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Futera Z, Blumberger J. Adsorption of Amino Acids on Gold: Assessing the Accuracy of the GolP-CHARMM Force Field and Parametrization of Au-S Bonds. J Chem Theory Comput 2018; 15:613-624. [PMID: 30540462 DOI: 10.1021/acs.jctc.8b00992] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The interaction of amino acids with metal electrodes plays a crucial role in bioelectrochemistry and the emerging field of bionanoelectronics. Here we present benchmark calculations of the adsorption structure and energy of all natural amino acids on Au(111) in vacuum using a van-der-Waals density functional (revPBE-vdW) that showed good performance on the S22 set of weakly bound dimers (mean relative unsigned error (MRUE) wrt CCSD(T)/CBS = 13.3%) and adsorption energies of small organic molecules on Au(111) (MRUE wrt experiment = 11.2%). The vdW-DF results are then used to assess the accuracy of a popular force field for Au-amino acid interactions, GolP-CHARMM, which explicitly describes image charge interactions via rigid-rod dipoles. We find that while the force field underestimates adsorption distances, it does reproduce the binding energy rather well (MRUE wrt revPBE-vdW = 11.3%) with the MRUE decreasing in the order Cys, Met > amines > aliphatic > carboxylic > aromatic. We also present a parametrization of the bonding interaction between sulfur-containing molecules and the Au(111) surface and report force field parameters that are compatible with GolP-CHARMM. We believe the vdW-DF calculations presented herein will provide useful reference data for further force field development, and that the new Au-S bonding parameters will enable improved simulations of proteins immobilized on Au-electrodes via S-linkages.
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Affiliation(s)
- Zdenek Futera
- Department of Physics and Astronomy and Thomas-Young-Centre , University College London , Gower Street , London , WC1E 6BT , U.K
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas-Young-Centre , University College London , Gower Street , London , WC1E 6BT , U.K.,Institute for Advanced Study , Technische Universität München , Lichtenbergstrasse 2 a , D-85748 Garching , Germany
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Steinmann SN, Ferreira De Morais R, Götz AW, Fleurat-Lessard P, Iannuzzi M, Sautet P, Michel C. Force Field for Water over Pt(111): Development, Assessment, and Comparison. J Chem Theory Comput 2018; 14:3238-3251. [PMID: 29660272 DOI: 10.1021/acs.jctc.7b01177] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric, or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force-field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water, (ii) a Gaussian term to improve the surface corrugation, and (iii) two terms describing the angular dependence of the interaction energy. The 12 parameters of this force field are fitted against a set of 210 adsorption geometries of water on Pt(111). The performance of GAL17 is compared to several other approaches that have not been validated against extensive first-principles computations yet. Their respective accuracy is evaluated on an extended set of 802 adsorption geometries of H2O on Pt(111), 52 geometries derived from icelike layers, and an MD simulation of an interface between a c(4 × 6) Pt(111) surface and a water layer of 14 Å thickness. The newly developed GAL17 force field provides a significant improvement over previously existing force fields for Pt(111)/H2O interactions. Its well-balanced performance suggests that it is an ideal candidate to generate relevant geometries for the metal/water interface, paving the way to a representative sampling of the equilibrium distribution at the interface and to predict solvation free energies at the solid/liquid interface.
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Affiliation(s)
- Stephan N Steinmann
- Univ Lyon, Ecole Normale Supérieure de Lyon , CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182 , 46 allée d'Italie , F-69364 Lyon , France
| | - Rodrigo Ferreira De Morais
- Univ Lyon, Ecole Normale Supérieure de Lyon , CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182 , 46 allée d'Italie , F-69364 Lyon , France
| | - Andreas W Götz
- San Diego Supercomputer Center , University of California San Diego , La Jolla , California 92093 , United States
| | - Paul Fleurat-Lessard
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB, UMR 6302, CNRS) , Université de Bourgogne Franche-Comté , 9 Avenue Alain Savary , 21078 Dijon , France
| | - Marcella Iannuzzi
- Institut für Chemie , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zurich , Switzerland
| | | | - Carine Michel
- Univ Lyon, Ecole Normale Supérieure de Lyon , CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182 , 46 allée d'Italie , F-69364 Lyon , France
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Kayarkatte MK, Delikaya Ö, Roth C. Freestanding Catalyst Layers: A Novel Electrode Fabrication Technique for PEM Fuel Cells via Electrospinning. ChemElectroChem 2017. [DOI: 10.1002/celc.201600530] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Manoj Krishna Kayarkatte
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Takustraße 3 14195 Berlin Germany
| | - Öznur Delikaya
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Takustraße 3 14195 Berlin Germany
| | - Christina Roth
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Takustraße 3 14195 Berlin Germany
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Ayling SA, Burke DJ, Salter T, Brown WA. Desorption and crystallisation of binary 2-propanol and water ices adsorbed on graphite. RSC Adv 2017. [DOI: 10.1039/c7ra10410c] [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] Open
Abstract
Strong interactions between 2-propanol and water ice cause marked changes in the crystallisation kinetics and desorption of water.
