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Ambrosetti A, Silvestrelli PL, Salasnich L. Superfluidity Meets the Solid State: Frictionless Mass Transport through a (5,5) Carbon Nanotube. PHYSICAL REVIEW LETTERS 2023; 131:206301. [PMID: 38039458 DOI: 10.1103/physrevlett.131.206301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/17/2023] [Indexed: 12/03/2023]
Abstract
Superfluidity is a well-characterized quantum phenomenon which entails frictionless motion of mesoscopic particles through a superfluid, such as ^{4}He or dilute atomic gases at very low temperatures. As shown by Landau, the incompatibility between energy and momentum conservation, which ultimately stems from the spectrum of the elementary excitations of the superfluid, forbids quantum scattering between the superfluid and the moving mesoscopic particle, below a critical speed threshold. Here, we predict that frictionless motion can also occur in the absence of a standard superfluid, i.e., when a He atom travels through a narrow (5,5) carbon nanotube (CNT). Because of the quasilinear dispersion of the plasmon and phonon modes that could interact with He, the (5,5) CNT embodies a solid-state analog of the superfluid, thereby enabling straightforward transfer of Landau's criterion of superfluidity. As a result, Landau's equations acquire broader generality and may be applicable to other nanoscale friction phenomena, whose description has been so far purely classical.
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Affiliation(s)
- Alberto Ambrosetti
- Dipartimento di Fisica e Astronomia, Università degli Studi di Padova, via Marzolo 8, 35131 Padova, Italy
| | - Pier Luigi Silvestrelli
- Dipartimento di Fisica e Astronomia, Università degli Studi di Padova, via Marzolo 8, 35131 Padova, Italy
| | - Luca Salasnich
- Dipartimento di Fisica e Astronomia, Università degli Studi di Padova, via Marzolo 8, 35131 Padova, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Padova, via Marzolo 8, 35131 Padova, Italy and Istituto Nazionale di Ottica del Consiglio Nazionale delle Ricerche, Unità di Sesto Fiorentino, via Carrara 1, 50019 Sesto Fiorentino (Firenze), Italy
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2
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Li C, Paesani F, Voth GA. Static and Dynamic Correlations in Water: Comparison of Classical Ab Initio Molecular Dynamics at Elevated Temperature with Path Integral Simulations at Ambient Temperature. J Chem Theory Comput 2022; 18:2124-2131. [PMID: 35263110 PMCID: PMC9059465 DOI: 10.1021/acs.jctc.1c01223] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It is a common practice in ab initio molecular dynamics (AIMD) simulations of water to use an elevated temperature to overcome the overstructuring and slow diffusion predicted by most current density functional theory (DFT) models. The simulation results obtained in this distinct thermodynamic state are then compared with experimental data at ambient temperature based on the rationale that a higher temperature effectively recovers nuclear quantum effects (NQEs) that are missing in the classical AIMD simulations. In this work, we systematically examine the foundation of this assumption for several DFT models as well as for the many-body MB-pol model. We find for the cases studied that a higher temperature does not correctly mimic NQEs at room temperature, which is especially manifest in significantly different three-molecule correlations as well as hydrogen bond dynamics. In many of these cases, the effects of NQEs are the opposite of the effects of carrying out the simulations at an elevated temperature.
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Affiliation(s)
- Chenghan Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, Materials Science and Engineering, and San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637
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3
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Li C, Voth GA. Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics. J Chem Theory Comput 2022; 18:599-604. [PMID: 34982562 PMCID: PMC8864787 DOI: 10.1021/acs.jctc.1c01085] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ab initio molecular dynamics (AIMD) has become one of the most popular and robust approaches for modeling complicated chemical, liquid, and material systems. However, the formidable computational cost often limits its widespread application in simulations of the largest-scale systems. The situation becomes even more severe in cases where the hydrogen nuclei may be better described as quantized particles using a path integral representation. Here, we present a computational approach that combines machine learning with recent advances in path integral contraction schemes, and we achieve a 2 orders of magnitude acceleration over direct path integral AIMD simulation while at the same time maintaining its accuracy.
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4
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Calio PB, Li C, Voth GA. Resolving the Structural Debate for the Hydrated Excess Proton in Water. J Am Chem Soc 2021; 143:18672-18683. [PMID: 34723507 DOI: 10.1021/jacs.1c08552] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It has long been proposed that the hydrated excess proton in water (aka the solvated "hydronium" cation) likely has two limiting forms, that of the Eigen cation (H9O4+) and that of the Zundel cation (H5O2+). There has been debate over which of these two is the more dominant species and/or whether intermediate (or "distorted") structures between these two limits are the more realistic representation. Spectroscopy experiments have recently provided further results regarding the excess proton. These experiments show that the hydrated proton has an anisotropy reorientation time scale on the order of 1-2 ps. This time scale has been suggested to possibly contradict the picture of the more rapid "special pair dance" phenomenon for the hydrated excess proton, which is a signature of a distorted Eigen cation. The special pair dance was predicted from prior computational studies in which the hydrated central core hydronium structure continually switches (O-H···O)* special pair hydrogen-bond partners with the closest three water molecules, yielding on average a distorted Eigen cation with three equivalent and dynamically exchanging distortions. Through state-of-art simulations it is shown here that anisotropy reorientation time scales of the same magnitude are obtained that also include structural reorientations associated with the special pair dance, leading to a reinterpretation of the experimental results. These results and additional analyses point to a distorted and dynamic Eigen cation as the most prevalent hydrated proton species in aqueous acid solutions of dilute to moderate concentration, as opposed to a stabilized or a distorted (but not "dancing") Zundel cation.
