1
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Palos E, Bull-Vulpe EF, Zhu X, Agnew H, Gupta S, Saha S, Paesani F. Current Status of the MB-pol Data-Driven Many-Body Potential for Predictive Simulations of Water Across Different Phases. J Chem Theory Comput 2024. [PMID: 39401055 DOI: 10.1021/acs.jctc.4c01005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Developing a molecular-level understanding of the properties of water is central to numerous scientific and technological applications. However, accurately modeling water through computer simulations has been a significant challenge due to the complex nature of the hydrogen-bonding network that water molecules form under different thermodynamic conditions. This complexity has led to over five decades of research and many modeling attempts. The introduction of the MB-pol data-driven many-body potential energy function marked a significant advancement toward a universal molecular model capable of predicting the structural, thermodynamic, dynamical, and spectroscopic properties of water across all phases. By integrating physics-based and data-driven (i.e., machine-learned) components, which correctly capture the delicate balance among different many-body interactions, MB-pol achieves chemical and spectroscopic accuracy, enabling realistic molecular simulations of water, from gas-phase clusters to liquid water and ice. In this review, we present a comprehensive overview of the data-driven many-body formalism adopted by MB-pol, highlight the main results and predictions made from computer simulations with MB-pol to date, and discuss the prospects for future extensions to data-driven many-body potentials of generic and reactive molecular 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
| | - Ethan F Bull-Vulpe
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Xuanyu Zhu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Henry Agnew
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Shreya Gupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Suman Saha
- 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
- Halicioǧlu Data Science Institute, 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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2
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Eraković M, Cvitaš MT. Tunneling splittings in the vibrationally excited states of water trimer. Phys Chem Chem Phys 2024; 26:12965-12981. [PMID: 38634688 DOI: 10.1039/d4cp00013g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Tunneling splitting (TS) patterns in vibrationally excited states of the water trimer are calculated, taking into account six tunneling pathways that describe the flips of free OH bonds and five bifurcation mechanisms that break and reform hydrogen bonds in the trimer ring. A tunneling matrix (TM) model is used to derive the energy shifts due to tunneling in terms of the six distinct TM elements in symbolic form. TM elements are calculated using the recently-developed modified WKB (Wentzel-Kramers-Brillouin) method in full dimensionality. Convergence was achieved for the lowest six excited vibrational modes. Bifurcation widths of the pseudorotational quartets are shown to be of comparable size to the ground-state widths, obtained using instanton theory, or increased for some particular modes of vibration. The largest increase is obtained for the excited out-of-phase flip of two adjacent water monomers with free OH bonds pointing in opposite directions relative to the ring plane. Bifurcation widths in (D2O)3 are found to be two orders of magnitude smaller than in (H2O)3. Geometrical arguments were used to explain the order of states in some TS multiplets in vibrationally excited water trimers.
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Affiliation(s)
- Mihael Eraković
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Marko T Cvitaš
- Department of Physics, University of Zagreb Faculty of Science, Zagreb, Croatia.
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3
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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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4
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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: 13] [Impact Index Per Article: 13.0] [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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5
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Trenins G, Meuser L, Bertschi H, Vavourakis O, Flütsch R, Richardson JO. Exact tunneling splittings from symmetrized path integrals. J Chem Phys 2023; 159:034108. [PMID: 37466233 DOI: 10.1063/5.0158879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
We develop a new simulation technique based on path-integral molecular dynamics for calculating ground-state tunneling splitting patterns from ratios of symmetrized partition functions. In particular, molecular systems are rigorously projected onto their J = 0 rotational state by an "Eckart spring" that connects two adjacent beads in a ring polymer. Using this procedure, the tunneling splitting can be obtained from thermodynamic integration at just one (sufficiently low) temperature. Converged results are formally identical to the values that would have been obtained by solving the full rovibrational Schrödinger equation on a given Born-Oppenheimer potential energy surface. The new approach is showcased with simulations of hydronium and methanol, which are in good agreement with wavefunction-based calculations and experimental measurements. The method will be of particular use for the study of low-barrier methyl rotations and other floppy modes, where instanton theory is not valid.
