1
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Montero de Hijes P, Dellago C, Jinnouchi R, Schmiedmayer B, Kresse G. Comparing machine learning potentials for water: Kernel-based regression and Behler-Parrinello neural networks. J Chem Phys 2024; 160:114107. [PMID: 38506284 DOI: 10.1063/5.0197105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/03/2024] [Indexed: 03/21/2024] Open
Abstract
In this paper, we investigate the performance of different machine learning potentials (MLPs) in predicting key thermodynamic properties of water using RPBE + D3. Specifically, we scrutinize kernel-based regression and high-dimensional neural networks trained on a highly accurate dataset consisting of about 1500 structures, as well as a smaller dataset, about half the size, obtained using only on-the-fly learning. This study reveals that despite minor differences between the MLPs, their agreement on observables such as the diffusion constant and pair-correlation functions is excellent, especially for the large training dataset. Variations in the predicted density isobars, albeit somewhat larger, are also acceptable, particularly given the errors inherent to approximate density functional theory. Overall, this study emphasizes the relevance of the database over the fitting method. Finally, this study underscores the limitations of root mean square errors and the need for comprehensive testing, advocating the use of multiple MLPs for enhanced certainty, particularly when simulating complex thermodynamic properties that may not be fully captured by simpler tests.
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Affiliation(s)
- Pablo Montero de Hijes
- University of Vienna, Faculty of Physics, Kolingasse 14, A-1090 Vienna, Austria
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Josef-Holaubuek-Platz 2, 1090 Vienna, Austria
| | - Christoph Dellago
- University of Vienna, Faculty of Physics, Kolingasse 14, A-1090 Vienna, Austria
| | - Ryosuke Jinnouchi
- Toyota Central R&D Labs., Inc., 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
| | | | - Georg Kresse
- University of Vienna, Faculty of Physics, Kolingasse 14, A-1090 Vienna, Austria
- VASP Software GmbH, Berggasse 21, A-1090 Vienna, Austria
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2
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Palos E, Caruso A, Paesani F. Consistent density functional theory-based description of ion hydration through density-corrected many-body representations. J Chem Phys 2023; 159:181101. [PMID: 37947509 DOI: 10.1063/5.0174577] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
Delocalization error constrains the accuracy of density functional theory in describing molecular interactions in ion-water systems. Using Na+ and Cl- in water as model systems, we calculate the effects of delocalization error in the SCAN functional for describing ion-water and water-water interactions in hydrated ions, and demonstrate that density-corrected SCAN (DC-SCAN) predicts n-body and interaction energies with an accuracy approaching coupled cluster theory. The performance of DC-SCAN is size-consistent, maintaining an accurate description of molecular interactions well beyond the first solvation shell. Molecular dynamics simulations at ambient conditions with many-body MB-SCAN(DC) potentials, derived from the many-body expansion, predict the solvation structure of Na+ and Cl- in quantitative agreement with reference data, while simultaneously reproducing the structure of liquid water. Beyond rationalizing the accuracy of density-corrected models of ion hydration, our findings suggest that our unified density-corrected MB formalism holds great promise for efficient DFT-based simulations of condensed-phase systems with chemical accuracy.
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Affiliation(s)
- Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Alessandro Caruso
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
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3
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Zhang C, Yue S, Panagiotopoulos AZ, Klein ML, Wu X. Why Dissolving Salt in Water Decreases Its Dielectric Permittivity. PHYSICAL REVIEW LETTERS 2023; 131:076801. [PMID: 37656852 DOI: 10.1103/physrevlett.131.076801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/30/2023] [Accepted: 07/07/2023] [Indexed: 09/03/2023]
Abstract
The dielectric permittivity of salt water decreases on dissolving more salt. For nearly a century, this phenomenon has been explained by invoking saturation in the dielectric response of the solvent water molecules. Herein, we employ an advanced deep neural network (DNN), built using data from density functional theory, to study the dielectric permittivity of sodium chloride solutions. Notably, the decrease in the dielectric permittivity as a function of concentration, computed using the DNN approach, agrees well with experiments. Detailed analysis of the computations reveals that the dominant effect, caused by the intrusion of ionic hydration shells into the solvent hydrogen-bond network, is the disruption of dipolar correlations among water molecules. Accordingly, the observed decrease in the dielectric permittivity is mostly due to increasing suppression of the collective response of solvent waters.
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Affiliation(s)
- Chunyi Zhang
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Shuwen Yue
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | | | - Michael L Klein
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Xifan Wu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
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4
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Fidanyan K, Liu G, Rossi M. Ab initio study of water dissociation on a charged Pd(111) surface. J Chem Phys 2023; 158:094707. [PMID: 36889966 DOI: 10.1063/5.0139082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The interactions between molecules and electrode surfaces play a key role in electrochemical processes and are a subject of extensive research, both experimental and theoretical. In this paper, we address the water dissociation reaction on a Pd(111) electrode surface, modeled as a slab embedded in an external electric field. We aim at unraveling the relationship between surface charge and zero-point energy in aiding or hindering this reaction. We calculate the energy barriers with dispersion-corrected density-functional theory and an efficient parallel implementation of the nudged-elastic-band method. We show that the lowest dissociation barrier and consequently the highest reaction rate take place when the field reaches a strength where two different geometries of the water molecule in the reactant state are equally stable. The zero-point energy contributions to this reaction, on the other hand, remain nearly constant across a wide range of electric field strengths, despite significant changes in the reactant state. Interestingly, we show that the application of electric fields that induce a negative charge on the surface can make nuclear tunneling more significant for these reactions.
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Affiliation(s)
- Karen Fidanyan
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Guoyuan Liu
- Department of Materials Science and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Mariana Rossi
- Department of Materials Science and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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5
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Song M, Zhu S, Jiao Z, Ou Z, Liu Y, Guo L. Search for the superiority of supercritical water with ab initio molecular dynamics simulation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Neufeld O, Nourbakhsh Z, Tancogne-Dejean N, Rubio A. Ab Initio Cluster Approach for High Harmonic Generation in Liquids. J Chem Theory Comput 2022; 18:4117-4126. [PMID: 35699241 PMCID: PMC9281394 DOI: 10.1021/acs.jctc.2c00235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High harmonic generation (HHG) takes place in all phases of matter. In gaseous atomic and molecular media, it has been extensively studied and is very well understood. In solids, research is ongoing, but a consensus is forming for the dominant microscopic HHG mechanisms. In liquids, on the other hand, no established theory yet exists, and approaches developed for gases and solids are generally inapplicable, hindering our current understanding. We develop here a powerful and reliable ab initio cluster-based approach for describing the nonlinear interactions between isotropic bulk liquids and intense laser pulses. The scheme is based on time-dependent density functional theory and utilizes several approximations that make it feasible yet accurate in realistic systems. We demonstrate our approach with HHG calculations in water, ammonia, and methane liquids and compare the characteristic response of polar and nonpolar liquids. We identify unique features in the HHG spectra of liquid methane that could be utilized for ultrafast spectroscopy of its chemical and physical properties, including a structural minimum at 15-17 eV that is associated solely with the liquid phase. Our results pave the way to accessible calculations of HHG in liquids and illustrate the unique nonlinear nature of liquid systems.
