1
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Pederson JP, McDaniel JG. PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics. J Chem Phys 2024; 161:034103. [PMID: 39007371 DOI: 10.1063/5.0219851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100 ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.
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Affiliation(s)
- John P Pederson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Jesse G McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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2
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Zhai Z, Chen Q, Wang Y, Ren W, Guo P. Orientational dynamics of the water layer adjacent to Au surface accelerated by polarization effect. J Chem Phys 2024; 160:234704. [PMID: 38884408 DOI: 10.1063/5.0198777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
The orientation and rearrangement of water on a gold electrode significantly influences its physicochemical heterogeneous performance. Despite numerous experimental and theoretical studies aimed at uncovering the structural characteristics of interfacial water, the orientational behavior resulting from electrode-induced rearrangements remains a subject of ongoing debate. Here, we employed molecular dynamics simulations to investigate the adaptive structure and dynamics properties of interfacial water on Au(111) and Au(100) surfaces by considering a polarizable model for Au atoms in comparison with the non-polarizable model. Compared to the nonpolarizable systems, the polarization effect can enhance the interaction between water molecules and the gold surface. Unexpectedly, the rotational dynamics directly associated with the orientational behavior of water adjacent to the gold surface is accelerated, thereby reducing the hydrogen bond lifetime. The underlying mechanism for this anomalous phenomenon originates from the polarization effect, which induces the attraction of the positive hydrogen atoms to the surface by the negative image charge. This leads to a change in orientation that disrupts the hydrogen bonds in the first water layer and subsequently accelerates reorientation dynamics of water molecules adjacent to the gold surface. These results shed light on the intricate interplay between polarization effects and water molecule dynamics on metal surfaces, establishing the foundation for the rational regulation of the orientation of interfacial water.
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Affiliation(s)
- Zhidong Zhai
- Department of Physics, Shanghai Key Laboratory of High Temperature Superconductors, International Centre of Quantum and Molecular Structures, Shanghai University, Shanghai 200444, China
| | - Qun Chen
- Department of Physics, Shanghai Key Laboratory of High Temperature Superconductors, International Centre of Quantum and Molecular Structures, Shanghai University, Shanghai 200444, China
| | - Yin Wang
- Department of Physics, Shanghai Key Laboratory of High Temperature Superconductors, International Centre of Quantum and Molecular Structures, Shanghai University, Shanghai 200444, China
| | - Wei Ren
- Department of Physics, Shanghai Key Laboratory of High Temperature Superconductors, International Centre of Quantum and Molecular Structures, Shanghai University, Shanghai 200444, China
| | - Pan Guo
- Department of Physics, Shanghai Key Laboratory of High Temperature Superconductors, International Centre of Quantum and Molecular Structures, Shanghai University, Shanghai 200444, China
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3
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Fyta M. Functionalized electrodes embedded in nanopores: read-out enhancement? Chem Asian J 2023; 18:e202200916. [PMID: 36372991 PMCID: PMC10107472 DOI: 10.1002/asia.202200916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/12/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
In this review, functionalized nanogaps embedded in nanopores are discussed in view of their high biosensitivity in detecting biomolecules, their length, type, and sequence. Specific focus is given on nanoelectrodes functionalized with tiny nanometer-sized diamond-like particles offering vast functionalization possibilities for gold junction electrodes. This choice of the functionalization, in turn, offers nucleotide-specific binding possibilities improving the detection signals arising from such functionalized electrodes potentially embedded in a nanopore. The review sheds light onto the use and enhancement of the tunnelling recognition in functionalized nanogaps towards sensing DNA nucleotides and mutation detection, providing important input for a practical realization.
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Affiliation(s)
- Maria Fyta
- Computational Biotechnology, RWTH-Aachen University, Worringerweg 3, 52072, Aachen, Germany
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4
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Takahashi K, Nakano H, Sato H. Accelerated constant-voltage quantum mechanical/molecular mechanical method for molecular systems at electrochemical interfaces. J Chem Phys 2022; 157:234107. [PMID: 36550044 DOI: 10.1063/5.0128358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The structure and electronic properties of a molecule at an electrochemical interface are changed by interactions with the electrode surface and the electrolyte solution, which can be significantly modulated by an applied voltage. We present an efficient self-consistent quantum mechanics/molecular mechanics (QM/MM) approach to study a physisorbed molecule at a metal electrode-electrolyte interface under the constant-voltage condition. The approach employs a classical polarizable double electrode model, which enables us to study the QM/MM system in the constant-voltage ensemble. A mean-field embedding approximation is further introduced in order to overcome the difficulties associated with statistical sampling of the electrolyte configurations. The results of applying the method to a test system indicate that the adsorbed molecule is no less or slightly more polarized at the interface than in the bulk electrolyte solution. The geometry of the horizontally adsorbed molecule is modulated by their electrostatic interactions with the polarizable electrode surfaces and also the interactions with cations attracted toward the interface when the adsorbate is reduced. We also demonstrate that the approach can be used to quantitatively evaluate the reorganization energy of a one electron reduction reaction of a molecule in an electrochemical cell.