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Affiliation(s)
- George Trenins
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Lars Meuser
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Hannah Bertschi
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Odysseas Vavourakis
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Reto Flütsch
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jeremy O Richardson
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
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6
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Zhu YC, Yang S, Zeng JX, Fang W, Jiang L, Zhang DH, Li XZ. Accurate calculation of tunneling splittings in water clusters using path-integral based methods. J Chem Phys 2023; 158:2895223. [PMID: 37290067 DOI: 10.1063/5.0146562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/03/2023] [Indexed: 06/10/2023] Open
Abstract
Tunneling splittings observed in molecular rovibrational spectra are significant evidence for tunneling motion of hydrogen nuclei in water clusters. Accurate calculations of the splitting sizes from first principles require a combination of high-quality inter-atomic interactions and rigorous methods to treat the nuclei with quantum mechanics. Many theoretical efforts have been made in recent decades. This Perspective focuses on two path-integral based tunneling splitting methods whose computational cost scales well with the system size, namely, the ring-polymer instanton method and the path-integral molecular dynamics (PIMD) method. From a simple derivation, we show that the former is a semiclassical approximation to the latter, despite that the two methods are derived very differently. Currently, the PIMD method is considered to be an ideal route to rigorously compute the ground-state tunneling splitting, while the instanton method sacrifices some accuracy for a significantly smaller computational cost. An application scenario of such a quantitatively rigorous calculation is to test and calibrate the potential energy surfaces of molecular systems by spectroscopic accuracy. Recent progress in water clusters is reviewed, and the current challenges are discussed.
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Affiliation(s)
- Yu-Cheng Zhu
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Frontier Science Center for Nano-optoelectronics and School of Physics, Peking University, Beijing 100871, People's Republic of China
- Interdisciplinary Institute of Light-Element Quantum Materials, Research Center for Light-Element Advanced Materials, and Collaborative Innovation Center of Quantum Materials, Peking University, Beijing 100871, People's Republic of China
| | - Shuo Yang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jia-Xi Zeng
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Frontier Science Center for Nano-optoelectronics and School of Physics, Peking University, Beijing 100871, People's Republic of China
- Interdisciplinary Institute of Light-Element Quantum Materials, Research Center for Light-Element Advanced Materials, and Collaborative Innovation Center of Quantum Materials, Peking University, Beijing 100871, People's Republic of China
| | - Wei Fang
- Department of Chemistry, Fudan University, Shanghai 200438, People's Republic of China
| | - Ling Jiang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
| | - Xin-Zheng Li
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Frontier Science Center for Nano-optoelectronics and School of Physics, Peking University, Beijing 100871, People's Republic of China
- Interdisciplinary Institute of Light-Element Quantum Materials, Research Center for Light-Element Advanced Materials, and Collaborative Innovation Center of Quantum Materials, Peking University, Beijing 100871, People's Republic of China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, People's Republic of China
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7
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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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8
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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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9
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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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10
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Eraković M, Cvitaš MT. Vibrational Tunneling Spectra of Molecules with Asymmetric Wells: A Combined Vibrational Configuration Interaction and Instanton Approach. J Chem Theory Comput 2022; 18:2785-2802. [PMID: 35439012 PMCID: PMC9097297 DOI: 10.1021/acs.jctc.2c00124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A combined approach
that uses the vibrational configuration interaction
(VCI) and semiclassical instanton theory was developed to study vibrational
tunneling spectra of molecules with multiple wells in full dimensionality.
The method can be applied to calculate low-lying vibrational states in the systems with an
arbitrary number of minima, which are not necessarily equal in energy
or shape. It was tested on a two-dimensional double-well model system
and on malonaldehyde, and the calculations reproduced the exact quantum
mechanical (QM) results with high accuracy. The method was subsequently
applied to calculate the vibrational spectrum of the asymmetrically
deuterated malonaldehyde with nondegenerate vibrational frequencies
in the two wells. The spectrum is obtained at a cost of single-well
VCI calculations used to calculate the local energies. The interactions
between states of different wells are computed semiclassically using
the instanton theory at a comparatively negligible computational cost.
The method is particularly suited to systems in which the wells are
separated by large potential barriers and tunneling splittings are
small, for example, in some water clusters, when the exact QM methods
come at a prohibitive computational cost.