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Affiliation(s)
- Ofer Neufeld
- Max Planck Institute for the Structure and Dynamics of Matter and Center for Free-Electron Laser Science, Hamburg 22761, Germany
| | - Zahra Nourbakhsh
- Max Planck Institute for the Structure and Dynamics of Matter and Center for Free-Electron Laser Science, Hamburg 22761, Germany
| | - Nicolas Tancogne-Dejean
- Max Planck Institute for the Structure and Dynamics of Matter and Center for Free-Electron Laser Science, Hamburg 22761, Germany
| | - Angel Rubio
- Max Planck Institute for the Structure and Dynamics of Matter and Center for Free-Electron Laser Science, Hamburg 22761, Germany.,Center for Computational Quantum Physics (CCQ), The Flatiron Institute, New York, New York 10010, United States
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7
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Marracino P, Paffi A, d'Inzeo G. A rationale for non-linear responses to strong electric fields in molecular dynamics simulations. Phys Chem Chem Phys 2022; 24:11654-11661. [PMID: 35536147 DOI: 10.1039/d1cp04466d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many approaches for calculation of the field-dependent electric properties of water solutions rely on the Onsager and Kirkwood theories of polar dielectrics. Such basic theories implicitly consider the electric field intensity to fulfill the so-called 'weak field conditions', i.e. to produce a linear response in the system. In this work we made use of molecular dynamics simulations to investigate possible non-linear effects induced by high intensity electric fields, specifically continuous wave bursts with nanosecond duration, comparing them with the ones predicted by the theory. We found that field intensities above 0.15 V nm-1 produce remarkable nonlinear responses in the whole 100 MHz-100 GHz frequency window considered, with the onset of higher order polarization signals, which are the clear fingerprint of harmonic distorsions. That non-linear response turned out to depend on the considered frequency. We finally show that MD outcomes are consistent with a modelization based on an extended formulation of the Langevin function including a frequency-dependent parameter.
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Affiliation(s)
- Paolo Marracino
- Rise Technology S. R. L., L. Re Paolo Toscanelli 170, 00121 Rome, Italy.
| | - Alessandra Paffi
- University of Rome "La Sapienza", DIET, Rome, Italy.,Centre on the Interactions between Electromagnetic Fields and Biosystems (ICEmB), University of Genoa, Genoa, Italy
| | - Guglielmo d'Inzeo
- University of Rome "La Sapienza", DIET, Rome, Italy.,Centre on the Interactions between Electromagnetic Fields and Biosystems (ICEmB), University of Genoa, Genoa, Italy
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8
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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: 15] [Impact Index Per Article: 7.5] [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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9
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Palos E, Lambros E, Dasgupta S, Paesani F. Density Functional Theory of Water with the Machine-Learned DM21 Functional. J Chem Phys 2022; 156:161103. [DOI: 10.1063/5.0090862] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The delicate interplay between functional-driven and density-driven errors in density functional theory (DFT) has hindered traditional density functional approximations (DFAs) from providing an accurate description of water for over 30 years. Recently, the deep-learned DeepMind 21 (DM21) functional has been shown to overcome the limitations of traditional DFAs as it is free of delocalization error. To determine if DM21 can enable a molecular-level description of the physical properties of aqueous systems within Kohn-Sham DFT, we assess the accuracy of the DM21 functional for neutral, protonated, and deprotonated water clusters. We find that the ability of DM21 to accurately predict the energetics of aqueous clusters varies significantly with cluster size. Additionally, we introduce the many-body MB-DM21 potential derived from DM21 data within the many-body expansion of the energy and use it in simulations of liquid water as a function of temperature at ambient pressure. We find that size-dependent functional-driven errors identified in the analysis of the energetics of small clusters calculated with the DM21 functional result in the MB-DM21 potential systematically overestimating the hydrogen-bond strength and, consequently, predicting a more ice-like local structure of water at room temperature.
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Affiliation(s)
- Etienne Palos
- Chemistry and Biochemistry, University of California San Diego, United States of America
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10
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Yang Y, Peltier CR, Zeng R, Schimmenti R, Li Q, Huang X, Yan Z, Potsi G, Selhorst R, Lu X, Xu W, Tader M, Soudackov AV, Zhang H, Krumov M, Murray E, Xu P, Hitt J, Xu L, Ko HY, Ernst BG, Bundschu C, Luo A, Markovich D, Hu M, He C, Wang H, Fang J, DiStasio RA, Kourkoutis LF, Singer A, Noonan KJT, Xiao L, Zhuang L, Pivovar BS, Zelenay P, Herrero E, Feliu JM, Suntivich J, Giannelis EP, Hammes-Schiffer S, Arias T, Mavrikakis M, Mallouk TE, Brock JD, Muller DA, DiSalvo FJ, Coates GW, Abruña HD. Electrocatalysis in Alkaline Media and Alkaline Membrane-Based Energy Technologies. Chem Rev 2022; 122:6117-6321. [PMID: 35133808 DOI: 10.1021/acs.chemrev.1c00331] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen energy-based electrochemical energy conversion technologies offer the promise of enabling a transition of the global energy landscape from fossil fuels to renewable energy. Here, we present a comprehensive review of the fundamentals of electrocatalysis in alkaline media and applications in alkaline-based energy technologies, particularly alkaline fuel cells and water electrolyzers. Anion exchange (alkaline) membrane fuel cells (AEMFCs) enable the use of nonprecious electrocatalysts for the sluggish oxygen reduction reaction (ORR), relative to proton exchange membrane fuel cells (PEMFCs), which require Pt-based electrocatalysts. However, the hydrogen oxidation reaction (HOR) kinetics is significantly slower in alkaline media than in acidic media. Understanding these phenomena requires applying theoretical and experimental methods to unravel molecular-level thermodynamics and kinetics of hydrogen and oxygen electrocatalysis and, particularly, the proton-coupled electron transfer (PCET) process that takes place in a proton-deficient alkaline media. Extensive electrochemical and spectroscopic studies, on single-crystal Pt and metal oxides, have contributed to the development of activity descriptors, as well as the identification of the nature of active sites, and the rate-determining steps of the HOR and ORR. Among these, the structure and reactivity of interfacial water serve as key potential and pH-dependent kinetic factors that are helping elucidate the origins of the HOR and ORR activity differences in acids and bases. Additionally, deliberately modulating and controlling catalyst-support interactions have provided valuable insights for enhancing catalyst accessibility and durability during operation. The design and synthesis of highly conductive and durable alkaline membranes/ionomers have enabled AEMFCs to reach initial performance metrics equal to or higher than those of PEMFCs. We emphasize the importance of using membrane electrode assemblies (MEAs) to integrate the often separately pursued/optimized electrocatalyst/support and membranes/ionomer components. Operando/in situ methods, at multiscales, and ab initio simulations provide a mechanistic understanding of electron, ion, and mass transport at catalyst/ionomer/membrane interfaces and the necessary guidance to achieve fuel cell operation in air over thousands of hours. We hope that this Review will serve as a roadmap for advancing the scientific understanding of the fundamental factors governing electrochemical energy conversion in alkaline media with the ultimate goal of achieving ultralow Pt or precious-metal-free high-performance and durable alkaline fuel cells and related technologies.
