1
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Morishita T, Shiga M. Ab Initio Characterization of the CO 2-Water Interface Using Unsupervised Machine Learning for Dimensionality Reduction. J Phys Chem B 2024; 128:5781-5791. [PMID: 38829554 DOI: 10.1021/acs.jpcb.4c01526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Precise characterization of the supercritical CO2-water interface under high pressure and temperature conditions is crucial for the geological storage of carbon dioxide (CO2) in deep saline aquifers. Molecular dynamics (MD) simulations offer a valuable approach to gaining insight into the CO2-water interface at a microscopic level. However, no attempt has been made to characterize the CO2-water interface with the accuracy afforded by ab initio calculations. In this study, we performed ab initio MD (AIMD) simulations to investigate the structural and dynamical properties of the CO2-water interface, comparing the results with those obtained from classical force-field MD (FF-MD) simulations. Molecular orientation at the interface was well reproduced in both AIMD and FF-MD simulations. Characteristic structural fluctuations of water at the interface were unveiled by applying multidimensional scaling and time-dependent principal component analysis to the AIMD trajectories; however, they were not prominent in the FF-MD simulations. Furthermore, our study demonstrated a marked difference in the residence time of molecules in the interface region between AIMD and FF-MD simulations, indicating that time-dependent properties of the CO2-water interface strongly depend on the description of the intermolecular forces.
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Affiliation(s)
- Tetsuya Morishita
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Masashige Shiga
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
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2
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Herzfeld J. Art, fact and artifact: reflections on the cross-talk between theory and experiment. Phys Chem Chem Phys 2024; 26:9848-9855. [PMID: 38502180 DOI: 10.1039/d4cp00005f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
With the increasing sophistication of each, theory and experiment have become highly specialized endeavors conducted by separate research groups. A result has been a weakening of the coupling between them and occasional hostility. Examples are given and suggestions are offered for strengthening the traditional synergy between theory and experiment.
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3
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Konstantinovsky D, Yan ECY, Hammes-Schiffer S. Characterizing Interfaces by Voronoi Tessellation. J Phys Chem Lett 2023; 14:5260-5266. [PMID: 37265175 PMCID: PMC10344600 DOI: 10.1021/acs.jpclett.3c01159] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The chemistry of interfaces differs markedly from that of the bulk. Calculation of interfacial properties depends strongly on the definition of the interface, which can lead to ambiguous results that vary between studies. There is a need for a method that can explicitly define the interfaces and boundaries in molecular systems. Voronoi tessellation offers an attractive solution to this problem through its ability to determine neighbors among specified groups of atoms. Here we discuss three cases where Voronoi tessellation combined with modeling of vibrational sum frequency generation (SFG) spectroscopy yields relevant insights: the breakdown of the air-water interface into clear and intuitive molecular layers, the study of the hydration shell in biological systems, and the acceleration of difficult spectral calculations where intermolecular vibrational couplings dominate. The utility of Voronoi tessellation has broad applications that extend beyond any single type of spectroscopy or system.
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Affiliation(s)
- Daniel Konstantinovsky
- Department of Chemistry, Yale University, New Haven, CT, USA 06511
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA 06511
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, New Haven, CT, USA 06511
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, CT, USA 06511
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA 06511
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4
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Palos E, Lambros E, Swee S, Hu J, Dasgupta S, Paesani F. Assessing the Interplay between Functional-Driven and Density-Driven Errors in DFT Models of Water. J Chem Theory Comput 2022; 18:3410-3426. [PMID: 35506889 DOI: 10.1021/acs.jctc.2c00050] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the interplay between functional-driven and density-driven errors in different density functional approximations within density functional theory (DFT) and the implications of these errors for simulations of water with DFT-based data-driven potentials. Specifically, we quantify density-driven errors in two widely used dispersion-corrected functionals derived within the generalized gradient approximation (GGA), namely BLYP-D3 and revPBE-D3, and two modern meta-GGA functionals, namely strongly constrained and appropriately normed (SCAN) and B97M-rV. The effects of functional-driven and density-driven errors on the interaction energies are first assessed for the water clusters of the BEGDB dataset. Further insights into the nature of functional-driven errors are gained from applying the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) to the interaction energies, which demonstrates that functional-driven errors are strongly correlated with the nature of the interactions. We discuss cases where density-corrected DFT (DC-DFT) models display higher accuracy than the original DFT models and cases where reducing the density-driven errors leads to larger deviations from the reference energies due to the presence of large functional-driven errors. Finally, molecular dynamics simulations are performed with data-driven many-body potentials derived from DFT and DC-DFT data to determine the effect that minimizing density-driven errors has on the description of liquid water. Besides rationalizing the performance of widely used DFT models of water, we believe that our findings unveil fundamental relations between the shortcomings of some common DFT approximations and the requirements for accurate descriptions of molecular interactions, which will aid the development of a consistent, DFT-based framework for the development of data-driven and machine-learned potentials for simulations of condensed-phase systems.