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Affiliation(s)
- Mihael Eraković
- Department of Physical Chemistry, Rud̵er Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Marko T Cvitaš
- Department of Physics, Faculty of Science, University of Zagreb, Bijenička Cesta 32, 10000 Zagreb, Croatia
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11
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Measurement of Donor-Acceptor Interchange Tunnelling in Ar(H2O)2 using Rotational Spectroscopy and a Re-look at Its Structure and Bonding. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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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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13
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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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14
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Eraković M, Cvitaš MT. Tunnelling splitting patterns in some partially deuterated water trimers. Phys Chem Chem Phys 2021; 23:4240-4254. [PMID: 33586727 DOI: 10.1039/d0cp06135b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We apply our recently developed semiclassical method for calculating tunnelling splittings (TS) in asymmetric systems to make the first characterization of the ground-state TS pattern of some partially deuterated water trimers. Similarly to homoisotopic water trimers, the ground-state TS patterns are explained in terms of six distinct rearrangement mechanisms. TS patterns in (D2O)(H2O)2 and (H2O)(D2O)2 are composed of sextets induced by the dynamics of flips, and each of its levels is further finely split into a quartet of doublets and a doublet of quartets, respectively, due to various bifurcation dynamics. The TS pattern is obtained using 18 distinct tunnelling matrix elements. TS patterns of (HOD)(H2O)2 and (HOD)(D2O)2 each consists of two sextets, belonging to in-bond and out-of-bond substituted isomers. These sextet levels are further split into quartets by bifurcations. The TS pattern is computed in terms of 13 matrix elements. We also derive analytic expressions for bifurcation tunnelling splittings in terms of tunnelling matrix elements using symmetry. The present approach can be applied to other water clusters and also to the low-lying vibrationally excited states and should help in the interpretation and assignment of experimental spectra in the future.
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Affiliation(s)
- Mihael Eraković
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
| | - Marko T Cvitaš
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
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15
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Sahu N, Richardson JO, Berger R. Instanton calculations of tunneling splittings in chiral molecules. J Comput Chem 2021; 42:210-221. [PMID: 33259074 DOI: 10.1002/jcc.26447] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 11/11/2022]
Abstract
We report the ground state tunneling splittings (ΔE± ) of a number of axially chiral molecules using the ring-polymer instanton (RPI) method (J. Chem. Phys., 2011, 134, 054109). The list includes isotopomers of hydrogen dichalcogenides H2 X2 (X = O, S, Se, Te, and Po), hydrogen thioperoxide HSOH and dichlorodisulfane S2 Cl2 . Ab initio electronic-structure calculations have been performed on the level of second-order Møller-Plesset perturbation (MP2) theory either with split-valance basis sets or augmented correlation-consistent basis sets on H, O, S, and Cl atoms. Energy-consistent pseudopotential and corresponding triple zeta basis sets of the Stuttgart group are used on Se, Te, and Po atoms. The results are further improved using single point calculations performed at the coupled cluster level with iterative singles and doubles and perturbative triples amplitudes. When available for comparison, our computed values of ΔE± are found to lie within the same order of magnitude as values reported in the literature, although RPI also provides predictions for H2 Po2 and S2 Cl2 , which have not previously been directly calculated. Since RPI is a single-shot method which does not require detailed prior knowledge of the optimal tunneling path, it offers an effective way for estimating the tunneling dynamics of more complex chiral molecules, and especially those with small tunneling splittings.