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Affiliation(s)
- Yao Yang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Cheyenne R Peltier
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Rui Zeng
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Roberto Schimmenti
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Qihao Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xin Huang
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Zhifei Yan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Georgia Potsi
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Ryan Selhorst
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xinyao Lu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Weixuan Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Mariel Tader
- Department of Physics, Cornell University, Ithaca, New York 14853, United States
| | - Alexander V Soudackov
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Hanguang Zhang
- Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Mihail Krumov
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ellen Murray
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Pengtao Xu
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy Hitt
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Linxi Xu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Hsin-Yu Ko
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Colin Bundschu
- Department of Physics, Cornell University, Ithaca, New York 14853, United States
| | - Aileen Luo
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Danielle Markovich
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Meixue Hu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Cheng He
- Chemical and Materials Science Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Hongsen Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jiye Fang
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York 13902, United States
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Lena F Kourkoutis
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States.,Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States
| | - Andrej Singer
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Kevin J T Noonan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Li Xiao
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Lin Zhuang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Bryan S Pivovar
- Chemical and Materials Science Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Piotr Zelenay
- Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Enrique Herrero
- Instituto de Electroquímica, Universidad de Alicante, Alicante E-03080, Spain
| | - Juan M Feliu
- Instituto de Electroquímica, Universidad de Alicante, Alicante E-03080, Spain
| | - Jin Suntivich
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States.,Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States
| | - Emmanuel P Giannelis
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | | | - Tomás Arias
- Department of Physics, Cornell University, Ithaca, New York 14853, United States
| | - Manos Mavrikakis
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Thomas E Mallouk
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Joel D Brock
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - David A Muller
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States.,Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States
| | - Francis J DiSalvo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Geoffrey W Coates
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Héctor D Abruña
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Center for Alkaline Based Energy Solutions (CABES), Cornell University, Ithaca, New York 14853, United States
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11
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Stratified diffusion of HOD-D2O inside COOH- and NH2-functionalized multi-walled carbon nanotubes studied by NMR spectroscopy. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Theoretical Description of Water from Single-Molecule to Condensed Phase: a Review of Recent Progress on Potential Energy Surfaces and Molecular Dynamics. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2201005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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13
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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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14
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Gallo P, Bachler J, Bove LE, Böhmer R, Camisasca G, Coronas LE, Corti HR, de Almeida Ribeiro I, de Koning M, Franzese G, Fuentes-Landete V, Gainaru C, Loerting T, de Oca JMM, Poole PH, Rovere M, Sciortino F, Tonauer CM, Appignanesi GA. Advances in the study of supercooled water. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:143. [PMID: 34825973 DOI: 10.1140/epje/s10189-021-00139-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
In this review, we report recent progress in the field of supercooled water. Due to its uniqueness, water presents numerous anomalies with respect to most simple liquids, showing polyamorphism both in the liquid and in the glassy state. We first describe the thermodynamic scenarios hypothesized for the supercooled region and in particular among them the liquid-liquid critical point scenario that has so far received more experimental evidence. We then review the most recent structural indicators, the two-state model picture of water, and the importance of cooperative effects related to the fact that water is a hydrogen-bonded network liquid. We show throughout the review that water's peculiar properties come into play also when water is in solution, confined, and close to biological molecules. Concerning dynamics, upon mild supercooling water behaves as a fragile glass former following the mode coupling theory, and it turns into a strong glass former upon further cooling. Connections between the slow dynamics and the thermodynamics are discussed. The translational relaxation times of density fluctuations show in fact the fragile-to-strong crossover connected to the thermodynamics arising from the existence of two liquids. When considering also rotations, additional crossovers come to play. Mobility-viscosity decoupling is also discussed in supercooled water and aqueous solutions. Finally, the polyamorphism of glassy water is considered through experimental and simulation results both in bulk and in salty aqueous solutions. Grains and grain boundaries are also discussed.
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Affiliation(s)
- Paola Gallo
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy.
| | - Johannes Bachler
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Livia E Bove
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
- Sorbonne Université, CNRS UMR 7590, IMPMC, 75005, Paris, France
| | - Roland Böhmer
- Fakultät Physik, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Gaia Camisasca
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy
| | - Luis E Coronas
- Secció de Física Estadística i Interdisciplinària-Departament de Física de la Matèria Condensada, Universitat de Barcelona, & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, C. Martí i Franquès 1, 08028, Barcelona, Spain
| | - Horacio R Corti
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
| | - Ingrid de Almeida Ribeiro
- Instituto de Física "Gleb Wataghin", Universidade Estadual de Campinas, UNICAMP, 13083-859, Campinas, São Paulo, Brazil
| | - Maurice de Koning
- Instituto de Física "Gleb Wataghin", Universidade Estadual de Campinas, UNICAMP, 13083-859, Campinas, São Paulo, Brazil
- Center for Computing in Engineering & Sciences, Universidade Estadual de Campinas, UNICAMP, 13083-861, Campinas, São Paulo, Brazil
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària-Departament de Física de la Matèria Condensada, Universitat de Barcelona, & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, C. Martí i Franquès 1, 08028, Barcelona, Spain
| | - Violeta Fuentes-Landete
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Catalin Gainaru
- Fakultät Physik, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Thomas Loerting
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | | | - Peter H Poole
- Department of Physics, St. Francis Xavier University, Antigonish, NS, B2G 2W5, Canada
| | - Mauro Rovere
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
| | - Christina M Tonauer
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Gustavo A Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
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15
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Pérez Ramírez L, Boucly A, Saudrais F, Bournel F, Gallet JJ, Maisonhaute E, Milosavljević AR, Nicolas C, Rochet F. The Fermi level as an energy reference in liquid jet X-ray photoelectron spectroscopy studies of aqueous solutions. Phys Chem Chem Phys 2021; 23:16224-16233. [PMID: 34304262 DOI: 10.1039/d1cp01511g] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To advance the understanding of key electrochemical and photocatalytic processes that depend on the electronic structure of aqueous solutions, X-ray photoemission spectroscopy has become an invaluable tool, especially when practiced with liquid microjet setups. Determining vertical ionization energies referenced to the vacuum level, and binding energies referenced to the Fermi level, including the much-coveted reorganization energy of the oxidized species of a redox couple, requires that energy levels be properly defined. The present paper addresses specifically how the vacuum level "just outside the surface" can be known through the energy position of the rising edge of the secondary electrons, and how the Fermi level reference is uniquely determined via the introduction of a redox couple. Taking the case of the ferricyanide/ferrocyanide and ferric/ferrous couples, this study also tackles issues related to the electrokinetic effects inherent to the production of a liquid jet in a vacuum, which has become the standard water sample environment for photoemission experiments.
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Affiliation(s)
- Lucía Pérez Ramírez
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique Matière et Rayonnement, UMR 7614, 4 Place Jussieu, 75005 Paris, France.
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16
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Yao Y, Kanai Y. Nuclear Quantum Effect and Its Temperature Dependence in Liquid Water from Random Phase Approximation via Artificial Neural Network. J Phys Chem Lett 2021; 12:6354-6362. [PMID: 34231366 DOI: 10.1021/acs.jpclett.1c01566] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report structural and dynamical properties of liquid water described by the random phase approximation (RPA) correlation together with the exact exchange energy (EXX) within density functional theory. By utilizing thermostated ring polymer molecular dynamics, we examine the nuclear quantum effects and their temperature dependence. We circumvent the computational limitation of performing direct first-principles molecular dynamics simulation at this high level of electronic structure theory by adapting an artificial neural network model. We show that the EXX+RPA level of theory accurately describes liquid water in terms of both dynamical and structural properties.
