring Homochirality at Surfaces: Going Beyond Molecular Handedness. J Am Chem Soc 2011; 133:15992-6000. [DOI: 10.1021/ja202986s] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew Forster
- Surface Science Research Centre and Department of Chemistry, University of Liverpool, Oxford Street, Liverpool L69 3BX, U.K
| | - Matthew S. Dyer
- Surface Science Research Centre and Department of Chemistry, University of Liverpool, Oxford Street, Liverpool L69 3BX, U.K
| | - Mats Persson
- Surface Science Research Centre and Department of Chemistry, University of Liverpool, Oxford Street, Liverpool L69 3BX, U.K
- Department of Applied Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Rasmita Raval
- Surface Science Research Centre and Department of Chemistry, University of Liverpool, Oxford Street, Liverpool L69 3BX, U.K
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26
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Smerieri M, Vattuone L, Kravchuk T, Costa D, Savio L. (S)-glutamic acid on Ag(100): self-assembly in the nonzwitterionic form. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:2393-2404. [PMID: 21338127 DOI: 10.1021/la1033993] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The fundamental understanding of adsorption and self-organization of biological molecules at surfaces is of greatest importance for a huge variety of possible applications, ranging from molecular electronics to the study of biocompatible materials, hygiene, and biofouling. In spite of that, the characterization of the interactions of organic molecules of biological interest with surfaces is far from being complete. In the present paper we report on a combined microscopic (scanning tunneling microscopy (STM)) and spectroscopic (X-ray photoemission spectroscopy and high-resolution electron energy loss spectroscopy) study of glutamic acid (Glu) adsorption and self-assembly on Ag(100) at different temperature. STM allows one to determine the structures of the Glu layers, for which empirical models are proposed, while photoemission spectra exclude adsorption in the zwitterionic form, which is the most common especially for weakly interacting substrates.
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Affiliation(s)
- M Smerieri
- IMEM-CNR , Via Dodecaneso 33, 16146 Genova, Italy
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27
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Vallee A, Humblot V, Pradier CM. Peptide interactions with metal and oxide surfaces. Acc Chem Res 2010; 43:1297-306. [PMID: 20672797 DOI: 10.1021/ar100017n] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Increasing interest in bio-interfaces for medical, diagnostic, or biotechnology applications has highlighted the critical scientific challenge behind both the understanding and control of protein-solid surface interactions. In this context, this Account focuses on the molecular-level characterization of the interactions of peptides, ranging in size from a few amino acids to long sequences, with metal and oxide surfaces. In this Account, we attempt to fill the gap between the well-known basic studies of the interaction of a single amino acid with well-defined metal surfaces and the investigations aimed at controlling biocompatibility or biofilm growth processes. We gather studies performed with surface science tools and macroscopic characterization techniques along with those that use modeling methods, and note the trends that emerge. Sulfur drives the interaction of cysteine-containing peptides with metal surfaces, particularly gold. Moreover, intermolecular interactions, such as hydrogen bonds may induce surface self assembly and chiral arrangements of the peptide layer. Depending on the solvent pH and composition, carboxylates or amino groups may also interact with the surface, which could involve conformational changes in the adsorbed peptide. On oxide surfaces such as titania or silica, researchers have identified carboxylate groups as the preferential peptide binding groups because of their strong electrostatic interactions with the charged surface. In high molecular weight peptides, systematic studies of their interaction with various oxide surfaces point to the preferential interaction of certain peptide sequences: basic residues such as arginine assume a special role. Researchers have successfully used these observations to synthesize adhesive sequences and initiate biomineralization. Studies of the interaction of peptides with nanoparticles have revealed similar binding trends. Sulfur-containing peptides adhere preferentially to gold nanoparticles. Peptides containing aromatic nitrogen also display a high affinity for various inorganic nanoparticles. Finally, we describe a novel class of peptides, genetically engineered peptides for inorganics (GEPIs), which are selected from a phage display protocol for their high binding affinity for inorganic surfaces. Extended investigations have focused on the mechanisms of the molecular binding of these peptides to solid surfaces, in particular the high binding affinity of some sulfur-free sequences of GEPIs to gold or platinum surfaces. We expect that this clearer view of the possible preferential interactions between peptides and inorganic surfaces will facilitate the development of new, more focused research in various fields of biotechnology, such as biocompatibility, biomimetics, or tissue engineering.
