1
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Mendonça BHS, de Moraes EE, Kirch A, Batista RJC, de Oliveira AB, Barbosa MC, Chacham H. Flow through Deformed Carbon Nanotubes Predicted by Rigid and Flexible Water Models. J Phys Chem B 2023; 127:8634-8643. [PMID: 37754781 DOI: 10.1021/acs.jpcb.3c02889] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
In this study, using nonequilibrium molecular dynamics simulation, the flow of water in deformed carbon nanotubes is studied for two water models TIP4P/2005 and simple point charge/FH (SPC/FH). The results demonstrated a nonuniform dependence of the flow on the tube deformation and the flexibility imposed on the water molecules, leading to an unexpected increase in the flow in some cases. The effects of the tube diameter and pressure gradient are investigated to explain the abnormal flow behavior with different degrees of structural deformation.
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Affiliation(s)
- Bruno H S Mendonça
- Departamento de Física, ICEX, Universidade Federal de Minas Gerais, CP 702, Belo Horizonte 30123-970, MG, Brazil
| | - Elizane E de Moraes
- Instituto de Física, Universidade Federal da Bahia, Campus Universitário de Ondina, Salvador 40210-340, BA, Brazil
| | - Alexsandro Kirch
- Instituto de Física, Universidade de São Paulo, CP 66318, São Paulo 05315-970, SP, Brazil
| | - Ronaldo J C Batista
- Departamento de Física, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto 35400-000, MG, Brazil
| | - Alan B de Oliveira
- Departamento de Física, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto 35400-000, MG, Brazil
| | - Marcia C Barbosa
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Hélio Chacham
- Departamento de Física, ICEX, Universidade Federal de Minas Gerais, CP 702, Belo Horizonte 30123-970, MG, Brazil
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2
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Riera M, Knight C, Bull-Vulpe EF, Zhu X, Agnew H, Smith DGA, Simmonett AC, Paesani F. MBX: A many-body energy and force calculator for data-driven many-body simulations. J Chem Phys 2023; 159:054802. [PMID: 37526156 PMCID: PMC10550339 DOI: 10.1063/5.0156036] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
Many-Body eXpansion (MBX) is a C++ library that implements many-body potential energy functions (PEFs) within the "many-body energy" (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of many-body interactions to achieve chemical accuracy from the gas to the condensed phases. MBX can be employed either as a stand-alone package or as an energy/force engine that can be integrated with generic software for molecular dynamics and Monte Carlo simulations. MBX is parallelized internally using Open Multi-Processing and can utilize Message Passing Interface when available in interfaced molecular simulation software. MBX enables classical and quantum molecular simulations with MB-nrg PEFs, as well as hybrid simulations that combine conventional force fields and MB-nrg PEFs, for diverse systems ranging from small gas-phase clusters to aqueous solutions and molecular fluids to biomolecular systems and metal-organic frameworks.
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Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Christopher Knight
- Argonne National Laboratory, Computational Science Division, Lemont, Illinois 60439, USA
| | - Ethan F. Bull-Vulpe
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Xuanyu Zhu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Henry Agnew
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | | | - Andrew C. Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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3
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Zhuang D, Riera M, Zhou R, Deary A, Paesani F. Hydration Structure of Na + and K + Ions in Solution Predicted by Data-Driven Many-Body Potentials. J Phys Chem B 2022; 126:9349-9360. [PMID: 36326071 DOI: 10.1021/acs.jpcb.2c05674] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The hydration structure of Na+ and K+ ions in solution is systematically investigated using a hierarchy of molecular models that progressively include more accurate representations of many-body interactions. We found that a conventional empirical pairwise additive force field that is commonly used in biomolecular simulations is unable to reproduce the extended X-ray absorption fine structure (EXAFS) spectra for both ions. In contrast, progressive inclusion of many-body effects rigorously derived from the many-body expansion of the energy allows the MB-nrg potential energy functions (PEFs) to achieve nearly quantitative agreement with the experimental EXAFS spectra, thus enabling the development of a molecular-level picture of the hydration structure of both Na+ and K+ in solution. Since the MB-nrg PEFs have already been shown to accurately describe isomeric equilibria and vibrational spectra of small ion-water clusters in the gas phase, the present study demonstrates that the MB-nrg PEFs effectively represent the long-sought-after models able to correctly predict the properties of ionic aqueous systems from the gas to the liquid phase, which has so far remained elusive.