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Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina at Chapel Hill, Durham, North Carolina 27599, United States
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Durham, North Carolina 27599, United States
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17
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Krishnamoorthy A, Nomura KI, Baradwaj N, Shimamura K, Rajak P, Mishra A, Fukushima S, Shimojo F, Kalia R, Nakano A, Vashishta P. Dielectric Constant of Liquid Water Determined with Neural Network Quantum Molecular Dynamics. PHYSICAL REVIEW LETTERS 2021; 126:216403. [PMID: 34114857 DOI: 10.1103/physrevlett.126.216403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
The static dielectric constant ϵ_{0} and its temperature dependence for liquid water is investigated using neural network quantum molecular dynamics (NNQMD). We compute the exact dielectric constant in canonical ensemble from NNQMD trajectories using fluctuations in macroscopic polarization computed from maximally localized Wannier functions (MLWF). Two deep neural networks are constructed. The first, NNQMD, is trained on QMD configurations for liquid water under a variety of temperature and density conditions to learn potential energy surface and forces and then perform molecular dynamics simulations. The second network, NNMLWF, is trained to predict locations of MLWF of individual molecules using the atomic configurations from NNQMD. Training data for both the neural networks is produced using a highly accurate quantum-mechanical method, DFT-SCAN that yields an excellent description of liquid water. We produce 280×10^{6} configurations of water at 7 temperatures using NNQMD and predict MLWF centers using NNMLWF to compute the polarization fluctuations. The length of trajectories needed for a converged value of the dielectric constant at 0°C is found to be 20 ns (40×10^{6} configurations with 0.5 fs time step). The computed dielectric constants for 0, 15, 30, 45, 60, 75, and 90°C are in good agreement with experiments. Our scalable scheme to compute dielectric constants with quantum accuracy is also applicable to other polar molecular liquids.
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Affiliation(s)
- Aravind Krishnamoorthy
- Collaboratory for Advanced Computing and Simulations, Department of Chemical Engineering and Materials Science, Department of Physics & Astronomy, and Department of Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Ken-Ichi Nomura
- Collaboratory for Advanced Computing and Simulations, Department of Chemical Engineering and Materials Science, Department of Physics & Astronomy, and Department of Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Nitish Baradwaj
- Collaboratory for Advanced Computing and Simulations, Department of Chemical Engineering and Materials Science, Department of Physics & Astronomy, and Department of Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Kohei Shimamura
- Department of Physics, Kumamoto University, Kumamoto 860-8555, Japan
| | - Pankaj Rajak
- Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Ankit Mishra
- Collaboratory for Advanced Computing and Simulations, Department of Chemical Engineering and Materials Science, Department of Physics & Astronomy, and Department of Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Shogo Fukushima
- Department of Physics, Kumamoto University, Kumamoto 860-8555, Japan
| | - Fuyuki Shimojo
- Department of Physics, Kumamoto University, Kumamoto 860-8555, Japan
| | - Rajiv Kalia
- Collaboratory for Advanced Computing and Simulations, Department of Chemical Engineering and Materials Science, Department of Physics & Astronomy, and Department of Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Aiichiro Nakano
- Collaboratory for Advanced Computing and Simulations, Department of Chemical Engineering and Materials Science, Department of Physics & Astronomy, and Department of Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Priya Vashishta
- Collaboratory for Advanced Computing and Simulations, Department of Chemical Engineering and Materials Science, Department of Physics & Astronomy, and Department of Computer Science, University of Southern California, Los Angeles, California 90089, USA
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18
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Lambros E, Hu J, Paesani F. Assessing the Accuracy of the SCAN Functional for Water through a Many-Body Analysis of the Adiabatic Connection Formula. J Chem Theory Comput 2021; 17:3739-3749. [DOI: 10.1021/acs.jctc.1c00141] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Eleftherios Lambros
- 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
| | - 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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19
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Zhu T, Van Voorhis T. Understanding the Dipole Moment of Liquid Water from a Self-Attractive Hartree Decomposition. J Phys Chem Lett 2021; 12:6-12. [PMID: 33296211 DOI: 10.1021/acs.jpclett.0c03300] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The dipole moment of a single water molecule in liquid water has been a critical concept for understanding water's dielectric properties. In this work, we investigate the dipole moment of liquid water through a self-attractive Hartree (SAH) decomposition of total electron density computed by density functional theory, on water clusters sampled from ab initio molecular dynamics simulation of bulk water. By adjusting one parameter that controls the degree of density localization, we reveal two distinct pictures of water dipoles that are consistent with bulk dielectric properties: a localized picture with smaller and less polarizable monomer dipoles and a delocalized picture with larger and more polarizable monomer dipoles. We further uncover that the collective dipole-dipole correlation is stronger in the localized picture and is key to connecting individual dipoles with bulk dielectric properties. On the basis of these findings, we suggest considering both individual and collective dipole behaviors when studying the dipole moment of liquid water and propose new design strategies for developing water models.
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Affiliation(s)
- Tianyu Zhu
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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20
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21
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Li M, Chen L, Gui L, Cao S, Liu D, Zhao G, Ding M, Yan J, Wang D. Born–Oppenheimer molecular dynamics simulations on structures of high-density and low-density water: a comparison of the SCAN meta-GGA and PBE GGA functionals. Phys Chem Chem Phys 2021; 23:2298-2304. [DOI: 10.1039/d0cp05707j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using Born–Oppenheimer ab initio molecular dynamics (BOAIMD) simulations, the high-density water (HDW) and low-density water (LDW) structures based on SCAN meta-GGA are compared with those based on PBE GGA.
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Affiliation(s)
- Mengli Li
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Lu Chen
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Lirong Gui
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Shuo Cao
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Di Liu
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Gang Zhao
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Mingcui Ding
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Jinliang Yan
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Dehua Wang
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
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22
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Frank I. Some simple facts about water: CPMD simulation. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1802074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Irmgard Frank
- Theoretical Chemistry, Leibniz Universität Hannover, Hannover, Germany
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23
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Akter S, Yamamoto Y, Diaz CM, Jackson KA, Zope RR, Baruah T. Study of self-interaction errors in density functional predictions of dipole polarizabilities and ionization energies of water clusters using Perdew–Zunger and locally scaled self-interaction corrected methods. J Chem Phys 2020; 153:164304. [DOI: 10.1063/5.0025601] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Sharmin Akter
- Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Yoh Yamamoto
- Department of Physics, University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Carlos M. Diaz
- Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Koblar A. Jackson
- Physics Department and Science of Advanced Materials Program, Central Michigan University, Mt. Pleasant, Michigan 48859, USA
| | - Rajendra R. Zope
- Department of Physics, University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Tunna Baruah
- Department of Physics, University of Texas at El Paso, El Paso, Texas 79968, USA
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24
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Koizumi K, Hashizume D, Umeda J, Kimura M, Yokota T, Ito M, Iguchi A, Nakamura S. A comparison of geometries and electronic structure of plumbogummite (PbAl3P2O14H6), Pb2P4O12 and Pb2P2O7. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Cuny J, Cerda Calatayud J, Ansari N, Hassanali AA, Rapacioli M, Simon A. Simulation of Liquids with the Tight-Binding Density-Functional Approach and Improved Atomic Charges. J Phys Chem B 2020; 124:7421-7432. [PMID: 32696649 DOI: 10.1021/acs.jpcb.0c04167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Theoretical description of liquids, especially liquid water, is an ongoing subject with important implications in various domains such as homogeneous catalysis; solvation of molecular, ionic, and biomolecular species; and reactivity. Various formalisms exist to describe liquids, each one displaying its own balance between accuracy and computational cost that defines its range of applications. The present article revisits the ability of the density-functional-based tight-binding (SCC-DFTB) approach to model liquids by focusing on liquid water and liquid benzene under ambient conditions. To do so, we benchmark a recent correction for the SCC-DFTB atomic charges that allows for a drastic improvement of the pair radial distribution functions of liquid water as compared to both experimental data and density-functional theory results performed in the generalized-gradient approximation. We also report the coupling of the deMonNano and i-PI codes to perform path-integral molecular dynamics. This allows us to rationalize the impact of nuclear quantum effects on the SCC-DFTB description of liquid water. This study evidences the rather good ability of SCC-DFTB to describe liquid water and liquid benzene. As the first example of application, we also present results for a benzene molecule solvated in water with the perspectives of further studies devoted to solvent/water interfaces.