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Golze D, Iannuzzi M, Nguyen MT, Passerone D, Hutter J. Simulation of Adsorption Processes at Metallic Interfaces: An Image Charge Augmented QM/MM Approach. J Chem Theory Comput 2013; 9:5086-97. [DOI: 10.1021/ct400698y] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dorothea Golze
- Institute of Physical Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Marcella Iannuzzi
- Institute of Physical Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Manh-Thuong Nguyen
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, I-34151 Trieste, Italy
| | - Daniele Passerone
- Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces Laboratory, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland
| | - Jürg Hutter
- Institute of Physical Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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Herbers CR, Li C, van der Vegt NFA. Grand challenges in quantum-classical modeling of molecule-surface interactions. J Comput Chem 2013; 34:1177-88. [DOI: 10.1002/jcc.23247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/27/2012] [Accepted: 01/03/2013] [Indexed: 11/11/2022]
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Fritsch S, Poblete S, Junghans C, Ciccotti G, Delle Site L, Kremer K. Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir. PHYSICAL REVIEW LETTERS 2012; 108:170602. [PMID: 22680848 DOI: 10.1103/physrevlett.108.170602] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Indexed: 05/04/2023]
Abstract
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an interpretation in terms of an effective generalized grand canonical approach. The method is applied to liquid water at ambient conditions.
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Affiliation(s)
- S Fritsch
- Max Planck Institut für Polymerforschung, Ackermannweg 10, D-55128 Mainz, Germany
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Paredis K, Ono LK, Mostafa S, Li L, Zhang Z, Yang JC, Barrio L, Frenkel AI, Cuenya BR. Structure, Chemical Composition, And Reactivity Correlations during the In Situ Oxidation of 2-Propanol. J Am Chem Soc 2011; 133:6728-35. [DOI: 10.1021/ja200178f] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kristof Paredis
- Department of Physics, University of Central Florida, Orlando, Florida 32816, United States
| | - Luis K. Ono
- Department of Physics, University of Central Florida, Orlando, Florida 32816, United States
| | - Simon Mostafa
- Department of Physics, University of Central Florida, Orlando, Florida 32816, United States
| | - Long Li
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhongfan Zhang
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Judith C. Yang
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Laura Barrio
- Instituto de Catálisis y Petroleoquímica, CSIC, Madrid 28049
| | - Anatoly I. Frenkel
- Department of Physics, Yeshiva University, New York, New York 10016, United States
| | - Beatriz Roldan Cuenya
- Department of Physics, University of Central Florida, Orlando, Florida 32816, United States
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Comparative Theoretical Study of Adsorption and Dehydrogenation of Formic Acid, Hydrazine and Isopropanol on Pd(111) Surface. Catal Letters 2011. [DOI: 10.1007/s10562-011-0553-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Youngs TGA, Hardacre C. Effect of hydrophobic nanopatches within an ionic surface on the structure of liquids. Phys Chem Chem Phys 2011; 13:582-5. [DOI: 10.1039/c0cp01838d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Poblete S, Praprotnik M, Kremer K, Delle Site L. Coupling different levels of resolution in molecular simulations. J Chem Phys 2010; 132:114101. [DOI: 10.1063/1.3357982] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Rossinsky E, Tarmyshov KB, Böhm MC, Müller-Plathe F. Properties of Polyvinyl Alcohol Oligomers: A Molecular Dynamics Study. MACROMOL THEOR SIMUL 2009. [DOI: 10.1002/mats.200900030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Xu Y, Zhang B, Wu S, Xia Y. The adsorption of dopamine on gold and its interactions with iron(III) ions studied by microcantilevers. Anal Chim Acta 2009; 649:117-22. [DOI: 10.1016/j.aca.2009.06.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 05/23/2009] [Accepted: 06/22/2009] [Indexed: 10/20/2022]
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14
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Iori F, Corni S. Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces. J Comput Chem 2008; 29:1656-66. [DOI: 10.1002/jcc.20928] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ghiringhelli LM, Delle Site L. Phenylalanine near Inorganic Surfaces: Conformational Statistics vs Specific Chemistry. J Am Chem Soc 2008; 130:2634-8. [DOI: 10.1021/ja077817d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luca M. Ghiringhelli
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Luigi Delle Site
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Tarmyshov KB, Müller-Plathe F. Treatment of electrostatic interactions in simulations of the interface between transition metal surfaces and organic matter: the discrete classical model and the reaction-field dielectric method. Phys Chem Chem Phys 2008; 10:442-8. [DOI: 10.1039/b708570b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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