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Affiliation(s)
- Anne Vallee
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Université Pierre et Marie Curie Paris 6, 4 place Jussieu, Case 178, 75252 Paris Cedex 05, France
| | - Vincent Humblot
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Université Pierre et Marie Curie Paris 6, 4 place Jussieu, Case 178, 75252 Paris Cedex 05, France
| | - Claire-Marie Pradier
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Université Pierre et Marie Curie Paris 6, 4 place Jussieu, Case 178, 75252 Paris Cedex 05, France
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28
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Smerieri M, Vattuone L, Costa D, Tielens F, Savio L. Self-assembly of (S)-glutamic acid on Ag(100): a combined LT-STM and ab initio investigation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:7208-7215. [PMID: 20158258 DOI: 10.1021/la904331d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Self-assembly of organic molecules at metal surfaces is of greatest importance in nanoscience; in fact, it opens new perspectives in the field of molecular electronics and in the study of biocompatible materials. Combining an experimental low-temperature scanning tunneling microscopy investigation with ab initio calculations, we succeeded to describe in detail (S)-glutamic acid adsorption on Ag(100) at T = 350 K. We find that (S)-glutamic acid organizes in a squared structure and, at variance with the majority of cases reported in literature, it adsorbs in the neutral form, 4.6 A above the surface plane. The interaction with the poorly reactive Ag substrate is only due to weak van der Waals forces, while H-bonds between carboxyl groups and the formation of a OCOH-OCOH-OCOH-OCOH cycle at the vertex of the squares are the main responsible for the self-assembly.
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Affiliation(s)
- M Smerieri
- Dipartimento di Fisica dell'Università di Genova, Italy
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29
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Forster M, Dyer M, Persson M, Raval R. 2D Random Organization of Racemic Amino Acid Monolayers Driven by Nanoscale Adsorption Footprints: Proline on Cu(110). Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904979] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Forster M, Dyer M, Persson M, Raval R. 2D Random Organization of Racemic Amino Acid Monolayers Driven by Nanoscale Adsorption Footprints: Proline on Cu(110). Angew Chem Int Ed Engl 2010; 49:2344-8. [DOI: 10.1002/anie.200904979] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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Kitadai N, Yokoyama T, Nakashima S. In situ ATR-IR investigation of L-lysine adsorption on montmorillonite. J Colloid Interface Sci 2009; 338:395-401. [DOI: 10.1016/j.jcis.2009.06.061] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 06/25/2009] [Accepted: 06/27/2009] [Indexed: 10/20/2022]
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32
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Forster M, Dyer MS, Persson M, Raval R. Probing Conformers and Adsorption Footprints at the Single-Molecule Level in a Highly Organized Amino Acid Assembly of (S)-Proline on Cu(110). J Am Chem Soc 2009; 131:10173-81. [DOI: 10.1021/ja9020364] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew Forster
- Surface Science Research Centre and Department of Chemistry, University of Liverpool, Liverpool, L69 3BX, U.K., and Department of Applied Physics, Chalmers University of Technology, SE-412 96, Göteborg, Sweden
| | - Matthew S. Dyer
- Surface Science Research Centre and Department of Chemistry, University of Liverpool, Liverpool, L69 3BX, U.K., and Department of Applied Physics, Chalmers University of Technology, SE-412 96, Göteborg, Sweden
| | - Mats Persson
- Surface Science Research Centre and Department of Chemistry, University of Liverpool, Liverpool, L69 3BX, U.K., and Department of Applied Physics, Chalmers University of Technology, SE-412 96, Göteborg, Sweden
| | - Rasmita Raval
- Surface Science Research Centre and Department of Chemistry, University of Liverpool, Liverpool, L69 3BX, U.K., and Department of Applied Physics, Chalmers University of Technology, SE-412 96, Göteborg, Sweden
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33
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Schennach R, Hirschmugl C, Gilli E, Tysoe WT. A new method for performing polarization modulation infrared reflection-adsorption spectroscopy of surfaces. APPLIED SPECTROSCOPY 2009; 63:369-372. [PMID: 19281654 DOI: 10.1366/000370209787598960] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A new and relatively simple polarization modulation technique is presented and tested that enables the whole spectral range to be detected between 400 and 4000 cm(-1). This experiment is conventionally carried out using a photoelastic modulator that modulates incident plane polarized light through 90 degrees . This suffers from the drawback that it enables spectra to be collected only over a relatively narrow spectral range. As an alternative, a polarizer is placed in the beam and oriented at 45 degrees to the sample normal. This produces incident radiation fluxes with identical intensities for both s- and p-polarized light. A second polarizer is then modulated through 90 degrees and the surface spectrum is then extracted in the usual manner from the difference between these signals, normalized to their sum. The method is demonstrated for a self-assembled monolayer of 11-mercapto-undecanoicacid (11-MUA) on gold on mica, and it is shown that, while the resulting spectra are extremely sensitive to optical alignment, the method yields spectra that are in excellent agreement with published data.