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Affiliation(s)
- Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jesus Cerda Calatayud
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Narjes Ansari
- The Abdus Salam International Center for Theoretical Physics, Condensed Matter and Statistical Physics Section, Strada Costiera 11, 34151 Trieste, Italy.,Department of Chemistry and Applied Biosciences, ETH Zurich, 3 c/o USI Campus, Via Giuseppe Buffi13, 6900 Lugano, Switzerland.,Facoltà di informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland
| | - Ali A Hassanali
- The Abdus Salam International Center for Theoretical Physics, Condensed Matter and Statistical Physics Section, Strada Costiera 11, 34151 Trieste, Italy
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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26
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Yao Y, Kanai Y. Temperature dependence of nuclear quantum effects on liquid water via artificial neural network model based on SCAN meta-GGA functional. J Chem Phys 2020; 153:044114. [DOI: 10.1063/5.0012815] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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27
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Blumberger J, Gaigeot MP, Sulpizi M, Vuilleumier R. Frontiers in molecular simulation of solvated ions, molecules and interfaces. Phys Chem Chem Phys 2020; 22:10393-10396. [PMID: 32352136 DOI: 10.1039/d0cp90091e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This themed collection is a collection of articles on frontiers in molecular simulation of solvated ions, molecules and interfaces.
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Affiliation(s)
- J Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, UK.
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28
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Jindal A, Vasudevan S. Hydrogen Bonding in the Liquid State of Linear Alcohols: Molecular Dynamics and Thermodynamics. J Phys Chem B 2020; 124:3548-3555. [PMID: 32242419 DOI: 10.1021/acs.jpcb.0c01199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Linear monohydroxy alcohols are strongly hydrogen-bonded liquids that are considered to be homologues of water. Here, we report ab initio molecular dynamics simulations of the liquid alcohols, methanol to pentanol, and from the combined radial-angular probability distribution of the intermolecular O···O distances and HO···O angles determine the geometrical parameters that define the hydrogen bonds in these systems. The key feature of hydrogen bonds in the liquid alcohols, irrespective of the size of the alkyl group, is the strong orientation dependence with the donor-acceptor HO···O angle being close to zero, similar to that observed in liquid water. Hydrogen bond formation is consequently considered to be the passage from a state where donor-acceptor pairs show no preferred orientation to one where they are almost linear. The potential of mean force, the reversible work associated with this process, is computed from the pair probability density distributions obtained from the simulations and that for a hypothetical state where donor-acceptor pairs are randomly oriented. We find that the magnitude of the free energy for hydrogen bond formation is maximum for ethanol and show that this arises from a larger electrostatic contribution to hydrogen bond formation in ethanol as compared to the other alcohols.
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Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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29
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Schienbein P, Marx D. Assessing the properties of supercritical water in terms of structural dynamics and electronic polarization effects. Phys Chem Chem Phys 2020; 22:10462-10479. [DOI: 10.1039/c9cp05610f] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Evolution of water's structural dynamics from ambient liquid to supercritical dense liquid-like and dilute gas-like conditions.
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Affiliation(s)
- Philipp Schienbein
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
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30
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Mehnaz, Yang LH, Zou YB, Da B, Mao SF, Li HM, Zhao YF, Ding ZJ. A comparative study on Monte Carlo simulations of electron emission from liquid water. Med Phys 2019; 47:759-771. [PMID: 31702062 DOI: 10.1002/mp.13913] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/06/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Liquid water being the major constituent of the human body, is of fundamental importance in radiobiological research. Hence, the knowledge of electron-water interaction physics and particularly the secondary electron yield is essential. However, to date, only very little is known experimentally on the low energy electron interaction with liquid water because of certain practical limitations. The purpose of this study was to gain some useful information about electron emission from water using a Monte Carlo (MC) simulation technique that can numerically model electron transport trajectories in water. METHODS In this study, we have performed MC simulations of electron emission from liquid water in the primary energy range of 50 eV-30 keV by using two different codes, i.e., a classical trajectory MC (CMC) code developed in our laboratory and the Geant4-DNA (G4DNA) code. The calculated secondary electron yield and electron backscattering coefficient are compared with experimental results wherever applicable to verify the validity of physical models for the electron-water interaction. RESULTS The secondary electron yield vs. primary energy curves calculated using the two codes present the same generic curve shape as that of metals but in rather different absolute values. G4DNA underestimates the secondary electron yield due to the application of one step thermalization model by setting a cutoff energy at 10 eV so that the low energy losses due to phonon excitations are omitted. Our CMC code, using a full energy loss spectrum to model electron inelastic scattering, allows the simulation of individual phonon scattering events for very low energy losses down to 10 meV, which then enables the calculated secondary electron yields much closer to the experimental data and also gives quite reasonable energy distribution curve of secondary electrons. CONCLUSIONS It is concluded that full dielectric function data at low energy loss values below 10 eV are recommended for modeling of low energy electrons in liquid water.