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Affiliation(s)
- Ken Takahashi
- Department of Molecular Engineering, Kyoto University, Kyoto Daigaku Katsura, Kyoto 615-8246, Japan
| | - Hiroshi Nakano
- CD-FMat, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba Central 2, Tsukuba, Ibaraki 305-8568, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto Daigaku Katsura, Kyoto 615-8246, Japan
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5
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Seeber P, Seidenath S, Steinmetzer J, Gräfe S. Growing Spicy
ONIOMs
: Extending and generalizing concepts of
ONIOM
and many body expansions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Phillip Seeber
- Institute of Physical Chemistry Friedrich Schiller University Jena Jena Germany
| | - Sebastian Seidenath
- Institute of Physical Chemistry Friedrich Schiller University Jena Jena Germany
| | | | - Stefanie Gräfe
- Institute of Physical Chemistry Friedrich Schiller University Jena Jena Germany
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6
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Li P, Liu Y, Chen S. Microscopic EDL Structures and Charge-Potential Relation on Stepped Platinum Surface: Insights from the Ab Initio Molecular Dynamics Simulations. J Chem Phys 2022; 156:104701. [DOI: 10.1063/5.0080104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Peng Li
- College of Chemistry and Molecular Sciences, Wuhan University, China
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7
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Wang C, Wang Y, Gan Z, Lu Y, Qian C, Huo F, He H, Zhang S. Topological engineering of two-dimensional ionic liquid islands for high structural stability and CO 2 adsorption selectivity. Chem Sci 2021; 12:15503-15510. [PMID: 35003578 PMCID: PMC8654070 DOI: 10.1039/d1sc05431g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/29/2021] [Indexed: 11/21/2022] Open
Abstract
Ionic liquids (ILs) as green solvents and catalysts are highly attractive in the field of chemistry and chemical engineering. Their interfacial assembly structure and function are still far less well understood. Herein, we use coupling first-principles and molecular dynamics simulations to resolve the structure, properties, and function of ILs deposited on the graphite surface. Four different subunits driven by hydrogen bonds are identified first, and can assemble into close-packed and sparsely arranged annular 2D IL islands (2DIIs). Meanwhile, we found that the formation energy and HOMO–LUMO gap decrease exponentially as the island size increases via simulating a series of 2DIIs with different topological features. However, once the size is beyond the critical value, both the structural stability and electrical structure converge. Furthermore, the island edges are found to be dominant adsorption sites for CO2 and better than other pure metal surfaces, showing an ultrahigh adsorption selectivity (up to 99.7%) for CO2 compared with CH4, CO, or N2. Such quantitative structure–function relations of 2DIIs are meaningful for engineering ILs to efficiently promote their applications, such as the capture and conversion of CO2. Multi-scale simulations reveal the structure and properties of the two-dimensional ionic liquid islands supported by graphite, and the island edges show an ultrahigh adsorption selectivity for CO2 compared with CH4, CO, or N2.![]()
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Affiliation(s)
- Chenlu Wang
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | - Yanlei Wang
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhongdong Gan
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
| | - Yumiao Lu
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
| | - Cheng Qian
- School of Materials Science and Engineering, Ulsan National Institute of Science and Technology Ulsan 44919 South Korea
| | - Feng Huo
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
| | - Hongyan He
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China.,Innovation Academy for Green Manufacture, Chinese Academy of Sciences Beijing 100190 China.,Dalian National Laboratory for Clean Energy Dalian 116023 Liaoning China
| | - Suojiang Zhang
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
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8
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Yang X, Zhuang Y, Zhu J, Le J, Cheng J. Recent progress on multiscale modeling of electrochemistry. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1559] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xiao‐Hui Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces iChEM, College of Chemistry and Chemical Engineering, Xiamen University Xiamen China
| | - Yong‐Bin Zhuang
- State Key Laboratory of Physical Chemistry of Solid Surfaces iChEM, College of Chemistry and Chemical Engineering, Xiamen University Xiamen China
| | - Jia‐Xin Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces iChEM, College of Chemistry and Chemical Engineering, Xiamen University Xiamen China
| | - Jia‐Bo Le
- Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo China
| | - Jun Cheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces iChEM, College of Chemistry and Chemical Engineering, Xiamen University Xiamen China
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9
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Abstract
QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.
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Affiliation(s)
- Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Tanmoy Pal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Luke Xie
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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10
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Clabaut P, Staub R, Galiana J, Antonetti E, Steinmann SN. Water adlayers on noble metal surfaces: Insights from energy decomposition analysis. J Chem Phys 2020; 153:054703. [DOI: 10.1063/5.0013040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Paul Clabaut
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - Ruben Staub
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - Joachim Galiana
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - Elise Antonetti
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - 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
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11
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Takahashi K, Nakano H, Sato H. A polarizable molecular dynamics method for electrode–electrolyte interfacial electron transfer under the constant chemical-potential-difference condition on the electrode electrons. J Chem Phys 2020; 153:054126. [DOI: 10.1063/5.0020619] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Ken Takahashi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hiroshi Nakano
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan
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12
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Tocci G, Bilichenko M, Joly L, Iannuzzi M. Ab initio nanofluidics: disentangling the role of the energy landscape and of density correlations on liquid/solid friction. NANOSCALE 2020; 12:10994-11000. [PMID: 32426791 DOI: 10.1039/d0nr02511a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Despite relevance to water purification and renewable energy conversion membranes, the molecular mechanisms underlying water slip are poorly understood. We disentangle the static and dynamical origin of water slippage on graphene, hBN and MoS2 by means of large-scale ab initio molecular dynamics. Accounting for the role of the electronic structure of the interface is essential to determine that water slips five and eleven times faster on graphene compared to hBN and to MoS2, respectively. Intricate changes in the water energy landscape as well as in the density correlations of the fluid provide, respectively, the main static and dynamical origin of water slippage. Surprisingly, the timescales of the density correlations are the same on graphene and hBN, whereas they are longer on MoS2 and yield a 100% slowdown in the flow of water on this material. Our results pave the way for an in silico first principles design of materials with enhanced water slip, through the modification of properties connected not only to the structure, but also to the dynamics of the interface.