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Affiliation(s)
- Robert Schennach
- Graz University of Technology, Institute of Solid State Physics, Petersgasse 16/2, 8010 Graz, Austria
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34
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ATR-IR spectroscopic study of L-lysine adsorption on amorphous silica. J Colloid Interface Sci 2009; 329:31-7. [DOI: 10.1016/j.jcis.2008.09.072] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 09/24/2008] [Accepted: 09/25/2008] [Indexed: 11/20/2022]
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35
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Jones G, Jenkins SJ. Insight into the Reduction of Pyruvic Acid to Lactic Acid over Cu{110}: The Crucial Role of Intramolecular Tunneling in Direct Hydrogenation. J Am Chem Soc 2008; 130:14483-92. [DOI: 10.1021/ja077786m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Glenn Jones
- The University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Stephen J. Jenkins
- The University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, U.K
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36
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Feyer V, Plekan O, Skála T, Cháb V, Matolín V, Prince KC. The Electronic Structure and Adsorption Geometry of l-Histidine on Cu(110). J Phys Chem B 2008; 112:13655-60. [DOI: 10.1021/jp805671h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vitaliy Feyer
- Sincrotrone Trieste S.C.p.A., Area Science Park, Strada Statale 14, km 163.5, I-34012 Basovizza, Trieste, Italy, Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, 16253 Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Vholešovičkách 2, 18000 Prague 8, Czech Republic
| | - Oksana Plekan
- Sincrotrone Trieste S.C.p.A., Area Science Park, Strada Statale 14, km 163.5, I-34012 Basovizza, Trieste, Italy, Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, 16253 Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Vholešovičkách 2, 18000 Prague 8, Czech Republic
| | - Tomáš Skála
- Sincrotrone Trieste S.C.p.A., Area Science Park, Strada Statale 14, km 163.5, I-34012 Basovizza, Trieste, Italy, Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, 16253 Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Vholešovičkách 2, 18000 Prague 8, Czech Republic
| | - Vladimír Cháb
- Sincrotrone Trieste S.C.p.A., Area Science Park, Strada Statale 14, km 163.5, I-34012 Basovizza, Trieste, Italy, Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, 16253 Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Vholešovičkách 2, 18000 Prague 8, Czech Republic
| | - Vladimír Matolín
- Sincrotrone Trieste S.C.p.A., Area Science Park, Strada Statale 14, km 163.5, I-34012 Basovizza, Trieste, Italy, Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, 16253 Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Vholešovičkách 2, 18000 Prague 8, Czech Republic
| | - Kevin C. Prince
- Sincrotrone Trieste S.C.p.A., Area Science Park, Strada Statale 14, km 163.5, I-34012 Basovizza, Trieste, Italy, Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, 16253 Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Vholešovičkách 2, 18000 Prague 8, Czech Republic
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37
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Vallée A, Humblot V, Méthivier C, Pradier CM. Glutathione adsorption from UHV to the liquid phase at various pH on gold and subsequent modification of protein interaction. SURF INTERFACE ANAL 2008. [DOI: 10.1002/sia.2636] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Haq S, Massey A, Moslemzadeh N, Robin A, Barlow SM, Raval R. Racemic versus enantiopure alanine on Cu(110): an experimental study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:10694-700. [PMID: 17803322 DOI: 10.1021/la700965d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The adsorption of racemic alanine on the