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Affiliation(s)
- Mehnaz
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
| | - L H Yang
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
| | - Y B Zou
- School of Physics & Electronic Engineering, Xinjiang Normal University, Urumqi, Xinjiang, 830054, P.R. China
| | - B Da
- Center for Materials Research by Information Integration (CMI2), Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki, 305-0047, Japan
| | - S F Mao
- Department of Engineering and Applied Physics, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
| | - H M Li
- Supercomputing Center, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
| | - Y F Zhao
- Radiotherapy Department, Anhui Provincial Hospital, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
| | - Z J Ding
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
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31
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LaCount MD, Gygi F. Ensemble first-principles molecular dynamics simulations of water using the SCAN meta-GGA density functional. J Chem Phys 2019; 151:164101. [DOI: 10.1063/1.5124957] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Michael D. LaCount
- Department of Computer Science, University of California, Davis, California 95616, USA
| | - François Gygi
- Department of Computer Science, University of California, Davis, California 95616, USA
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32
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Miyazaki K, Takenaka N, Watanabe E, Iizuka S, Yamada Y, Tateyama Y, Yamada A. First-Principles Study on the Peculiar Water Environment in a Hydrate-Melt Electrolyte. J Phys Chem Lett 2019; 10:6301-6305. [PMID: 31512877 DOI: 10.1021/acs.jpclett.9b02207] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Aqueous electrolytes have great potential to improve the safety and production costs of Li-ion batteries. Our recent materials exploration led to the discovery of the Li-salt dihydrate melt Li(TFSI)0.7(BETI)0.3·2H2O, which possesses an extremely wide potential window. To clarify the detailed liquid structure and electronic states of this unique aqueous system, a first-principles molecular dynamics study has been conducted. We found that water molecules in the hydrate melt exist as isolated monomers or clusters consisting of only a few (at most five) H2O molecules. Both the monomers and the clusters have electronic structures largely deviating from that in bulk water, where the lowest unoccupied states are higher in energy than that of the Li-salt anions, which preferentially cause anion reduction leading to formation of an anion-derived stable solid-electrolyte interphase. This clearly shows the role of characteristic electronic structure inherent to the peculiar water environment for the extraordinary electrochemical stability of hydrate melts.
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Affiliation(s)
- Kasumi Miyazaki
- Department of Chemical System Engineering , The University of Tokyo , 7-3-1, Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Norio Takenaka
- Department of Chemical System Engineering , The University of Tokyo , 7-3-1, Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
- Elements Strategy Initiative for Catalysts & Batteries (ESICB) , Kyoto University , 1-30 Goryo-Ohara , Nishikyo-ku, Kyoto 615-8545 , Japan
| | - Eriko Watanabe
- Department of Chemical System Engineering , The University of Tokyo , 7-3-1, Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Shota Iizuka
- Center for Green Research on Energy and Environmental Materials and International Center for Materials Nanoarchitectonics , National Institute for Materials Science (NIMS) , Tsukuba 305-0044 , Japan
| | - Yuki Yamada
- Department of Chemical System Engineering , The University of Tokyo , 7-3-1, Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
- Elements Strategy Initiative for Catalysts & Batteries (ESICB) , Kyoto University , 1-30 Goryo-Ohara , Nishikyo-ku, Kyoto 615-8545 , Japan
| | - Yoshitaka Tateyama
- Elements Strategy Initiative for Catalysts & Batteries (ESICB) , Kyoto University , 1-30 Goryo-Ohara , Nishikyo-ku, Kyoto 615-8545 , Japan
- Center for Green Research on Energy and Environmental Materials and International Center for Materials Nanoarchitectonics , National Institute for Materials Science (NIMS) , Tsukuba 305-0044 , Japan
| | - Atsuo Yamada
- Department of Chemical System Engineering , The University of Tokyo , 7-3-1, Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
- Elements Strategy Initiative for Catalysts & Batteries (ESICB) , Kyoto University , 1-30 Goryo-Ohara , Nishikyo-ku, Kyoto 615-8545 , Japan
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33
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Wang LP, Song C. Car-Parrinello Monitor for More Robust Born-Oppenheimer Molecular Dynamics. J Chem Theory Comput 2019; 15:4454-4467. [PMID: 31318557 PMCID: PMC9749491 DOI: 10.1021/acs.jctc.9b00439] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Born-Oppenheimer molecular dynamics (BOMD) is a promising simulation method for exploring the possible reaction pathways of a chemical system, but one significant challenge is the increased difficulty of converging the self-consistent field (SCF) calculation that often accompanies the breaking and forming of chemical bonds. To address this challenge, we developed an enhancement to the BOMD simulation method called the Car-Parrinello monitor (CPMonitor) that uses Car-Parrinello molecular dynamics (CPMD) to recover from SCF convergence failures. CPMonitor works by detecting SCF convergence failures in BOMD and switching to a CPMD Hamiltonian to propagate through the region of configuration space where the SCF calculation is unable to converge, then switching back to BOMD when good convergence behavior is re-established. We present a series of simulation studies that use CPMonitor, including detailed studies of the thermodynamic and dynamical properties of simple systems, as well as ab initio nanoreactor simulations containing transition metal atoms that were previously not possible to simulate using standard BOMD methods. Our studies show that CPMonitor can make BOMD simulations robust to SCF convergence difficulties and improve simulation performance and stability in reaction discovery applications.
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Affiliation(s)
- Lee-Ping Wang
- Department of Chemistry, University of California; 1 Shields Ave; Davis, CA 95616
| | - Chenchen Song
- Department of Chemistry and the PULSE Institute, Stanford University; Stanford, CA 94305.,SLAC National Accelerator Laboratory; Menlo Park, CA 94025
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34
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Choudhary A, Chandra A. An ab initio molecular dynamics study of benzene in water at supercritical conditions: Structure, dynamics, and polarity of hydration shell water and the solute. J Chem Phys 2019; 151:044508. [PMID: 31370512 DOI: 10.1063/1.5094570] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Anisotropic structure and dynamics of the hydration shell of a benzene solute in supercritical water are investigated by means of ab initio molecular dynamics simulations. The polarity and structural distortion of the benzene solute in supercritical water are also investigated in this study. Calculations are done at 673 K for three different densities of the solvent. The simulations are carried out using the Becke-Lee-Yang-Parr (BLYP) and also the Becke-Lee-Yang-Parr functional including dispersion corrections of Grimme (BYLP-D). The structural anisotropy is found to exist even at supercritical conditions as elucidated by the radial distribution functions of different conical regions and also by angular and spatial distribution functions. The benzene-water πH-bond and also the water-water hydrogen bonds are found to exist even at the supercritical temperature of 673 K. However, the numbers of these hydrogen bonds are reduced substantially with a decrease in water density. The water molecules in the axial region of benzene are found to be preferably oriented with one OH vector pointing toward the benzene ring, whereas the water molecules located in the equatorial region are found to orient their dipoles mostly parallel to the ring plane. The orientational distributions, however, are found to be rather broad at the supercritical temperature due to thermal fluctuations. Although the water molecules have faster dynamics at these supercritical conditions, a slight difference is observed in the dynamics of the solvation shell and bulk molecules. The conformational flexibility of the ring is found to be enhanced which causes an increase in polarity of the benzene solute in water under supercritical conditions.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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35
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Pagliai M, Funghi G, Vassetti D, Procacci P, Chelli R, Cardini G. Imidazole in Aqueous Solution: Hydrogen Bond Interactions and Structural Reorganization with Concentration. J Phys Chem B 2019; 123:4055-4064. [DOI: 10.1021/acs.jpcb.9b01611] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Pagliai
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Giada Funghi
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Dario Vassetti
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Piero Procacci
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Riccardo Chelli
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Gianni Cardini
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
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36
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Koizumi K, Nobusada K, Boero M. Hydrogen storage mechanism and diffusion in metal-organic frameworks. Phys Chem Chem Phys 2019; 21:7756-7764. [PMID: 30638226 DOI: 10.1039/c8cp07467d] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diffusion and storage of hydrogen molecules in metal-organic frameworks are crucial for the development of next-generation energy storage devices. By resorting to the first principles modeling, we compute the diffusion coefficient of molecular hydrogen in these systems in a range of temperatures where MOF-based devices are expected to operate. The explicit inclusion of the electronic structure shows that diffusivities are one order of magnitude smaller than those reported by classical simulations, evidencing the insufficiency of the empirical force fields used so far. We show that hydrogen is mainly rolled up around the metal oxide nodes both in MOF-5 and IRMOF-6, and partly around the carbon atoms in the case of IRMOF-6, where charged linkers are present. Metal ions embedded in the junction sites exert an electrostatic attraction toward hydrogen and the resulting distribution shows some ordering around these same sites at low temperature, whereas this tendency vanishes at room temperature. The induced polarization of hydrogen molecules generates an electrostatic interaction with charged atoms inside these nano-scaffolds and this is a key factor for the enhancement in hydrogen storage both in MOF-5 and IRMOF-6. The mechanism discussed hereby provides a novel understanding of metal-organic frameworks and acts as a guide to tune their efficiency for hydrogen storage. Moreover it paves the way to a computer-aided design of effective MOFs indicating that a fine control of the distribution of electrostatic charges inside the hydrogen hosting structure is crucial.