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Affiliation(s)
- Debbie Zhuang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California92093, United States
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California92093, United States
| | - Ruihan Zhou
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California92093, United States
| | - Alexander Deary
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California92093, United States.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California92093, United States
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4
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Bull-Vulpe EF, Riera M, Bore SL, Paesani F. Data-Driven Many-Body Potential Energy Functions for Generic Molecules: Linear Alkanes as a Proof-of-Concept Application. J Chem Theory Comput 2022. [PMID: 36113028 DOI: 10.1021/acs.jctc.2c00645] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a generalization of the many-body energy (MB-nrg) theoretical/computational framework that enables the development of data-driven potential energy functions (PEFs) for generic covalently bonded molecules, with arbitrary quantum mechanical accuracy. The "nearsightedness of electronic matter" is exploited to define monomers as "natural building blocks" on the basis of their distinct chemical identity. The energy of generic molecules is then expressed as a sum of individual many-body energies of incrementally larger subsystems. The MB-nrg PEFs represent the low-order n-body energies, with n = 1-4, using permutationally invariant polynomials derived from electronic structure data carried out at an arbitrary quantum mechanical level of theory, while all higher-order n-body terms (n > 4) are represented by a classical many-body polarization term. As a proof-of-concept application of the general MB-nrg framework, we present MB-nrg PEFs for linear alkanes. The MB-nrg PEFs are shown to accurately reproduce reference energies, harmonic frequencies, and potential energy scans of alkanes, independently of their length. Since, by construction, the MB-nrg framework introduced here can be applied to generic covalently bonded molecules, we envision future computer simulations of complex molecular systems using data-driven MB-nrg PEFs, with arbitrary quantum mechanical accuracy.
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Affiliation(s)
- Ethan F. Bull-Vulpe
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Sigbjørn L. Bore
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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5
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Méndez E, Videla PE, Laria D. Equilibrium and Dynamical Characteristics of Hydrogen Bond Bifurcations in Water-Water and Water-Ammonia Dimers: A Path Integral Molecular Dynamics Study. J Phys Chem A 2022; 126:4721-4733. [PMID: 35834556 DOI: 10.1021/acs.jpca.2c02525] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present path integral molecular dynamics results that describe the effects of nuclear quantum fluctuations on equilibrium and dynamical characteristics pertaining to bifurcation pathways in hydrogen bonded dimers combining water and ammonia, at cryogenic temperatures of the order of 20 K. Along these isomerizations, the hydrogen atoms in the molecules acting as hydrogen-bond donors interchange their original dangling/connective characters. Our results reveal that the resulting quantum transition paths comprise three stages: the initial and final ones involve overall rotations during which the two protons retain their classical-like characteristics. Effects from quantum fluctuation are clearly manifested in the changes operated at the intermediate passages over transition states, as the spatial extents of the protons stretch over typical lengths comparable to the distances between connective and dangling basins of attractions. Consequently, the classical over-the-hill path is replaced by a tunneling controlled mechanism which, within the path integral perspective, can be cast in terms of concerted inter-basin migrations of polymer beads from dangling-to-connective and from connective-to-dangling, at practically no energy costs. We also estimated the characteristic timescales describing such interconversions within the approximate ring polymer rate theory. Effects derived from full and partial deuteration are also discussed.
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Affiliation(s)
- Emilio Méndez
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Ciudad Universitaria, Pabellón II, 1428 Buenos Aires, Argentina
| | - Pablo E Videla
- Department of Chemistry and Energy Sciences Institute, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Daniel Laria
- Departamento de Física de la Materia Condensada, Comisión Nacional de Energía Atómica, Avenida Libertador 8250, 1429 Buenos Aires, Argentina
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6
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Serwatka T, Roy PN. Ground state of asymmetric tops with DMRG: Water in one dimension. J Chem Phys 2022; 156:044116. [DOI: 10.1063/5.0078770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tobias Serwatka
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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7
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Schmidt M, Millar J, Roy PN. Path integral simulations of confined parahydrogen molecules within clathrate hydrates: Merging low temperature dynamics with the zero-temperature limit. J Chem Phys 2022; 156:014303. [PMID: 34998330 DOI: 10.1063/5.0076386] [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
Clathrate hydrates, or cages comprised solely of water molecules, have long been investigated as a clean storage facility for hydrogen molecules. A breakthrough occurred when hydrogen molecules were experimentally placed within a structure-II clathrate hydrate, which sparked much interest to determine their feasibility for energy storage [Mao et al., Science 297, 2247-2249 (2002)]. We use Path Integral Molecular Dynamics (PIMD) and Langevin equation Path Integral Ground State (LePIGS) for finite temperature and zero-temperature studies, respectively, to determine parahydrogen occupancy properties in the small dodecahedral (512) and large hexakaidecahedral (51264) sized cages that comprise the structure-II unit cell. We look at energetic and structural properties of small clusters of hydrogen, treated as point-like particles, confined within each of the different sized clathrates, and treated as rigid, to determine energetic and structural properties in the zero-temperature limit. Our predicted hydrogen occupancy within these two cage sizes is consistent with previous literature values. We then calculate the energies as a function of temperature and merge the low temperature results calculated using finite temperature PIMD with the zero-temperature results using LePIGS, demonstrating that the two methods are compatible.