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Affiliation(s)
- Gabriele Tocci
- Department of Chemistry, Universität Zürich, 8057 Zürich, Switzerland.
| | - Maria Bilichenko
- Department of Chemistry, Universität Zürich, 8057 Zürich, Switzerland.
| | - Laurent Joly
- Univ Lyon, Univ Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France and Institut Universitaire de France (IUF), France
| | - Marcella Iannuzzi
- Department of Chemistry, Universität Zürich, 8057 Zürich, Switzerland.
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13
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Kühne TD, Iannuzzi M, Del Ben M, Rybkin VV, Seewald P, Stein F, Laino T, Khaliullin RZ, Schütt O, Schiffmann F, Golze D, Wilhelm J, Chulkov S, Bani-Hashemian MH, Weber V, Borštnik U, Taillefumier M, Jakobovits AS, Lazzaro A, Pabst H, Müller T, Schade R, Guidon M, Andermatt S, Holmberg N, Schenter GK, Hehn A, Bussy A, Belleflamme F, Tabacchi G, Glöß A, Lass M, Bethune I, Mundy CJ, Plessl C, Watkins M, VandeVondele J, Krack M, Hutter J. CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations. J Chem Phys 2020; 152:194103. [PMID: 33687235 DOI: 10.1063/5.0007045] [Citation(s) in RCA: 966] [Impact Index Per Article: 241.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.
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Affiliation(s)
- Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Mauro Del Ben
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Patrick Seewald
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Frederick Stein
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Teodoro Laino
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | - Rustam Z Khaliullin
- Department of Chemistry, McGill University, CH-801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Ole Schütt
- Department of Materials, ETH Zürich, CH-8092 Zürich, Switzerland
| | | | - Dorothea Golze
- Department of Applied Physics, Aalto University, Otakaari 1, FI-02150 Espoo, Finland
| | - Jan Wilhelm
- Institute of Theoretical Physics, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Sergey Chulkov
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | | | - Valéry Weber
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | | | | | | | | | - Hans Pabst
- Intel Extreme Computing, Software and Systems, Zürich, Switzerland
| | - Tiziano Müller
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Robert Schade
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Manuel Guidon
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Samuel Andermatt
- Integrated Systems Laboratory, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Nico Holmberg
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Gregory K Schenter
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Anna Hehn
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Augustin Bussy
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Fabian Belleflamme
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Gloria Tabacchi
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100 Como, Italy
| | - Andreas Glöß
- BASF SE, Carl-Bosch-Straße 38, D-67056 Ludwigshafen am Rhein, Germany
| | - Michael Lass
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Iain Bethune
- Hartree Centre, Science and Technology Facilities Council, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Christopher J Mundy
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Christian Plessl
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Matt Watkins
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | - Joost VandeVondele
- Swiss National Supercomputing Centre (CSCS), ETH Zürich, Zürich, Switzerland
| | - Matthias Krack
- Laboratory for Scientific Computing and Modelling, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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14
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Schwarz K, Sundararaman R. The electrochemical interface in first-principles calculations. SURFACE SCIENCE REPORTS 2020; 75:10.1016/j.surfrep.2020.100492. [PMID: 34194128 PMCID: PMC8240516 DOI: 10.1016/j.surfrep.2020.100492] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
First-principles predictions play an important role in understanding chemistry at the electrochemical interface. Electronic structure calculations are straightforward for vacuum interfaces, but do not easily account for the interfacial fields and solvation that fundamentally change the nature of electrochemical reactions. Prevalent techniques for first-principles prediction of electrochemical processes range from expensive explicit solvation using ab initio molecular dynamics, through a hierarchy of continuum solvation techniques, to neglecting solvation and interfacial field effects entirely. Currently, no single approach reliably captures all relevant effects of the electrochemical double layer in first-principles calculations. This review systematically lays out the relation between all major approaches to first-principles electrochemistry, including the key approximations and their consequences for accuracy and computational cost. Focusing on ab initio methods for thermodynamic properties of aqueous interfaces, we first outline general considerations for modeling electrochemical interfaces, including solvent and electrolyte dynamics and electrification. We then present the specifics of various explicit and implicit models of the solvent and electrolyte. Finally, we discuss the compromise between computational efficiency and accuracy, and identify key outstanding challenges and future opportunities in the wide range of techniques for first-principles electrochemistry.
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Affiliation(s)
- Kathleen Schwarz
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, Maryland 20899, USA
| | - Ravishankar Sundararaman
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 8th St., Troy, New York 12180, USA
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15
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Scarbath-Evers LK, Hammer R, Golze D, Brehm M, Sebastiani D, Widdra W. From flat to tilted: gradual interfaces in organic thin film growth. NANOSCALE 2020; 12:3834-3845. [PMID: 31995082 DOI: 10.1039/c9nr06592j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We investigate domain formation and local morphology of thin films of α-sexithiophene (α-6T) on Au(100) beyond monolayer coverage by combining high resolution scanning tunneling microscopy (STM) experiments with electronic structure theory calculations and computational structure search. We report a layerwise growth of highly-ordered enantiopure domains. For the second and third layer, we show that the molecular orbitals of individual α-6T molecules can be well resolved by STM, providing access to detailed information on the molecular orientation. We find that already in the second layer the molecules abandon the flat adsorption structure of the monolayer and adopt a tilted conformation. Although the observed tilted arrangement resembles the orientation of α-6T in the bulk, the observed morphology does not yet correspond to a well-defined surface of the α-6T bulk structure. A similar behavior is found for the third layer indicating a growth mechanism where the bulk structure is gradually adopted over several layers.