Cu(110) surface has been compared to that of enantiopure alanine using low-energy electron diffraction (LEED), reflection absorption infrared spectroscopy (RAIRS), and scanning tunneling microscopy (STM). No evidence of chiral resolution at the surface was observed for the racemic system, indicating that the formation of separate enantiopure areas is not preferred. Also, in contrast to the enantiopure system, no chirally organized phase was observed for the racemic system. LEED shows that both systems display a common (3 x 2) phase at high coverage. However, the pathway and kinetic barriers to this phase differ markedly for the racemic and the enantiopure systems, with the racemic (3 x 2) appearing at a temperature that is more than 100 K below that required for the enantiopure system. In addition, we report intriguing complexities for the (3 x 2) LEED structure that is ubiquitous in amino acid/Cu(110) systems. First, a common (3 x 2) pattern with a zigzag distortion can be associated with both the racemic and enantiopure systems. For the racemic system, the coverage can be increased further to give a "true" (3 x 2) LEED pattern, which is a transformation that is impossible to enact for the enantiopure system. Most importantly, STM images of the "distorted" and "true" (3 x 2) structures created in the racemic system show subtle differences with neither arrangement being fully periodic over distances greater than a few molecules. Thus, the (3 x 2) phase appears to be more complicated than at first indicated and will require more complex models for a full interpretation.
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Affiliation(s)
- Sam Haq
- Surface Science Research Centre, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
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Cadwell KD, Alf ME, Abbott NL. Infrared Spectroscopy of Competitive Interactions between Liquid Crystals, Metal Salts, and Dimethyl Methylphosphonate at Surfaces. J Phys Chem B 2006; 110:26081-8. [PMID: 17181261 DOI: 10.1021/jp063211k] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the use of Fourier transform polarization modulation infrared reflection-absorption spectroscopy (PM-IRRAS) to characterize the influence of dimethyl methylphosphonate (DMMP) on the molecular interactions occurring within thin films of nitrile-containing liquid crystals supported on surfaces presenting metal perchlorate salts. Infrared spectra obtained using thin films of 4'-octyl-4-biphenylcarbonitrile (8CB) supported on copper(II) perchlorate salts reveal the nitrile groups of 8CB to be coordinated to the copper(II) on these surfaces, and subsequent exposure of the system to DMMP to result in the elimination of these coordinated nitrile groups. Concurrently, evidence of coordination of the phosphoryl group of DMMP with copper(II) is provided by measurement of a shift of the phosphoryl stretch from 1246 to 1198 cm(-1). In contrast, surfaces presenting nickel(II) perchlorate salts only weakly coordinate with DMMP [the phosphoryl peak shifts from 1246 to 1213 cm(-1) in the presence of nickel(II)], and exposure of 8CB to DMMP results in only partial loss of coordination of the nitrile groups of 8CB with nickel(II). These PM-IRRAS measurements and others reported in this article provide insights into the molecular origins of macroscopic ordering transitions that are observed when micrometer-thick films of nitrile-containing liquid crystals supported on copper(II) or nickel(II) perchlorate are exposed to DMMP: Upon exposure to DMMP, nematic phases of 4'-pentyl-4-biphenylcarbonitrile (5CB) supported on copper(II) perchlorate salts undergo ordering transitions, whereas 5CB supported on nickel(II) perchlorate salts do not. Our IR results support the hypothesis that these ordering transitions reflect the relative strengths of coordination interactions occurring between the 5CB, DMMP, and the metal salts at these interfaces.
