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Mauger N, Plé T, Lagardère L, Huppert S, Piquemal JP. Improving Condensed-Phase Water Dynamics with Explicit Nuclear Quantum Effects: The Polarizable Q-AMOEBA Force Field. J Phys Chem B 2022; 126:8813-8826. [PMID: 36270033 DOI: 10.1021/acs.jpcb.2c04454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We introduce a new parametrization of the AMOEBA polarizable force field for water denoted Q-AMOEBA, for use in simulations that explicitly account for nuclear quantum effects (NQEs). This study is made possible thanks to the recently introduced adaptive Quantum Thermal Bath (adQTB) simulation technique which computational cost is comparable to classical molecular dynamics. The flexible Q-AMOEBA model conserves the initial AMOEBA functional form, with an intermolecular potential including an atomic multipole description of electrostatic interactions (up to quadrupole), a polarization contribution based on the Thole interaction model and a buffered 14-7 potential to model van der Waals interactions. It has been obtained by using a ForceBalance fitting strategy including high-level quantum chemistry reference energies and selected condensed-phase properties targets. The final Q-AMOEBA model is shown to accurately reproduce both gas-phase and condensed-phase properties, notably improving the original AMOEBA water model. This development allows the fine study of NQEs on water liquid phase properties such as the average H-O-H angle compared to its gas-phase equilibrium value, isotope effects, and so on. Q-AMOEBA also provides improved infrared spectroscopy prediction capabilities compared to AMOEBA03. Overall, we show that the impact of NQEs depends on the underlying model functional form and on the associated strength of hydrogen bonds. Since adQTB simulations can be performed at near classical computational cost using the Tinker-HP package, Q-AMOEBA can be extended to organic molecules, proteins, and nucleic acids opening the possibility for the large-scale study of the importance of NQEs in biophysics.
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Affiliation(s)
- Nastasia Mauger
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Thomas Plé
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Simon Huppert
- Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
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Wang C, Zhang L, Liu J, Shao J. Generalized fourth-order decompositions of imaginary time path integral: Implications of the harmonic oscillator. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2205089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The imaginary time path integral formalism offers a powerful numerical tool for simulating thermodynamic properties of realistic systems. We show that, when second-order and fourth-order decompositions are employed, they share a remarkable unified analytic form for the partition function of the harmonic oscillator. We are then able to obtain the expression of the thermodynamic property and the leading error terms as well. In order to obtain reasonably optimal values of the free parameters in the generalized symmetric fourth-order decomposition scheme, we eliminate the leading error terms to achieve the accuracy of desired order for the thermodynamic property of the harmonic system. Such a strategy leads to an efficient fourth-order decomposition that produces third-order accurate thermodynamic properties for general systems.
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Affiliation(s)
- Cong Wang
- College of Chemistry and Center for Advanced Quantum Studies, Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Lihan Zhang
- Institute of Condensed Matter and Material Physics, School of Physics, Peking University, Beijing 100871, China
| | - Jian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiushu Shao
- College of Chemistry and Center for Advanced Quantum Studies, Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
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Gaigeot MP. Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119864. [PMID: 34052762 DOI: 10.1016/j.saa.2021.119864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/13/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput 'decoding' of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France.
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Mauger N, Plé T, Lagardère L, Bonella S, Mangaud É, Piquemal JP, Huppert S. Nuclear Quantum Effects in Liquid Water at Near Classical Computational Cost Using the Adaptive Quantum Thermal Bath. J Phys Chem Lett 2021; 12:8285-8291. [PMID: 34427440 DOI: 10.1021/acs.jpclett.1c01722] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We demonstrate the accuracy and efficiency of a recently introduced approach to account for nuclear quantum effects (NQEs) in molecular simulations: the adaptive quantum thermal bath (adQTB). In this method, zero-point energy is introduced through a generalized Langevin thermostat designed to precisely enforce the quantum fluctuation-dissipation theorem. We propose a refined adQTB algorithm with improved accuracy and report adQTB simulations of liquid water. Through extensive comparison with reference path integral calculations, we demonstrate that it provides excellent accuracy for a broad range of structural and thermodynamic observables as well as infrared vibrational spectra. The adQTB has a computational cost comparable to that of classical molecular dynamics, enabling simulations of up to millions of degrees of freedom.
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Affiliation(s)
- Nastasia Mauger
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Thomas Plé
- CNRS, Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588, 4 Place Jussieu, F-75005 Paris, France
| | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Sara Bonella
- CECAM Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lausanne, Batochimie, Avenue Forel 2, 1015 Lausanne, Switzerland
| | - Étienne Mangaud
- CNRS, Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588, 4 Place Jussieu, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
- Institut Universitaire de France, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Simon Huppert
- CNRS, Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588, 4 Place Jussieu, F-75005 Paris, France
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Drużbicki K, Gaboardi M, Fernandez-Alonso F. Dynamics & Spectroscopy with Neutrons-Recent Developments & Emerging Opportunities. Polymers (Basel) 2021; 13:1440. [PMID: 33947108 PMCID: PMC8125526 DOI: 10.3390/polym13091440] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/27/2021] [Indexed: 12/19/2022] Open
Abstract
This work provides an up-to-date overview of recent developments in neutron spectroscopic techniques and associated computational tools to interrogate the structural properties and dynamical behavior of complex and disordered materials, with a focus on those of a soft and polymeric nature. These have and continue to pave the way for new scientific opportunities simply thought unthinkable not so long ago, and have particularly benefited from advances in high-resolution, broadband techniques spanning energy transfers from the meV to the eV. Topical areas include the identification and robust assignment of low-energy modes underpinning functionality in soft solids and supramolecular frameworks, or the quantification in the laboratory of hitherto unexplored nuclear quantum effects dictating thermodynamic properties. In addition to novel classes of materials, we also discuss recent discoveries around water and its phase diagram, which continue to surprise us. All throughout, emphasis is placed on linking these ongoing and exciting experimental and computational developments to specific scientific questions in the context of the discovery of new materials for sustainable technologies.
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Affiliation(s)
- Kacper Drużbicki
- Materials Physics Center, CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastian, Spain;
- Polish Academy of Sciences, Center of Molecular and Macromolecular Studies, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Mattia Gaboardi
- Elettra—Sincrotrone Trieste S.C.p.A., S.S. 14 km 163.5 in Area Science Park, 34149 Trieste, Italy;
| | - Felix Fernandez-Alonso
- Materials Physics Center, CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastian, Spain;
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastian, Spain
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
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Remsing RC, Bates JE. Effective mass path integral simulations of quasiparticles in condensed phases. J Chem Phys 2020; 153:121104. [PMID: 33003737 DOI: 10.1063/5.0020555] [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
The quantum many-body problem in condensed phases is often simplified using a quasiparticle description, such as effective mass theory for electron motion in a periodic solid. These approaches are often the basis for understanding many fundamental condensed phase processes, including the molecular mechanisms underlying solar energy harvesting and photocatalysis. Despite the importance of these effective particles, there is still a need for computational methods that can explore their behavior on chemically relevant length and time scales. This is especially true when the interactions between the particles and their environment are important. We introduce an approach for studying quasiparticles in condensed phases by combining effective mass theory with the path integral treatment of quantum particles. This framework incorporates the generally anisotropic electronic band structure of materials into path integral simulation schemes to enable modeling of quasiparticles in quantum confinement, for example. We demonstrate the utility of effective mass path integral simulations by modeling an exciton in solid potassium chloride and electron trapping by a sulfur vacancy in monolayer molybdenum disulfide.
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Affiliation(s)
- Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Jefferson E Bates
- A. R. Smith Department of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, USA
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