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Affiliation(s)
| | - René Hammer
- Martin-Luther University Halle-Wittenberg, Institute of Physics, Halle/Saale, Germany.
| | - Dorothea Golze
- Department of Applied Physics, Aalto University School of Science, FI-00076 Aalto, Finland
| | - Martin Brehm
- Martin-Luther University Halle-Wittenberg, Institute of Chemistry, Halle/Saale, Germany
| | - Daniel Sebastiani
- Martin-Luther University Halle-Wittenberg, Institute of Chemistry, Halle/Saale, Germany
| | - Wolf Widdra
- Martin-Luther University Halle-Wittenberg, Institute of Physics, Halle/Saale, Germany.
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16
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Dufils T, Jeanmairet G, Rotenberg B, Sprik M, Salanne M. Simulating Electrochemical Systems by Combining the Finite Field Method with a Constant Potential Electrode. PHYSICAL REVIEW LETTERS 2019; 123:195501. [PMID: 31765198 DOI: 10.1103/physrevlett.123.195501] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Indexed: 06/10/2023]
Abstract
A better understanding of interfacial mechanisms is needed to improve the performances of electrochemical devices. Yet, simulating an electrode surface at fixed electrolyte composition remains a challenge. Here, we apply a finite electric field to a single electrode held at constant potential and in contact with an aqueous ionic solution, using classical molecular dynamics. The polarization yields two electrochemical interfaces on opposite sides of the same metal slab. The net charge on one electrode surface is the opposite of the net charge on the other, maintaining overall charge neutrality of the metal. The electrode surface charge fluctuations are compensated by the adsorption of ions from the electrolyte, forming a pair of electric double layers with aligned dipoles. This opens the way towards the efficient simulation of electrochemical interfaces using any flavor of molecular dynamics, from classical to first-principles-based methods.
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Affiliation(s)
- Thomas Dufils
- Sorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
| | - Guillaume Jeanmairet
- Sorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
| | - Benjamin Rotenberg
- Sorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
| | - Michiel Sprik
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Mathieu Salanne
- Sorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
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17
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Dou M, Maier FC, Fyta M. The influence of a solvent on the electronic transport across diamondoid-functionalized biosensing electrodes. NANOSCALE 2019; 11:14216-14225. [PMID: 31317158 DOI: 10.1039/c9nr03235e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Electrodes embedded in nanopores have the potential to detect the identity of biomolecules, such as DNA. This identification is typically being done through electronic current measurements across the electrodes in a solvent. In this work, using quantum-mechanical calculations, we qualitatively present the influence of this solvent on the current signals. For this, we model electrodes functionalized with a small diamond-like molecule known as diamondoid and place a DNA nucleotide within the electrode gap. The influence of an aqueous solvent is taken explicitly into account through Quantum-Mechanics/Molecular Mechanics (QM/MM) simulations. From these, we could clearly reveal that at the (111) surface of the Au electrode, water molecules form an adlayer-like structure through hydrogen bond networks. From the temporal evolution of the hydrogen bond between a nucleotide and the functionalizing diamondoid, we could extract information on the conductance across the device. In order to evaluate the influence of the solvent, we compare these results with ground-state electronic structure calculations in combination with the non-equilibrium Green's function (NEGF) approach. These allow access to the electronic transport across the electrodes and show a difference in the detection signals with and without the aqueous solution. We analyze the results with respect to the density of states in the device. In the end, we demonstrate that the presence of water does not hinder the detection of a mutation over a healthy DNA nucleotide. We discuss these results in view of sequencing DNA with nanopores.
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Affiliation(s)
- Maofeng Dou
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
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18
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Bedrov D, Piquemal JP, Borodin O, MacKerell AD, Roux B, Schröder C. Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields. Chem Rev 2019; 119:7940-7995. [PMID: 31141351 PMCID: PMC6620131 DOI: 10.1021/acs.chemrev.8b00763] [Citation(s) in RCA: 284] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Indexed: 11/30/2022]
Abstract
Many applications in chemistry, biology, and energy storage/conversion research rely on molecular simulations to provide fundamental insight into structural and transport properties of materials with high ionic concentrations. Whether the system is comprised entirely of ions, like ionic liquids, or is a mixture of a polar solvent with a salt, e.g., liquid electrolytes for battery applications, the presence of ions in these materials results in strong local electric fields polarizing solvent molecules and large ions. To predict properties of such systems from molecular simulations often requires either explicit or mean-field inclusion of the influence of polarization on electrostatic interactions. In this manuscript, we review the pros and cons of different treatments of polarization ranging from the mean-field approaches to the most popular explicit polarization models in molecular dynamics simulations of ionic materials. For each method, we discuss their advantages and disadvantages and emphasize key assumptions as well as their adjustable parameters. Strategies for the development of polarizable models are presented with a specific focus on extracting atomic polarizabilities. Finally, we compare simulations using polarizable and nonpolarizable models for several classes of ionic systems, discussing the underlying physics that each approach includes or ignores, implications for implementation and computational efficiency, and the accuracy of properties predicted by these methods compared to experiments.