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Affiliation(s)
- Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Steven Swee
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Jie Hu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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5
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Liu J, He X. Ab initio molecular dynamics simulation of liquid water with fragment-based quantum mechanical approach under periodic boundary conditions. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2110183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai 200062, China
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6
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Tang F, Ohto T, Sun S, Rouxel JR, Imoto S, Backus EHG, Mukamel S, Bonn M, Nagata Y. Molecular Structure and Modeling of Water-Air and Ice-Air Interfaces Monitored by Sum-Frequency Generation. Chem Rev 2020; 120:3633-3667. [PMID: 32141737 PMCID: PMC7181271 DOI: 10.1021/acs.chemrev.9b00512] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Indexed: 12/26/2022]
Abstract
From a glass of water to glaciers in Antarctica, water-air and ice-air interfaces are abundant on Earth. Molecular-level structure and dynamics at these interfaces are key for understanding many chemical/physical/atmospheric processes including the slipperiness of ice surfaces, the surface tension of water, and evaporation/sublimation of water. Sum-frequency generation (SFG) spectroscopy is a powerful tool to probe the molecular-level structure of these interfaces because SFG can specifically probe the topmost interfacial water molecules separately from the bulk and is sensitive to molecular conformation. Nevertheless, experimental SFG has several limitations. For example, SFG cannot provide information on the depth of the interface and how the orientation of the molecules varies with distance from the surface. By combining the SFG spectroscopy with simulation techniques, one can directly compare the experimental data with the simulated SFG spectra, allowing us to unveil the molecular-level structure of water-air and ice-air interfaces. Here, we present an overview of the different simulation protocols available for SFG spectra calculations. We systematically compare the SFG spectra computed with different approaches, revealing the advantages and disadvantages of the different methods. Furthermore, we account for the findings through combined SFG experiments and simulations and provide future challenges for SFG experiments and simulations at different aqueous interfaces.
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Affiliation(s)
- Fujie Tang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department
of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Tatsuhiko Ohto
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Shumei Sun
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department
of Physical Chemistry, University of Vienna, Währinger Strasse 42, 1090 Vienna, Austria
| | - Jérémy R. Rouxel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Sho Imoto
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Ellen H. G. Backus
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department
of Physical Chemistry, University of Vienna, Währinger Strasse 42, 1090 Vienna, Austria
| | - Shaul Mukamel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Yuki Nagata
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department
of Physics, State Key Laboratory of Surface Physics and Key Laboratory
of Micro- and Nano-Photonic Structures (MOE), Fudan University, Shanghai 200433, China
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7
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Zhong K, Yu CC, Dodia M, Bonn M, Nagata Y, Ohto T. Vibrational mode frequency correction of liquid water in density functional theory molecular dynamics simulations with van der Waals correction. Phys Chem Chem Phys 2020; 22:12785-12793. [DOI: 10.1039/c9cp06335h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We develop a frequency correction scheme for the stretch and bending modes of liquid water, which substantially improves the prediction of the vibrational spectra.