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Affiliation(s)
- Nityananda Sahu
- Fachbereich Chemie, Theoretische Chemie, Philipps Universität Marburg, Marburg, Germany
| | | | - Robert Berger
- Fachbereich Chemie, Theoretische Chemie, Philipps Universität Marburg, Marburg, Germany
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Eraković M, Cvitaš MT. Tunneling splittings of vibrationally excited states using general instanton paths. J Chem Phys 2020; 153:134106. [PMID: 33032414 DOI: 10.1063/5.0024210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A multidimensional semiclassical method for calculating tunneling splittings in vibrationally excited states of molecules using Cartesian coordinates is developed. It is an extension of the theory by Mil'nikov and Nakamura [J. Chem. Phys. 122, 124311 (2005)] to asymmetric paths that are necessary for calculating tunneling splitting patterns in multi-well systems, such as water clusters. Additionally, new terms are introduced in the description of the semiclassical wavefunction that drastically improves the splitting estimates for certain systems. The method is based on the instanton theory and builds the semiclassical wavefunction of the vibrationally excited states from the ground-state instanton wavefunction along the minimum action path and its harmonic neighborhood. The splittings of excited states are thus obtained at a negligible added numerical effort. The cost is concentrated, as for the ground-state splittings, in the instanton path optimization and the hessian evaluation along the path. The method can thus be applied without modification to many mid-sized molecules in full dimensionality and in combination with on-the-fly evaluation of electronic potentials. The tests were performed on several model potentials and on the water dimer.
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Affiliation(s)
- Mihael Eraković
- Department of Physical Chemistry, Ruder Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Marko T Cvitaš
- Department of Physical Chemistry, Ruder Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
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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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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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Eraković M, Vaillant CL, Cvitaš MT. Instanton theory of ground-state tunneling splittings with general paths. J Chem Phys 2020; 152:084111. [PMID: 32113369 DOI: 10.1063/1.5145278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We derive a multidimensional instanton theory for calculating ground-state tunneling splittings in Cartesian coordinates for general paths. It is an extension of the method by Mil'nikov and Nakamura [J. Chem. Phys. 115, 6881 (2001)] to include asymmetric paths that are necessary for calculating tunneling splitting patterns in multi-well systems, such as water clusters. The approach avoids multiple expensive matrix diagonalizations to converge the fluctuation prefactor in the ring-polymer instanton (RPI) method, and instead replaces them by an integration of a Riccati differential equation. When combined with the string method for locating instantons, we avoid the need to converge the calculation with respect to the imaginary time period of the semiclassical orbit, thereby reducing the number of convergence parameters of the optimized object to just one: the number of equally spaced system replicas used to represent the instanton path. The entirety of the numerical effort is thus concentrated in optimizing the shape of the path and evaluating hessians along the path, which is a dramatic improvement over RPI. In addition to the standard instanton approximations, we neglect the coupling of vibrational modes to external rotations. The method is tested on the model potential of malonaldehyde and on the water dimer and trimer, giving close agreement with RPI at a much-reduced cost.
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Affiliation(s)
- Mihael Eraković
- Department of Physical Chemistry, Rudđđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Christophe L Vaillant
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marko T Cvitaš
- Department of Physical Chemistry, Rudđđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
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Cvitaš MT, Richardson JO. Quantum tunnelling pathways of the water pentamer. Phys Chem Chem Phys 2020; 22:1035-1044. [DOI: 10.1039/c9cp05561d] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Five tunnelling rearrangement pathways in water pentamer are responsible for the ground-state tunnelling splitting pattern of 320 states.
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Affiliation(s)
- Marko T. Cvitaš
- Department of Physical Chemistry
- Ruđer Bošković Institute
- Croatia
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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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Kuenzer U, Hofer TS. A periodic Numerov approach applied to the torsional tunneling splitting in hydrogen peroxide, aliphatic alcohols and phenol. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.04.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Vaillant CL, Althorpe SC, Wales DJ. Path Integral Energy Landscapes for Water Clusters. J Chem Theory Comput 2019; 15:33-42. [PMID: 30550261 DOI: 10.1021/acs.jctc.8b00675] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The energy landscapes for a discretized path integral representation of the water dimer, trimer and pentamer are characterized in terms of the localized (classical) and delocalized minima and transition states. The transition states are finite-temperature approximations to the exact instanton path, and they are typically used to calculate the tunneling splittings or reaction rates. The features of the path integral landscape are explored, thus elucidating procedures that could usefully be automated when searching for instantons in larger systems. Our work not only clarifies the role of minima and transition states in path integral calculations but also enables us to analyze the quantum-to-classical transition.
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Affiliation(s)
- Christophe L Vaillant
- University Chemical Laboratories , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Stuart C Althorpe
- University Chemical Laboratories , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - David J Wales
- University Chemical Laboratories , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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