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Affiliation(s)
- Dmitry Bedrov
- Department
of Materials Science & Engineering, University of Utah, 122 South Central Campus Drive, Room 304, Salt Lake City, Utah 84112, United States
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, CC137, 4 Place Jussieu, Tour 12-13, 4ème étage, 75252 Paris Cedex 05, France
- Institut
Universitaire de France, 75005, Paris Cedex 05, France
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Oleg Borodin
- Electrochemistry
Branch, Sensors and Electron Devices Directorate, Army Research Laboratory, 2800 Powder Mill Road, Adelphi, Maryland 20703, United
States
| | - Alexander D. MacKerell
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Benoît Roux
- Department
of Biochemistry and Molecular Biology, Gordon Center for Integrative
Science, University of Chicago, 929 57th Street, Chicago, Illinois 60637, United States
| | - Christian Schröder
- Department
of Computational Biological Chemistry, University
of Vienna, Währinger Strasse 17, A-1090 Vienna, Austria
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19
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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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20
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Hofer TS, de Visser SP. Editorial: Quantum Mechanical/Molecular Mechanical Approaches for the Investigation of Chemical Systems - Recent Developments and Advanced Applications. Front Chem 2018; 6:357. [PMID: 30271768 PMCID: PMC6146044 DOI: 10.3389/fchem.2018.00357] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/30/2018] [Indexed: 12/28/2022] Open
Affiliation(s)
- Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Sam P de Visser
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
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21
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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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22
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Geada IL, Ramezani-Dakhel H, Jamil T, Sulpizi M, Heinz H. Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential. Nat Commun 2018; 9:716. [PMID: 29459638 PMCID: PMC5818522 DOI: 10.1038/s41467-018-03137-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/22/2018] [Indexed: 12/11/2022] Open
Abstract
Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard–Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals. Molecular dynamics models for predicting the behavior of metallic nanostructures typically do not take into account polarization effects in metals. Here, the authors introduce a polarizable Lennard–Jones potential that provides quantitative insight into the role of induced charges at metal surfaces and related complex material interfaces.
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Affiliation(s)
- Isidro Lorenzo Geada
- Department of Physics, University of Mainz, Staudingerweg 7, D-55128, Mainz, Germany
| | - Hadi Ramezani-Dakhel
- Department of Polymer Engineering, University of Akron, 250S Forge St, Akron, OH, 44325, USA.,Institute for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL, 60637, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Tariq Jamil
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, 3415 Colorado Ave, Boulder, CO, 80309, USA
| | - Marialore Sulpizi
- Department of Physics, University of Mainz, Staudingerweg 7, D-55128, Mainz, Germany.
| | - Hendrik Heinz
- Department of Polymer Engineering, University of Akron, 250S Forge St, Akron, OH, 44325, USA. .,Department of Chemical and Biological Engineering, University of Colorado-Boulder, 3415 Colorado Ave, Boulder, CO, 80309, USA.
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23
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Feldt J, Miranda S, Pratas F, Roma N, Tomás P, Mata RA. Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program. J Chem Phys 2017; 147:244105. [PMID: 29289129 DOI: 10.1063/1.5009820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.
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Affiliation(s)
- Jonas Feldt
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Sebastião Miranda
- INESC-ID/IST, Universidade de Lisboa, Rua Alves Redol, 1000-029 Lisboa, Portugal
| | - Frederico Pratas
- INESC-ID/IST, Universidade de Lisboa, Rua Alves Redol, 1000-029 Lisboa, Portugal
| | - Nuno Roma
- INESC-ID/IST, Universidade de Lisboa, Rua Alves Redol, 1000-029 Lisboa, Portugal
| | - Pedro Tomás
- INESC-ID/IST, Universidade de Lisboa, Rua Alves Redol, 1000-029 Lisboa, Portugal
| | - Ricardo A Mata
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
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24
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Dohn AO, Jónsson EÖ, Levi G, Mortensen JJ, Lopez-Acevedo O, Thygesen KS, Jacobsen KW, Ulstrup J, Henriksen NE, Møller KB, Jónsson H. Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex. J Chem Theory Comput 2017; 13:6010-6022. [PMID: 29083921 DOI: 10.1021/acs.jctc.7b00621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt2(P2O5H2)4]4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.
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Affiliation(s)
- A O Dohn
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland
| | - E Ö Jónsson
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland
| | - G Levi
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - J J Mortensen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - O Lopez-Acevedo
- Department of Applied Physics, Aalto University , 02150 Espoo, Finland
| | - K S Thygesen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - K W Jacobsen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - J Ulstrup
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - N E Henriksen
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - K B Møller
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - H Jónsson
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland.,Department of Applied Physics, Aalto University , 02150 Espoo, Finland
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25
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Le J, Iannuzzi M, Cuesta A, Cheng J. Determining Potentials of Zero Charge of Metal Electrodes versus the Standard Hydrogen Electrode from Density-Functional-Theory-Based Molecular Dynamics. PHYSICAL REVIEW LETTERS 2017; 119:016801. [PMID: 28731734 DOI: 10.1103/physrevlett.119.016801] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Indexed: 05/12/2023]
Abstract
We develop a computationally efficient scheme to determine the potentials of zero charge (PZC) of metal-water interfaces with respect to the standard hydrogen electrode. We calculate the PZC of Pt(111), Au(111), Pd(111) and Ag(111) at a good accuracy using this scheme. Moreover, we find that the interface dipole potentials are almost entirely caused by charge transfer from water to the surfaces, the magnitude of which depends on the bonding strength between water and the metals, while water orientation hardly contributes at the PZC conditions.