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Affiliation(s)
- Matthew Schmidt
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jayme Millar
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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8
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Bull-Vulpe EF, Riera M, Götz AW, Paesani F. MB-Fit: Software infrastructure for data-driven many-body potential energy functions. J Chem Phys 2021; 155:124801. [PMID: 34598567 DOI: 10.1063/5.0063198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.
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Affiliation(s)
- Ethan F Bull-Vulpe
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, 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
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9
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Caruso A, Paesani F. Data-driven many-body models enable a quantitative description of chloride hydration from clusters to bulk. J Chem Phys 2021; 155:064502. [PMID: 34391363 DOI: 10.1063/5.0059445] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We present a new data-driven potential energy function (PEF) describing chloride-water interactions, which is developed within the many-body-energy (MB-nrg) theoretical framework. Besides quantitatively reproducing low-order many-body energy contributions, the new MB-nrg PEF is able to correctly predict the interaction energies of small chloride-water clusters calculated at the coupled cluster level of theory. Importantly, classical and quantum molecular dynamics simulations of a single chloride ion in water demonstrate that the new MB-nrg PEF predicts x-ray spectra in close agreement with the experimental results. Comparisons with an popular empirical model and a polarizable PEF emphasize the importance of an accurate representation of short-range many-body effect while demonstrating that pairwise additive representations of chloride-water and water-water interactions are inadequate for correctly representing the hydration structure of chloride in both gas-phase clusters and solution. We believe that the analyses presented in this study provide additional evidence for the accuracy and predictive ability of the MB-nrg PEFs, which can then enable more realistic simulations of ionic aqueous systems in different environments.
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Affiliation(s)
- 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
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10
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DiRisio RJ, Lu F, McCoy AB. GPU-Accelerated Neural Network Potential Energy Surfaces for Diffusion Monte Carlo. J Phys Chem A 2021; 125:5849-5859. [PMID: 34165989 DOI: 10.1021/acs.jpca.1c03709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Diffusion Monte Carlo (DMC) provides a powerful method for understanding the vibrational landscape of molecules that are not well-described by conventional methods. The most computationally demanding step of these calculations is the evaluation of the potential energy. In this work, a general approach is developed in which a neural network potential energy surface is trained by using data generated from a small-scale DMC calculation. Once trained, the neural network can be evaluated by using highly parallelizable calls to a graphics processing unit (GPU). The power of this approach is demonstrated for DMC simulations on H2O, CH5+, and (H2O)2. The need to include permutation symmetry in the neural network potentials is explored and incorporated into the molecular descriptors of CH5+ and (H2O)2. It is shown that the zero-point energies and wave functions obtained by using the neural network potentials are nearly identical to the results obtained when using the potential energy surfaces that were used to train the neural networks at a substantial savings in the computational requirements of the simulations.
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Affiliation(s)
- Ryan J DiRisio
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Fenris Lu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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11
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Sahoo T, Serwatka T, Roy PN. A path integral ground state approach for asymmetric top rotors with nuclear spin symmetry: Application to water chains. J Chem Phys 2021; 154:244305. [PMID: 34241367 DOI: 10.1063/5.0053051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A path integral ground state (PIGS) approach for the simulation of asymmetric top rotors is presented. The method is based on Monte Carlo sampling of angular degrees of freedom. A symmetry-adapted rotational density matrix is used to account for nuclear spin statistics. To illustrate the method, ground-state properties of collections of para-water molecules confined to a one-dimensional lattice are computed. Those include energetic and structural observables. An advantage of the PIGS method is that expectation values can be obtained directly since the square of the wavefunction is sampled during a simulation. To benchmark the method, ground state energies and orientational distributions are computed using exact diagonalization for a single para-water molecule in an external field using a finite basis of symmetric top eigenfunctions. Benchmark results are also provided for N = 2 para-water molecules pinned to lattice sites at various distances to sample the crossover from hydrogen bonding to the dipole-dipole interaction regime. Excellent agreement between the PIGS results and the finite basis set calculations is observed. A thorough analysis of the convergence in terms of the imaginary time propagation length and systematic Trotter error is performed. The PIGS approach is then applied to a chain of N = 11 water molecules, and an equation of state is constructed in terms of the intermolecular separation. Ordering effects are also studied, and a transition between hydrogen bonding to dipole-dipole alignment is observed. The method is scalable and can also be applied in higher dimensions.