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Affiliation(s)
- Kenichi Koizumi
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan.
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37
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Milne AW, Jorge M. Polarization Corrections and the Hydration Free Energy of Water. J Chem Theory Comput 2018; 15:1065-1078. [DOI: 10.1021/acs.jctc.8b01115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Andrew W. Milne
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow G1 1XQ, United Kingdom
| | - Miguel Jorge
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow G1 1XQ, United Kingdom
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38
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Santos JCC, Negreiros FR, Pedroza LS, Dalpian GM, Miranda PB. Interaction of Water with the Gypsum (010) Surface: Structure and Dynamics from Nonlinear Vibrational Spectroscopy and Ab Initio Molecular Dynamics. J Am Chem Soc 2018; 140:17141-17152. [DOI: 10.1021/jacs.8b09907] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jaciara C. C. Santos
- Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, São Carlos, São Paulo 13560-970, Brazil
| | - Fabio R. Negreiros
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo 09210-580, Brazil
| | - Luana S. Pedroza
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo 09210-580, Brazil
| | - Gustavo M. Dalpian
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo 09210-580, Brazil
| | - Paulo B. Miranda
- Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, São Carlos, São Paulo 13560-970, Brazil
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39
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Tsimpanogiannis IN, Moultos OA, Franco LFM, Spera MBDM, Erdős M, Economou IG. Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1511903] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ioannis N. Tsimpanogiannis
- Environmental Research Laboratory, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
| | - Othonas A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Luís F. M. Franco
- School of Chemical Engineering, University of Campinas, Campinas, Brazil
| | | | - Máté Erdős
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Ioannis G. Economou
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Chemical Engineering Program, Texas A&M University at Qatar, Doha, Qatar
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40
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Neto APV, Machado DFS, Lopes TO, Camargo AJ, de Oliveira HCB. Explicit Aqueous Solvation Treatment of Epinephrine from Car–Parrinello Molecular Dynamics: Effect of Hydrogen Bonding on the Electronic Absorption Spectrum. J Phys Chem B 2018; 122:8439-8450. [DOI: 10.1021/acs.jpcb.8b06110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Arsênio P. V. Neto
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular (LEEDMOL), Instituto de Química, Universidade Federal de Goiás, 70904-970 Brasília, DF, Brazil
| | - Daniel F. Scalabrini Machado
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular (LEEDMOL), Instituto de Química, Universidade Federal de Goiás, 70904-970 Brasília, DF, Brazil
| | - Thiago O. Lopes
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular (LEEDMOL), Instituto de Química, Universidade Federal de Goiás, 70904-970 Brasília, DF, Brazil
| | - Ademir J. Camargo
- Grupo de Química Teórica de Anápolis (GQTEA), Universidade Estadual de Goiás, 75132-903 Anápolis, Goiás, Brazil
| | - Heibbe C. B. de Oliveira
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular (LEEDMOL), Instituto de Química, Universidade Federal de Goiás, 70904-970 Brasília, DF, Brazil
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular (LEEDMOL), Instituto de Química, Universidade de Brasília, 74690-900 Goiânia, Goiás, Brazil
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41
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Cuny J, Jolibois F, Gerber IC. Evaluation of Gas-to-Liquid 17O Chemical Shift of Water: A Test Case for Molecular and Periodic Approaches. J Chem Theory Comput 2018; 14:4041-4051. [DOI: 10.1021/acs.jctc.8b00243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC), Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Franck Jolibois
- LPCNO, Université Fédérale de Toulouse Midi-Pyrénées, INSA-CNRS-UPS, 135 avenue de Rangueil, 31077 Cedex 4 Toulouse, France
| | - Iann C. Gerber
- LPCNO, Université Fédérale de Toulouse Midi-Pyrénées, INSA-CNRS-UPS, 135 avenue de Rangueil, 31077 Cedex 4 Toulouse, France
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42
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Singraber A, Morawietz T, Behler J, Dellago C. Density anomaly of water at negative pressures from first principles. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:254005. [PMID: 29762140 DOI: 10.1088/1361-648x/aac4f4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Using molecular dynamics simulations based on ab initio trained high-dimensional neural network potentials, we study the equation of state of liquid water at negative pressures. From density isobars computed for various pressures down to p = -230 MPa we determine the line of density maxima for two potentials based on the BLYP and the RPBE functionals, respectively. In both cases, dispersion corrections are included to account for non-local long-range correlations that give rise to van der Waals forces. We have followed the density maximum down to negative pressures close to the spinodal instability. For both functionals, the temperature of maximum density increases with decreasing pressure under moderate stretching, but changes slope at [Formula: see text] MPa and [Formula: see text] MPa for BLYP and RPBE, respectively. Our calculations confirm qualitatively the retracing shape of the line of density maxima found for empirical water models, indicating that the spinodal line maintains a positive slope even at strongly negative pressures.
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Affiliation(s)
- Andreas Singraber
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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43
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Li F, Li Z, Li S, Fang W, Sun C, Men Z. Influence of the hydrogen bond quantum nature in liquid water and heavy water on stimulated Raman scattering. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 199:462-464. [PMID: 29133131 DOI: 10.1016/j.saa.2017.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 06/07/2023]
Abstract
Stimulated Raman scattering (SRS) of liquid water and heavy water have been investigated using Nd:YAG laser. The SRS spectra of liquid heavy water indicate that ice-VII and ice-VIII structures are formed by shock-induced compression (SIC) in forward and backward directions, respectively. Simultaneously, the SRS spectra reveal of liquid water that only ice-VII structure is formed in the backward direction. The difference in ice structures formed by SIC in liquid water and heavy water could be attributed to the effect of the hydrogen bond quantum nature with H+. SRS spectra of 2M NaOH water solution with ice-VII and ice-VIII structures have been successfully obtained in forward and backward, respectively, as OH- greatly reduce the quantum nature of hydrogen bonds by neutralizing H+ in water. The hydrogen bond quantum nature is important for understanding isotope calibration test structure and isotopic effect.
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Affiliation(s)
- Fabing Li
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Zhanlong Li
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Shuo Li
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Wenhui Fang
- School of Science, Changchun University of Science and Technology, Changchun 130012, China
| | - Chenglin Sun
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Zhiwei Men
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China.