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Affiliation(s)
- Paul B Calio
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Chenghan Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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5
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Kadaoluwa Pathirannahalage SP, Meftahi N, Elbourne A, Weiss ACG, McConville CF, Padua A, Winkler DA, Costa Gomes M, Greaves TL, Le TC, Besford QA, Christofferson AJ. Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:4521-4536. [PMID: 34406000 DOI: 10.1021/acs.jcim.1c00794] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions, mixtures, and materials settings. It therefore forms the basis for all molecular dynamics simulations of biological phenomena, as well as for many chemical, industrial, and materials investigations. Over the years, many water models have been developed, and it remains a challenge to find a single water model that accurately reproduces all experimental properties of water simultaneously. Here, we report a comprehensive comparison of structural and dynamic properties of 30 commonly used 3-point, 4-point, 5-point, and polarizable water models simulated using consistent settings and analysis methods. For the properties of density, coordination number, surface tension, dielectric constant, self-diffusion coefficient, and solvation free energy of methane, models published within the past two decades consistently show better agreement with experimental values compared to models published earlier, albeit with some notable exceptions. However, no single model reproduced all experimental values exactly, highlighting the need to carefully choose a water model for a particular study, depending on the phenomena of interest. Finally, machine learning algorithms quantified the relationship between the water model force field parameters and the resulting bulk properties, providing insight into the parameter-property relationship and illustrating the challenges of developing a water model that can accurately reproduce all properties of water simultaneously.
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Affiliation(s)
- Sachini P Kadaoluwa Pathirannahalage
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia.,Laboratoire de Chimie, Ecole Normale Supérieure de Lyon, CNRS, Lyon 69342, France
| | - Nastaran Meftahi
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Aaron Elbourne
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Alessia C G Weiss
- Leibniz-Institut für Polymerforschung e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Chris F McConville
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia.,Institute for Frontier Materials, Deakin University, Geelong, Victoria 3220, Australia
| | - Agilio Padua
- Laboratoire de Chimie, Ecole Normale Supérieure de Lyon, CNRS, Lyon 69342, France
| | - David A Winkler
- School of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia.,Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.,School of Pharmacy, University of Nottingham, Nottingham NG7 2QL, U.K
| | | | - Tamar L Greaves
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Tu C Le
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Quinn A Besford
- Leibniz-Institut für Polymerforschung e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Andrew J Christofferson
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia.,ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, Victoria 3000, Australia
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Li C, Voth GA. Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface. J Chem Theory Comput 2021; 17:5759-5765. [PMID: 34468142 PMCID: PMC8444337 DOI: 10.1021/acs.jctc.1c00609] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Indexed: 11/30/2022]
Abstract
Ab initio molecular dynamics (AIMD) and quantum mechanics/molecular mechanics (QM/MM) methods are powerful tools for studying proton solvation, transfer, and transport processes in various environments. However, due to the high computational cost of such methods, achieving sufficient sampling of rare events involving excess proton motion-especially when Grotthuss proton shuttling is involved-usually requires enhanced free energy sampling methods to obtain informative results. Moreover, an appropriate collective variable (CV) that describes the effective position of the net positive charge defect associated with an excess proton is essential both for tracking the trajectory of the defect and for the free energy sampling of the processes associated with the resulting proton transfer and transport. In this work, such a CV is derived from first principles using constrained density functional theory (CDFT). This CV is applicable to a broad array of proton transport and transfer processes as studied via AIMD and QM/MM simulations.