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Affiliation(s)
- Jiabo Le
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Marcella Iannuzzi
- Department of Physical Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Angel Cuesta
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Jun Cheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
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26
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Vatamanu J, Bedrov D, Borodin O. On the application of constant electrode potential simulation techniques in atomistic modelling of electric double layers. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1279287] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Jenel Vatamanu
- Materials Science & Engineering Department, University of Utah, Salt Lake City, UT, USA
- Electrochemistry Branch, Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, MD, USA
| | - Dmitry Bedrov
- Materials Science & Engineering Department, University of Utah, Salt Lake City, UT, USA
| | - Oleg Borodin
- Electrochemistry Branch, Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, MD, USA
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27
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Golze D, Benedikter N, Iannuzzi M, Wilhelm J, Hutter J. Fast evaluation of solid harmonic Gaussian integrals for local resolution-of-the-identity methods and range-separated hybrid functionals. J Chem Phys 2017; 146:034105. [DOI: 10.1063/1.4973510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Dorothea Golze
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Niels Benedikter
- QMath, Department of Mathematical Sciences, University of Copenhagen, Universitetsparken 5, 2100 København, Denmark
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jan Wilhelm
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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28
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Bouju X, Mattioli C, Franc G, Pujol A, Gourdon A. Bicomponent Supramolecular Architectures at the Vacuum–Solid Interface. Chem Rev 2017; 117:1407-1444. [DOI: 10.1021/acs.chemrev.6b00389] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xavier Bouju
- CEMES-CNRS, 29 Rue J. Marvig, 31055 Toulouse, France
| | | | - Grégory Franc
- CEMES-CNRS, 29 Rue J. Marvig, 31055 Toulouse, France
| | - Adeline Pujol
- Université de Toulouse, UPS, CNRS, CEMES, 118 route de Narbonne, 31062 Toulouse, France
| | - André Gourdon
- CEMES-CNRS, 29 Rue J. Marvig, 31055 Toulouse, France
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29
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Hunt D, Sanchez VM, Scherlis DA. A quantum-mechanics molecular-mechanics scheme for extended systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:335201. [PMID: 27352028 DOI: 10.1088/0953-8984/28/33/335201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO2 anatase (1 0 1) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H2O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.
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Affiliation(s)
- Diego Hunt
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires (C1428EHA) Argentina
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30
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Li X, Carravetta V, Li C, Monti S, Rinkevicius Z, Ågren H. Optical Properties of Gold Nanoclusters Functionalized with a Small Organic Compound: Modeling by an Integrated Quantum-Classical Approach. J Chem Theory Comput 2016; 12:3325-39. [DOI: 10.1021/acs.jctc.6b00283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Xin Li
- Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vincenzo Carravetta
- CNR-IPCF, Institute of Chemical
and Physical Processes, via G. Moruzzi
1, I-56124 Pisa, Italy
| | - Cui Li
- CNR-IPCF, Institute of Chemical
and Physical Processes, via G. Moruzzi
1, I-56124 Pisa, Italy
| | - Susanna Monti
- Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- CNR-ICCOM, Institute of Chemistry
of Organometallic Compounds, via G.
Moruzzi 1, I-56124 Pisa, Italy
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
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Björneholm O, Hansen MH, Hodgson A, Liu LM, Limmer DT, Michaelides A, Pedevilla P, Rossmeisl J, Shen H, Tocci G, Tyrode E, Walz MM, Werner J, Bluhm H. Water at Interfaces. Chem Rev 2016; 116:7698-726. [PMID: 27232062 DOI: 10.1021/acs.chemrev.6b00045] [Citation(s) in RCA: 358] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The interfaces of neat water and aqueous solutions play a prominent role in many technological processes and in the environment. Examples of aqueous interfaces are ultrathin water films that cover most hydrophilic surfaces under ambient relative humidities, the liquid/solid interface which drives many electrochemical reactions, and the liquid/vapor interface, which governs the uptake and release of trace gases by the oceans and cloud droplets. In this article we review some of the recent experimental and theoretical advances in our knowledge of the properties of aqueous interfaces and discuss open questions and gaps in our understanding.
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Affiliation(s)
- Olle Björneholm
- Department of Physics and Astronomy, Uppsala University , Box 516, 751 20 Uppsala, Sweden
| | - Martin H Hansen
- Technical University of Denmark , 2800 Kongens Lyngby, Denmark.,Department of Chemistry, University of Copenhagen , Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Andrew Hodgson
- Department of Chemistry, University of Liverpool , Liverpool L69 7ZD, United Kingdom
| | - Li-Min Liu
- Thomas Young Centre, London Centre for Nanotechnology, Department of Physics and Astronomy, and Department of Chemistry, University College London , London WC1E 6BT, United Kingdom.,Beijing Computational Science Research Center , Beijing, 100193, China
| | - David T Limmer
- Princeton Center for Theoretical Science, Princeton University , Princeton, New Jersey 08544, United States
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology, Department of Physics and Astronomy, and Department of Chemistry, University College London , London WC1E 6BT, United Kingdom
| | - Philipp Pedevilla
- Thomas Young Centre, London Centre for Nanotechnology, Department of Physics and Astronomy, and Department of Chemistry, University College London , London WC1E 6BT, United Kingdom
| | - Jan Rossmeisl
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Huaze Shen
- International Center for Quantum Materials and School of Physics, Peking University , Beijing 100871, China
| | - Gabriele Tocci
- Thomas Young Centre, London Centre for Nanotechnology, Department of Physics and Astronomy, and Department of Chemistry, University College London , London WC1E 6BT, United Kingdom.,Laboratory for fundamental BioPhotonics, Laboratory of Computational Science and Modeling, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Eric Tyrode
- Department of Chemistry, KTH Royal Institute of Technology , 10044 Stockholm, Sweden
| | - Marie-Madeleine Walz
- Department of Physics and Astronomy, Uppsala University , Box 516, 751 20 Uppsala, Sweden
| | - Josephina Werner
- Department of Physics and Astronomy, Uppsala University , Box 516, 751 20 Uppsala, Sweden.,Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences , Box 7015, 750 07 Uppsala, Sweden
| | - Hendrik Bluhm
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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32
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Rinkevicius Z, Sandberg JAR, Li X, Linares M, Norman P, Ågren H. Hybrid Complex Polarization Propagator/Molecular Mechanics Method for Heterogeneous Environments. J Chem Theory Comput 2016; 12:2661-7. [DOI: 10.1021/acs.jctc.6b00255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Zilvinas Rinkevicius
- Division
of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
- Swedish
e-Science Research Centre, KTH Royal Institute of Technology, SE-104 50 Stockholm, Sweden
| | - Jaime A. R. Sandberg
- Division
of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Xin Li
- Division
of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Mathieu Linares
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
- Swedish
e-Science Research Centre, Linköping University, SE-581 83 Linköping, Sweden
| | - Patrick Norman
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Hans Ågren
- Division
of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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33
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Heinz H, Ramezani-Dakhel H. Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities. Chem Soc Rev 2016; 45:412-48. [PMID: 26750724 DOI: 10.1039/c5cs00890e] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.