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44
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Dawson W, Gygi F. Equilibration and analysis of first-principles molecular dynamics simulations of water. J Chem Phys 2018; 148:124501. [PMID: 29604876 DOI: 10.1063/1.5018116] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.
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Affiliation(s)
- William Dawson
- Department of Computer Science, University of California, Davis, Davis, California 95616, USA
| | - François Gygi
- Department of Computer Science, University of California, Davis, Davis, California 95616, USA
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45
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Gaiduk AP, Gustafson J, Gygi F, Galli G. First-Principles Simulations of Liquid Water Using a Dielectric-Dependent Hybrid Functional. J Phys Chem Lett 2018; 9:3068-3073. [PMID: 29768015 DOI: 10.1021/acs.jpclett.8b01017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We carried out first-principles simulations of liquid water under ambient conditions using a dielectric-dependent hybrid functional, where the fraction of exact exchange is set equal to the inverse of the high-frequency dielectric constant of the liquid. We found excellent agreement with experiment for the oxygen-oxygen partial correlation function at the experimental equilibrium density and 311 ± 3 K. Other structural and dynamical properties, such as the diffusion coefficient, molecular dipole moments, and vibrational spectra, are also in good agreement with experiment. Our results, together with previous findings on electronic properties of the liquid with the same functional, show that the dielectric-dependent hybrid functional accurately describes both the structural and electronic properties of liquid water.
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Affiliation(s)
- Alex P Gaiduk
- Institute for Molecular Engineering , The University of Chicago , Chicago , Illinois 60637 , United States
- Materials Science Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Jeffrey Gustafson
- Department of Chemistry , The University of Chicago , Chicago , Illinois 60637 , United States
| | - François Gygi
- Department of Computer Science , University of California , Davis , California 95616 , United States
| | - Giulia Galli
- Institute for Molecular Engineering , The University of Chicago , Chicago , Illinois 60637 , United States
- Materials Science Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
- Department of Chemistry , The University of Chicago , Chicago , Illinois 60637 , United States
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46
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Kakekhani A, Roling LT, Kulkarni A, Latimer AA, Abroshan H, Schumann J, AlJama H, Siahrostami S, Ismail-Beigi S, Abild-Pedersen F, Nørskov JK. Nature of Lone-Pair–Surface Bonds and Their Scaling Relations. Inorg Chem 2018; 57:7222-7238. [DOI: 10.1021/acs.inorgchem.8b00902] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arvin Kakekhani
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Luke T. Roling
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ambarish Kulkarni
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Allegra A. Latimer
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Hadi Abroshan
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Julia Schumann
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Hassan AlJama
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Samira Siahrostami
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Sohrab Ismail-Beigi
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, United States
| | - Frank Abild-Pedersen
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Jens K. Nørskov
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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47
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Zheng L, Chen M, Sun Z, Ko HY, Santra B, Dhuvad P, Wu X. Structural, electronic, and dynamical properties of liquid water by ab initio molecular dynamics based on SCAN functional within the canonical ensemble. J Chem Phys 2018; 148:164505. [DOI: 10.1063/1.5023611] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lixin Zheng
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Mohan Chen
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Zhaoru Sun
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Hsin-Yu Ko
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Biswajit Santra
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Pratikkumar Dhuvad
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Xifan Wu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
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48
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Liu J, He X, Zhang JZH, Qi LW. Hydrogen-bond structure dynamics in bulk water: insights from ab initio simulations with coupled cluster theory. Chem Sci 2018; 9:2065-2073. [PMID: 29675248 PMCID: PMC5885775 DOI: 10.1039/c7sc04205a] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/04/2017] [Indexed: 02/04/2023] Open
Abstract
An accurate and efficient ab initio molecular dynamics (AIMD) simulation of liquid water was made possible using the fragment-based approach (J. F. Liu, X. He and J. Z. H. Zhang, Phys. Chem. Chem. Phys., 2017, 19, 11931-11936). In this study, we advance the AIMD simulations using the fragment-based coupled cluster (CC) theory, more accurately revealing the structural and dynamical properties of liquid water under ambient conditions. The results show that the double-donor hydrogen-bond configurations in liquid water are nearly in balance with the single-donor configurations, with a slight bias towards the former. Our observation is in contrast to the traditional tetrahedral water structure. The hydrogen-bond switching dynamics in liquid water are very fast, with a hydrogen-bond life time of around 0.78 picoseconds, determined using AIMD simulation at the CCD/aug-cc-pVDZ level. This time scale is remarkably shorter than the ∼3.0 picoseconds that is commonly obtained from traditional nonpolarized force fields and density functional theory (DFT) based first-principles simulations. Additionally, the obtained radial distribution functions, triplet oxygen angular distribution, diffusion coefficient, and the dipole moment of the water molecule are uniformly in good agreement with the experimental observations. The current high-level AIMD simulation sheds light on the understanding of the structural and dynamical properties of liquid water.
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Affiliation(s)
- Jinfeng Liu
- State Key Laboratory of Natural Medicines , Department of Basic Medicine and Clinical Pharmacy , China Pharmaceutical University , Nanjing , 210009 , China .
| | - Xiao He
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China
- NYU-ECNU Center for Computational Chemistry , NYU Shanghai , Shanghai , 200062 , China
| | - John Z H Zhang
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China
- NYU-ECNU Center for Computational Chemistry , NYU Shanghai , Shanghai , 200062 , China
- Department of Chemistry , New York University , New York , NY 10003 , USA
| | - Lian-Wen Qi
- State Key Laboratory of Natural Medicines , Department of Basic Medicine and Clinical Pharmacy , China Pharmaceutical University , Nanjing , 210009 , China .
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49
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Liu J, He X, Zhang JZH. Structure of liquid water - a dynamical mixture of tetrahedral and 'ring-and-chain' like structures. Phys Chem Chem Phys 2018; 19:11931-11936. [PMID: 28440370 DOI: 10.1039/c7cp00667e] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The nature of the dynamical hydrogen-bond network of liquid water under ambient conditions has challenged both experimental and theoretical researchers for decades and remains a topic of intense debate. In this work, we addressed the structural issue of the hydrogen-bond network of liquid water based on an accurate ab initio molecular dynamics simulation. The present work showed clearly that liquid water is neither accurately described by a static picture of mostly tetrahedral water molecules nor dominated by "ring-and-chain" like structures. Instead, the structure of water is a dynamical mixture of tetrahedral and 'ring-and-chain' like structures with a slight bias toward the former. On average, each water molecule forms about three hydrogen bonds with the surrounding water molecules. The present accurate ab initio molecular dynamics simulation of liquid water was made possible by using a fragment-based second-order Møller-Plesset perturbation theory (MP2) with a large basis set to treat a large body of water molecules. This level of ab initio theory is sufficiently accurate for describing water interactions, and the simulated structural and dynamical properties of liquid water, including radial distribution functions, diffusion coefficient, dipole moment, etc., are uniformly in excellent agreement with experimental observations.
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Affiliation(s)
- Jinfeng Liu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
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50
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Yao Y, Kanai Y. Free Energy Profile of NaCl in Water: First-Principles Molecular Dynamics with SCAN and ωB97X-V Exchange–Correlation Functionals. J Chem Theory Comput 2018; 14:884-893. [DOI: 10.1021/acs.jctc.7b00846] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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