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Affiliation(s)
- Tapas Sahoo
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Tobias Serwatka
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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12
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Lambros E, Paesani F. How good are polarizable and flexible models for water: Insights from a many-body perspective. J Chem Phys 2020; 153:060901. [DOI: 10.1063/5.0017590] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Eleftherios Lambros
- 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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13
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Méndez E, Laria D. Nuclear quantum effects on the hydrogen bond donor-acceptor exchange in water-water and water-methanol dimers. J Chem Phys 2020; 153:054302. [PMID: 32770908 DOI: 10.1063/5.0016122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present results from path integral molecular dynamics simulations that describe effects from the explicit incorporation of nuclear quantum fluctuations on the topology of the free energy associated with the geared exchange of hydrogen bonds in the water-water dimer. Compared to the classical treatment, our results reveal important reductions in the free energy barriers and changes at a qualitative level in the overall profile. Most notable are those manifested by a plateau behavior, ascribed to nuclear tunneling, which bridges reactant and product states, contrasting with the usual symmetric double-well profile. The characteristics of the proton localizations along the pathway are examined. An imaginary time analysis of the rotational degrees of freedom of the partners in the dimer at the vicinities of transition states shows a clear "anticorrelation" between intermolecular interactions coupling beads localized in connective and dangling basins of attractions. As such, the transfer is operated by gradual concerted inter-basin migrations in opposite directions, at practically no energy costs. Modifications operated by partial deuteration and by the asymmetries in the hydrogen bonding characteristics prevailing in water-methanol heterodimers are also examined.
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Affiliation(s)
- Emilio Méndez
- Departamento de Química Inorgánica Analítica y Química-Física e INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, 1428 Buenos Aires, Argentina
| | - Daniel Laria
- Departamento de Química Inorgánica Analítica y Química-Física e INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, 1428 Buenos Aires, Argentina
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14
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Zhai Y, Caruso A, Gao S, Paesani F. Active learning of many-body configuration space: Application to the Cs+–water MB-nrg potential energy function as a case study. J Chem Phys 2020; 152:144103. [DOI: 10.1063/5.0002162] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Yaoguang Zhai
- Department of Computer Science and Engineering, 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
| | - Sicun Gao
- Department of Computer Science and Engineering, 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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15
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Ueno S, Tanimura Y. Modeling Intermolecular and Intramolecular Modes of Liquid Water Using Multiple Heat Baths: Machine Learning Approach. J Chem Theory Comput 2020; 16:2099-2108. [DOI: 10.1021/acs.jctc.9b01288] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seiji Ueno
- HPC Systems Inc., Nakagyoku, Kyoto 604, Japan
- Department of Chemistry, Kyoto University, Kyoto 606-8502, Japan
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16
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Vaillant CL, Wales DJ, Althorpe SC. Tunneling Splittings in Water Clusters from Path Integral Molecular Dynamics. J Phys Chem Lett 2019; 10:7300-7304. [PMID: 31682130 DOI: 10.1021/acs.jpclett.9b02951] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present calculations of tunneling splittings in selected small water clusters, based on a recently developed path integral molecular dynamics (PIMD) method. The ground-rotational-state tunneling motions associated with the largest splittings in the water dimer, trimer, and hexamer are considered, and we show that the PIMD predictions are in very good agreement with benchmark quantum and experimental results. As the tunneling spectra are highly sensitive to both the details of the quantum dynamics and the potential energy surface, our calculations are a validation of the MB-Pol surface as well as the accuracy of PIMD. The favorable scaling of PIMD with system size paves the way for calculations of tunneling splittings in large, nonrigid molecular systems with motions that cannot be treated accurately by other methods, such as the semiclassical instanton.
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Affiliation(s)
- C L Vaillant
- Laboratory of Theoretical Physical Chemistry , Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - D J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - S C Althorpe
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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17
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Lee VGM, McCoy AB. An Efficient Approach for Studies of Water Clusters Using Diffusion Monte Carlo. J Phys Chem A 2019; 123:8063-8070. [DOI: 10.1021/acs.jpca.9b06444] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Victor G. M. Lee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Anne B. McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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18
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Micciarelli M, Conte R, Suarez J, Ceotto M. Anharmonic vibrational eigenfunctions and infrared spectra from semiclassical molecular dynamics. J Chem Phys 2018; 149:064115. [DOI: 10.1063/1.5041911] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Marco Micciarelli
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Jaime Suarez
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
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Vaillant CL, Wales DJ, Althorpe SC. Tunneling splittings from path-integral molecular dynamics using a Langevin thermostat. J Chem Phys 2018; 148:234102. [DOI: 10.1063/1.5029258] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- C. L. Vaillant
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - D. J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - S. C. Althorpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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