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Affiliation(s)
- Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO 80309, USA.
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Natarajan SK, Behler J. Neural network molecular dynamics simulations of solid–liquid interfaces: water at low-index copper surfaces. Phys Chem Chem Phys 2016; 18:28704-28725. [DOI: 10.1039/c6cp05711j] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulation of the water–copper interface have been carried out using high-dimensional neural network potential based on density functional theory.
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Affiliation(s)
| | - Jörg Behler
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- D-44780 Bochum
- Germany
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Abstract
Recent advances in experimental and computational techniques have allowed for an accurate description of the adsorption of ionic liquids on metallic electrodes. It is now well-established that they adopt a multilayered structure and that the composition of the layers changes with the potential of the electrode. In some cases, potential-driven ordering transitions in the first adsorbed layer have been observed in experiments probing the interface on the molecular scale or by molecular simulations. This perspective gives an overview of the current understanding of such transitions and of their potential impact on the physical and (electro)chemical processes at the interface. In particular, peaks in the differential capacitance, slow dynamics at the interface, and changes in the reactivity have been reported in electrochemical studies. Interfaces between ionic liquids and metallic electrodes are also highly relevant for their friction properties, the voltage-dependence of which opens the way to exciting applications.
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Affiliation(s)
- Benjamin Rotenberg
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire PHENIX, F-75005, Paris, France
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, 80039 Amiens Cedex, France
| | - Mathieu Salanne
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire PHENIX, F-75005, Paris, France
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, 80039 Amiens Cedex, France
- Maison de la Simulation, USR 3441, CEA - CNRS - INRIA - Université Paris-Sud -Université de Versailles, F-91191 Gif-sur-Yvette, France
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Vatamanu J, Ni X, Liu F, Bedrov D. Tailoring graphene-based electrodes from semiconducting to metallic to increase the energy density in supercapacitors. NANOTECHNOLOGY 2015; 26:464001. [PMID: 26511198 DOI: 10.1088/0957-4484/26/46/464001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The semiconducting character of graphene and some carbon-based electrodes can lead to noticeably lower total capacitances and stored energy densities in electric double layer (EDL)capacitors. This paper discusses the chemical and electronic structure modifications that enhance the available energy bands, density of states and quantum capacitance of graphene substrates near the Fermi level, therefore restoring the conducting character of these materials. The doping of graphene with p or n dopants, such as boron and nitrogen atoms, or the introduction of vacancy defects that introduce zigzag edges, can significantly increase the quantum capacitance within the potential range of interest for the energy storage applications by either shifting the Dirac point away from the Fermi level or by eliminating the Dirac point. We show that a combination of doping and vacancies at realistic concentrations is sufficient to increase the capacitance of a graphene-based electrode to within 1 μF cm(−2) from that of a metallic surface.Using a combination of ab initio calculations and classical molecular dynamics simulations we estimate how the changes in the quantum capacitance of these electrode materials affect the total capacitance stored by the open structure EDL capacitors containing room temperature ionic liquid electrolytes.
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Hofer TS, Tirler AO. Combining 2d-Periodic Quantum Chemistry with Molecular Force Fields: A Novel QM/MM Procedure for the Treatment of Solid-State Surfaces and Interfaces. J Chem Theory Comput 2015; 11:5873-87. [DOI: 10.1021/acs.jctc.5b00548] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division,
Institute for General Inorganic and Theoretical Chemistry, Center
for Chemistry and Biomedicine, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Andreas O. Tirler
- Theoretical Chemistry Division,
Institute for General Inorganic and Theoretical Chemistry, Center
for Chemistry and Biomedicine, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
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Abstract
Capacitive energy storage devices are receiving increasing experimental and theoretical attention due to their enormous potential for energy applications. Current research in this field is focused on the improvement of both the energy and the power density of supercapacitors by optimizing the nanostructure of porous electrodes and the chemical structure/composition of the electrolytes. However, the understanding of the underlying correlations and the mechanisms of electric double layer formation near charged surfaces and inside nanoporous electrodes is complicated by the complex interplay of several molecular scale phenomena. This Perspective presents several aspects regarding the experimental and theoretical research in the field, discusses the current atomistic and molecular scale understanding of the mechanisms of energy and charge storage, and provides a brief outlook to the future developments and applications of these devices.