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Affiliation(s)
- Katie D Cadwell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706-1607, USA
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Weinhold M, Soubatch S, Temirov R, Rohlfing M, Jastorff B, Tautz FS, Doose C. Structure and Bonding of the Multifunctional Amino Acid l-DOPA on Au(110). J Phys Chem B 2006; 110:23756-69. [PMID: 17125337 DOI: 10.1021/jp064956t] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In investigations of the proteins which are responsible for the surface adhesion of the blue mussel Mytilus edulis, an unusually frequent appearance of the otherwise rare amino acid 3-(3,4-dihydroxyphenyl)-L-alanine (L-DOPA) has been observed. This amino acid is thought to play a major role in the mechanism of mussel adhesion. Here we report a detailed structural and spectroscopic investigation of the interface between L-DOPA and a single-crystalline Au(110) model surface, with the aim of understanding fundamentals about the surface bonding of this amino acid and its role in mussel adhesion. Molecular layers are deposited by organic molecular beam deposition (OMBD) in an ultrahigh-vacuum environment. The following experimental techniques have been applied: ex situ Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), low-energy electron diffraction (LEED), high-resolution electron energy loss spectroscopy (HREELS), and scanning tunneling microscopy (STM). Vibrational spectra of isolated L-DOPA molecules and the zwitterionic bulk have been calculated using density functional theory (DFT). The predicted modes are assigned to observed spectra, allowing conclusions regarding the molecule-substrate and molecule-molecule interactions at the L-DOPA/Au(110) interface. We find that zwitterionic L-DOPA forms a monochiral, one-domain commensurate monolayer on Au(110), with the catechol rings on top of [110] gold rows, oriented parallel to the surface. The (2 x 1)-Au(110) surface reconstruction is not lifted. The carboxylate group is found in a bidentate or bridging configuration, the amino group is tilted out of the surface plane, and the hydroxyl groups do not dehydrogenate on Au(110). Similar to the case for the bulk, molecules form dimers on Au(110). However, the number of hydrogen bridge bonds between L-DOPA molecules is reduced as compared to the bulk. Thicker layers which are deposited onto the commensurate interface do not order in the bulk structure. In conclusion, our study shows that the aromatic ring system of L-DOPA functions as a surface anchor. Since it is also known that the hydroxyl groups support cross-link reactions between L-DOPA residues in the mussel glue protein, we can conclude that the catechol ring supports surface adhesion of mussel proteins via two independent functions.
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Affiliation(s)
- M Weinhold
- School of Engineering and Science, International University Bremen, Campus Ring 8, 28759 Bremen, Germany
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Bieri M, Bürgi T. D-penicillamine adsorption on gold: an in situ ATR-IR spectroscopic and QCM study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:8379-86. [PMID: 16981752 DOI: 10.1021/la061454y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The adsorption of penicillamine from ethanol on gold was studied in situ by attenuated total reflection infrared (ATR-IR) and quartz crystal microbalance (QCM) experiments. Both ATR-IR and QCM reveal a fast mass uptake. In ethanol, the molecule adopts a zwitterionic form. Upon adsorption, part of the molecules deprotonate at the amine group, which is a relatively slow process that goes along with a strong shift of the nu(as)(COO(-)) mode. Both ATR-IR and QCM confirm a physisorbed layer. ATR-IR furthermore shows that the latter consists of zwitterionic molecules only, whereas both zwitterionic and anionic species are found in the chemisorbed layer. The infrared spectra of the physisorbed and chemisorbed layers are rather different, and the molecules within both layers seem to be oriented with respect to the surface. The ATR-IR spectra furthermore indicate that all three functional groups of penicillamine (i.e., thiol, carboxylate, and amine) interact with the surface, and density functional theory calculations support this finding. QCM also shows that the molecule uses considerably more space on the surface than molecules of similar size, which supports a three-point interaction. The latter leads to a strong anchoring of the molecule to the metal, which may explain the exceptional capability of penicillamine to bind metals.
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Affiliation(s)
- Marco Bieri
- Faculté des Sciences, Institut de Microtechnique, Université de Neuchâtel, Rue Emile Argand 11, Bâtiment G, 2009-Neuchâtel, Switzerland
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