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Affiliation(s)
- Kai Zhong
- Hefei National Laboratory for Physical Sciences at the Microscale
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Center for Excellence in Nanoscience
- School of Chemistry and Materials Science
- University of Science and Technology of China
| | - Chun-Chieh Yu
- Max Planck Institute for Polymer Research
- Ackermannweg 10
- 55128 Mainz
- Germany
| | - Mayank Dodia
- Max Planck Institute for Polymer Research
- Ackermannweg 10
- 55128 Mainz
- Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research
- Ackermannweg 10
- 55128 Mainz
- Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research
- Ackermannweg 10
- 55128 Mainz
- Germany
| | - Tatsuhiko Ohto
- Graduate School of Engineering Science
- Osaka University
- Osaka 560-8531
- Japan
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8
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Ohto T, Dodia M, Xu J, Imoto S, Tang F, Zysk F, Kühne TD, Shigeta Y, Bonn M, Wu X, Nagata Y. Accessing the Accuracy of Density Functional Theory through Structure and Dynamics of the Water-Air Interface. J Phys Chem Lett 2019; 10:4914-4919. [PMID: 31393136 PMCID: PMC6748669 DOI: 10.1021/acs.jpclett.9b01983] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/08/2019] [Indexed: 05/31/2023]
Abstract
Density functional theory-based molecular dynamics simulations are increasingly being used for simulating aqueous interfaces. Nonetheless, the choice of the appropriate density functional, critically affecting the outcome of the simulation, has remained arbitrary. Here, we assess the performance of various exchange-correlation (XC) functionals, based on the metrics relevant to sum-frequency generation spectroscopy. The structure and dynamics of water at the water-air interface are governed by heterogeneous intermolecular interactions, thereby providing a critical benchmark for XC functionals. We find that the XC functionals constrained by exact functional conditions (revPBE and revPBE0) with the dispersion correction show excellent performance. The poor performance of the empirically optimized density functional (M06-L) indicates the importance of satisfying the exact functional condition. Understanding the performance of different XC functionals can aid in resolving the controversial interpretation of the interfacial water structure and direct the design of novel, improved XC functionals better suited to describing the heterogeneous interactions in condensed phases.
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Affiliation(s)
- Tatsuhiko Ohto
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Mayank Dodia
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jianhang Xu
- Department
of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Sho Imoto
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Fujie Tang
- Department
of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Frederik Zysk
- Dynamics
of Condensed Matter and Center for Sustainable Systems Design, Chair
of Theoretical Chemistry, University of
Paderborn, Warburger Strasse 100, 33098 Paderborn, Germany
| | - Thomas D. Kühne
- Dynamics
of Condensed Matter and Center for Sustainable Systems Design, Chair
of Theoretical Chemistry, University of
Paderborn, Warburger Strasse 100, 33098 Paderborn, Germany
| | - Yasuteru Shigeta
- Graduate
School of Pure and Applied Sciences, University
of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8571, Japan
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Xifan Wu
- Department
of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Yuki Nagata
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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9
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Melani G, Nagata Y, Campen RK, Saalfrank P. Vibrational spectra of dissociatively adsorbed D 2O on Al-terminated α-Al 2O 3(0001) surfaces from ab initio molecular dynamics. J Chem Phys 2019; 150:244701. [PMID: 31255084 DOI: 10.1063/1.5099895] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water can adsorb molecularly or dissociatively onto different sites of metal oxide surfaces. These adsorption sites can be disentangled using surface-sensitive vibrational spectroscopy. Here, we model Vibrational Sum Frequency (VSF) spectra for various forms of dissociated, deuterated water on a reconstructed, Al-terminated α-Al2O3(0001) surface at submonolayer coverages (the so-called 1-2, 1-4, and 1-4' modes). Using an efficient scheme based on velocity-velocity autocorrelation functions, we go beyond previous normal mode analyses by including anharmonicity, mode coupling, and thermal surface motion in the framework of ab initio molecular dynamics. In this way, we calculate vibrational density of states curves, infrared, and VSF spectra. Comparing computed VSF spectra with measured ones, we find that relative frequencies of resonances are in quite good agreement and linewidths are reasonably well represented, while VSF intensities coincide not well. We argue that intensities are sensitively affected by local interactions and thermal fluctuations, even at such low coverage, while absolute peak positions strongly depend on the choice of the electronic structure method and on the appropriate inclusion of anharmonicity.