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Affiliation(s)
- Jenel Vatamanu
- Department of Materials Science & Engineering, The University of Utah , 122 S. Central Campus Drive, Salt Lake City, Utah 84112, United States
| | - Dmitry Bedrov
- Department of Materials Science & Engineering, The University of Utah , 122 S. Central Campus Drive, Salt Lake City, Utah 84112, United States
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Golze D, Hutter J, Iannuzzi M. Wetting of water on hexagonal boron nitride@Rh(111): a QM/MM model based on atomic charges derived for nano-structured substrates. Phys Chem Chem Phys 2015; 17:14307-16. [PMID: 25430062 DOI: 10.1039/c4cp04638b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The wetting of water on corrugated and flat hexagonal boron nitride (h-BN) monolayers on Rh(111) is studied within a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. Water is treated by QM methods, whereas the interactions between liquid and substrate are described at the MM level. The electrostatic properties of the substrate are reproduced by assigning specifically generated partial charges to each MM atom. We propose a method to determine restrained electrostatic potential (RESP) charges that can be applied to periodic systems. Our approach is based on the Gaussian and plane waves algorithm and allows an easy tuning of charges for nano-structured substrates. We have successfully applied it to reproduce the electrostatic potential of the corrugated and flat h-BN/Rh(111) known as nanomesh. Molecular dynamics simulations of water films in contact with these substrates are performed and structural and dynamic properties of the interfaces are analyzed. Based on this analysis and on the interaction energies between water film and substrate, we found that the corrugated nanomesh is slightly more hydrophilic. On a macroscopic scale, we expect a smaller contact angle for a droplet on the corrugated surface.
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Affiliation(s)
- Dorothea Golze
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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Vatamanu J, Vatamanu M, Bedrov D. Non-Faradaic Energy Storage by Room Temperature Ionic Liquids in Nanoporous Electrodes. ACS NANO 2015; 9:5999-6017. [PMID: 26038979 DOI: 10.1021/acsnano.5b00945] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The enhancement of non-Faradaic charge and energy density stored by ionic electrolytes in nanostructured electrodes is an intriguing issue of great practical importance for energy storage in electric double layer capacitors. On the basis of extensive molecular dynamics simulations of various carbon-based nanoporous electrodes and room temperature ionic liquid (RTIL) electrolytes, we identify atomistic mechanisms and correlations between electrode/electrolyte structures that lead to capacitance enhancement. In the symmetric electrode setup with nanopores having atomically smooth walls, most RTILs showed up to 50% capacitance increase compared to infinitely wide pore. Extensive simulations using asymmetric electrodes and pores with atomically rough surfaces demonstrated that tuning of electrode nanostructure could lead to further substantial capacitance enhancement. Therefore, the capacitance in nanoporous electrodes can be increased due to a combination of two effects: (i) the screening of ionic interactions by nanopore walls upon electrolyte nanoconfinement, and (ii) the optimization of nanopore structure (volume, surface roughness) to take into account the asymmetry between cation and anion chemical structures.
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Affiliation(s)
- Jenel Vatamanu
- Material Sciences and Engineering Department, University of Utah, 122 South Central Campus Drive, Salt Lake City, Utah 84112, United States
| | - Mihaela Vatamanu
- Material Sciences and Engineering Department, University of Utah, 122 South Central Campus Drive, Salt Lake City, Utah 84112, United States
| | - Dmitry Bedrov
- Material Sciences and Engineering Department, University of Utah, 122 South Central Campus Drive, Salt Lake City, Utah 84112, United States
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41
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Limmer DT, Willard AP. Nanoscale heterogeneity at the aqueous electrolyte–electrode interface. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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42
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Li X, Rinkevicius Z, Ågren H. Two-Photon Absorption of Metal-Assisted Chromophores. J Chem Theory Comput 2014; 10:5630-9. [DOI: 10.1021/ct500579n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Xin Li
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Zilvinas Rinkevicius
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
- Swedish
e-Science Research Centre, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
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Goyal P, Qian HJ, Irle S, Lu X, Roston D, Mori T, Elstner M, Cui Q. Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models. J Phys Chem B 2014; 118:11007-27. [PMID: 25166899 PMCID: PMC4174991 DOI: 10.1021/jp503372v] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We discuss the description of water and hydration effects that employs an approximate density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to explore, with the current formulation of DFTB3, the performance of this method for treating water in different chemical environments, the magnitude and nature of changes required to improve its performance, and factors that dictate its applicability to reactions in the condensed phase in a QM/MM framework. A relatively minor change (on the scale of kBT) in the O-H repulsive potential is observed to substantially improve the structural properties of bulk water under ambient conditions; modest improvements are also seen in dynamic properties of bulk water. This simple change also improves the description of protonated water clusters, a solvated proton, and to a more limited degree, a solvated hydroxide. By comparing results from DFTB3 models that differ in the description of water, we confirm that proton transfer energetics are adequately described by the standard DFTB3/3OB model for meaningful mechanistic analyses. For QM/MM applications, a robust parametrization of QM-MM interactions requires an explicit consideration of condensed phase properties, for which an efficient sampling technique was developed recently and is reviewed here. The discussions help make clear the value and limitations of DFTB3 based simulations, as well as the developments needed to further improve the accuracy and transferability of the methodology.
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Affiliation(s)
- Puja Goyal
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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Rinkevicius Z, Li X, Sandberg JAR, Mikkelsen KV, Ågren H. A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments. J Chem Theory Comput 2014; 10:989-1003. [DOI: 10.1021/ct400897s] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Zilvinas Rinkevicius
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
- KTH Royal Institute of Technology, Swedish e-Science
Research Centre, S-100 44 Stockholm, Sweden
| | - Xin Li
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Jaime A. R. Sandberg
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Kurt V. Mikkelsen
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Hans Ågren
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
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