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Affiliation(s)
- Chenghan Li
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, James Franck Institute,
and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, James Franck Institute,
and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
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7
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Duignan TT, Kathmann SM, Schenter GK, Mundy CJ. Toward a First-Principles Framework for Predicting Collective Properties of Electrolytes. Acc Chem Res 2021; 54:2833-2843. [PMID: 34137593 DOI: 10.1021/acs.accounts.1c00107] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Given the universal importance of electrolyte solutions, it is natural to expect that we have a nearly complete understanding of the fundamental properties of these solutions (e.g., the chemical potential) and that we can therefore explain, predict, and control the phenomena occurring in them. In fact, reality falls short of these expectations. But, recent advances in the simulation and modeling of electrolyte solutions indicate that it should soon be possible to make progress toward these goals. In this Account, we will discuss the use of first-principles interaction potentials based in quantum mechanics (QM) to enhance our understanding of electrolyte solutions. Specifically, we will focus on the use of quantum density functional theory (DFT) combined with molecular dynamics simulation (DFT-MD) as the foundation for our approach. The overarching concept is to understand and accurately reproduce the balance between local or short-ranged (SR) structural details and long-range (LR) correlations, allowing the prediction of the thermodynamics of both single ions in solution as well as the collective interactions characterized by activity/osmotic coefficients. In doing so, relevant collective motions and driving forces characterized by chemical potentials can be determined.In this Account, we will make the case that understanding electrolyte solutions requires a faithful QM representation of the SR nature of the ion-ion, ion-water, and water-water interactions. However, the number of molecules that is required for collective behavior makes the direct application of high-level QM methods that contain the best SR physics untenable, making methods that balance accuracy and efficiency a practical goal. Alternatives such as continuum solvent models (CSMs) and empirically based classical molecular dynamics have been extensively employed to resolve this problem but without yet overcoming the fundamental issue of SR accuracy. We will demonstrate that accurately describing the SR interaction is imperative for predicting both intrinsic properties, namely, at infinite dilution, and collective properties of electrolyte solutions.DFT has played an important role in our understanding of condensed phase systems, e.g., bulk liquid water, the air-water interface, ions in bulk, and at the air-water interface. This approach holds huge promise to provide benchmark calculations of electrolyte solution properties that will allow for the development and improvement of more efficient methods, as well as an enhanced understanding of fundamental phenomena. However, the standard protocol using the generalized gradient approximation with van der Waals (vdW) correction requires improvement in order to achieve a high level of quantitative accuracy. Simply simulating with higher level DFT functionals may not be the best route considering the significant computational cost. Alternative methods of incorporating information from higher levels of QM should be explored; e.g., using force matching techniques on small clusters, where high level benchmark calculations are possible, to develop ideal correction terms to the DFT functional is a promising possibility. We argue that DFT with statistical mechanics is becoming an increasingly useful framework enabling the prediction of collective electrolyte properties.
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Affiliation(s)
- Timothy T. Duignan
- School of Chemical Engineering, The University of Queensland, St Lucia, Brisbane 4072, Australia
| | - Shawn M. Kathmann
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Gregory K. Schenter
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Christopher J. Mundy
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
- Affiliate Professor, Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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8
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Arntsen C, Chen C, Calio PB, Li C, Voth GA. The hopping mechanism of the hydrated excess proton and its contribution to proton diffusion in water. J Chem Phys 2021; 154:194506. [PMID: 34240917 DOI: 10.1063/5.0040758] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this work, a series of analyses are performed on ab initio molecular dynamics simulations of a hydrated excess proton in water to quantify the relative occurrence of concerted hopping events and "rattling" events and thus to further elucidate the hopping mechanism of proton transport in water. Contrary to results reported in certain earlier papers, the new analysis finds that concerted hopping events do occur in all simulations but that the majority of events are the product of proton rattling, where the excess proton will rattle between two or more waters. The results are consistent with the proposed "special-pair dance" model of the hydrated excess proton wherein the acceptor water molecule for the proton transfer will quickly change (resonate between three equivalent special pairs) until a decisive proton hop occurs. To remove the misleading effect of simple rattling, a filter was applied to the trajectory such that hopping events that were followed by back hops to the original water are not counted. A steep reduction in the number of multiple hopping events is found when the filter is applied, suggesting that many multiple hopping events that occur in the unfiltered trajectory are largely the product of rattling, contrary to prior suggestions. Comparing the continuous correlation function of the filtered and unfiltered trajectories, we find agreement with experimental values for the proton hopping time and Eigen-Zundel interconversion time, respectively.
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Affiliation(s)
- Christopher Arntsen
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, USA
| | - Chen Chen
- Department of Mechanical and Nuclear Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul B Calio
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Chenghan Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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Rosenberger D, Smith JS, Garcia AE. Modeling of Peptides with Classical and Novel Machine Learning Force Fields: A Comparison. J Phys Chem B 2021; 125:3598-3612. [DOI: 10.1021/acs.jpcb.0c10401] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- David Rosenberger
- Los Alamos National Laboratory, Theoretical Division, Chemistry and Physics of Materials Group, Los Alamos, 87545 New Mexico, United States
- Los Alamos National Laboratory, Theoretical Division, Center for Nonlinear Studies, Los Alamos, 87545 New Mexico, United States
| | - Justin S. Smith
- Los Alamos National Laboratory, Theoretical Division, Chemistry and Physics of Materials Group, Los Alamos, 87545 New Mexico, United States
| | - Angel E. Garcia
- Los Alamos National Laboratory, Theoretical Division, Center for Nonlinear Studies, Los Alamos, 87545 New Mexico, United States
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