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Affiliation(s)
- Giacomo Melani
- Theoretische Chemie, Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam-Golm, Germany
| | - Yuki Nagata
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
| | - R Kramer Campen
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Peter Saalfrank
- Theoretische Chemie, Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam-Golm, Germany
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10
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Dodia M, Ohto T, Imoto S, Nagata Y. Structure and Dynamics of Water at the Water-Air Interface Using First-Principles Molecular Dynamics Simulations. II. NonLocal vs Empirical van der Waals Corrections. J Chem Theory Comput 2019; 15:3836-3843. [PMID: 31074989 PMCID: PMC6750744 DOI: 10.1021/acs.jctc.9b00253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
van der Waals (vdW) correction schemes
have been recognized to
be essential for an accurate description of liquid water in first-principles
molecular dynamics simulation. The description of the structure and
dynamics of water is governed by the type of the vdW corrections.
So far, two vdW correction schemes have been often used: empirical
vdW corrections and nonlocal vdW corrections. In this paper, we assess
the influence of the empirical vs nonlocal vdW correction schemes
on the structure and dynamics of water at the water–air interface.
Since the structure of water at the water–air interface is
established by a delicate balance of hydrogen bond formation and breaking,
the simulation at the water–air interface provides a unique
platform to testify as to the heterogeneous interaction of water.
We used the metrics [Ohto et al. J. Chem. Theory Comput., 2019, 15, 595−60230468702] which
are directly connected with the sum-frequency generation spectroscopic
measurement. We find that the overall performance of nonlocal vdW
methods is either similar or worse compared to the empirical vdW methods.
We also investigated the performance of the optB88-DRSLL functional,
which showed slightly less accuracy than the revPBE-D3 method. We
conclude that the revPBE-D3 method shows the best performance for
describing the interfacial water.
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Affiliation(s)
- Mayank Dodia
- Max Planck Institute for Polymer Research, Ackermannweg 10 , 55128 Mainz , Germany
| | - Tatsuhiko Ohto
- Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka, Osaka 560-8531 , Japan
| | - Sho Imoto
- Max Planck Institute for Polymer Research, Ackermannweg 10 , 55128 Mainz , Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10 , 55128 Mainz , Germany
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11
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González D, Heras-Domingo J, Pantaleone S, Rimola A, Rodríguez-Santiago L, Solans-Monfort X, Sodupe M. Water Adsorption on MO 2 (M = Ti, Ru, and Ir) Surfaces. Importance of Octahedral Distortion and Cooperative Effects. ACS OMEGA 2019; 4:2989-2999. [PMID: 31459524 PMCID: PMC6649029 DOI: 10.1021/acsomega.8b03350] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/25/2019] [Indexed: 06/10/2023]
Abstract
Understanding metal oxide MO2 (M = Ti, Ru, and Ir)-water interfaces is essential to assess the catalytic behavior of these materials. The present study analyzes the H2O-MO2 interactions at the most abundant (110) and (011) surfaces, at two different water coverages: isolated water molecules and full monolayer, by means of Perdew-Burke-Ernzerhof-D2 static calculations and ab initio molecular dynamics (AIMD) simulations. Results indicate that adsorption preferably occurs in its molecular form on (110)-TiO2 and in its dissociative form on (110)-RuO2 and (110)-IrO2. The opposite trend is observed at the (011) facet. This different behavior is related to the kind of octahedral distortion observed in the bulk of these materials (tetragonal elongation for TiO2 and tetragonal compression for RuO2 and IrO2) and to the different nature of the vacant sites created, axial on (110) and equatorial on (011). For the monolayer, additional effects such as cooperative H-bond interactions and cooperative adsorption come into play in determining the degree of deprotonation. For TiO2, AIMD indicates that the water monolayer is fully undissociated at both (110) and (011) surfaces, whereas for RuO2, water monolayer exhibits a 50% dissociation, the formation of H3O2 - motifs being essential. Finally, on (110)-IrO2, the main monolayer configuration is the fully dissociated one, whereas on (011)-IrO2, it exhibits a degree of dissociation that ranges between 50 and 75%. Overall, the present study shows that the degree of water dissociation results from a delicate balance between the H2O-MO2 intrinsic interaction and cooperative hydrogen bonding and adsorption effects.
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