1
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Mallick S, Mandal T, Kumari N, Roy L, De Sarkar S. Divergent Electrochemical Synthesis of Indoles through pK a Regulation of Amides: Synthetic and Mechanistic Insights. Chemistry 2024; 30:e202304002. [PMID: 38290995 DOI: 10.1002/chem.202304002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/15/2024] [Accepted: 01/30/2024] [Indexed: 02/01/2024]
Abstract
A divergent synthetic approach to access highly substituted indole scaffolds is illustrated. By virtue of a tunable electrochemical strategy, distinct control over the C-3 substitution pattern was achieved by employing two analogous 2-styrylaniline precursors. The chemoselectivity is governed by the fine-tuning of the acidity of the amide proton, relying on the appropriate selection of N-protecting groups, and assisted by the reactivity of the electrogenerated intermediates. Detailed mechanistic investigations based on cyclic voltametric experiments and computational studies revealed the crucial role of water additive, which assists the proton-coupled electron transfer event for highly acidic amide precursors, followed by an energetically favorable intramolecular C-N coupling, causing exclusive fabrication of the C-3 unsubstituted indoles. Alternatively, the implementation of an electrogenerated cationic olefin activator delivers the C-3 substituted indoles through the preferential nucleophilic nature of the N-acyl amides. This electrochemical approach of judicious selection of N-protecting groups to regulate pKa/E° provides an expansion in the domain of switchable generation of heterocyclic derivatives in a sustainable fashion, with high regio- and chemoselectivity.
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Affiliation(s)
- Samrat Mallick
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246, India
| | - Tanumoy Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246, India
| | - Nidhi Kumari
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246, India
| | - Lisa Roy
- Institute of Chemical Technology Mumbai-IOC Odisha Campus, Bhubaneswar, Bhubaneswar, 751013, India
| | - Suman De Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246, India
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2
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Shen H, Shen X, Wu Z. Simulating the isotropic Raman spectra of O-H stretching mode in liquid H 2O based on a machine learning potential: the influence of vibrational couplings. Phys Chem Chem Phys 2023; 25:28180-28188. [PMID: 37819214 DOI: 10.1039/d3cp03035k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
In this study, we trained a deep potential (DP) for H2O, an accurate machine learning (ML) potential. We performed molecular dynamics (MD) simulations of liquid water using the DP model (or DeePMD simulations). Our results showed that the DP model exhibits DFT-level accuracy, and the DeePMD simulation is a promising approach for modeling the structural properties of liquid water. Based on the DeePMD simulation trajectories, we calculated the isotropic Raman spectra of the O-H stretching mode using the surface-specific velocity-velocity correlation function (ssVVCF), showing that the DeePMD/ssVVCF approach can correctly capture the bimodal characteristics of the experimental Raman spectra, with one peak located near 3400 cm-1 and the other near 3250 cm-1. The success of the DeePMD/ssVVCF approach should be credited to (1) the DFT-level accuracy of the DP model for H2O, (2) the ssVVCF formulation considering the coupling between vibrational modes, and (3) non-Condon effects. Furthermore, the DeePMD simulations revealed that the anharmonic interactions between the coupled water molecules in the first and second hydration shells should play an essential role in the strong mixing of the H-O-H bending mode and the O-H stretching mode, leading to the delocalization of the O-H stretching band. In particular, increasing the strength of hydrogen bonds would enhance the bend-stretch coupling, leading to the red-shifting of the O-H vibrational spectra and the increase in the intensity of the shoulder around 3250 cm-1.
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Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang 550018, China.
| | - Xu Shen
- National Center of Technology Innovation for Intelligent Design and Numerical Control, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhenhua Wu
- Department of Big Data and Artificial Intelligence, Guizhou Vocational Technology College of Electronics & Information, Kaili, 556000, China
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3
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Herman KM, Stone AJ, Xantheas SS. Accurate Calculation of Many-Body Energies in Water Clusters Using a Classical Geometry-Dependent Induction Model. J Chem Theory Comput 2023; 19:6805-6815. [PMID: 37703063 DOI: 10.1021/acs.jctc.3c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
We incorporate geometry-dependent distributed multipole and polarizability surfaces into an induction model that is used to describe the 3- and 4-body terms of the interaction between water molecules. The moment expansion is carried out up to the hexadecapole with the multipoles distributed on the atom sites. Dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole distributed polarizabilities are used to represent the response of the multipoles to an electric field. We compare the model against two large databases consisting of 43,844 3-body terms and 3,603 4-body terms obtained from high level ab initio calculations previously used to fit the MB-pol and q-AQUA classical interaction potentials for water. The classical induction model with no adjustable parameters reproduces the ab initio 3-/4-body terms contained in these two databases with a root-mean-square error (RMSE) of 0.104/0.058 and a mean-absolute error (MAE) of 0.054/0.026 kcal/mol, respectively. These results are on par with the ones obtained by fitting the same data using over 14,000 (for the 3-body) and 200 (for the 4-body) parameters via Permutationally Invariant Polynomials (PIPs). This demonstrates the accuracy of this physically motivated model in describing the 3- and 4-body terms in the interactions between water molecules with no adjustable parameters. The triple-dipole-dispersion energy, included in the calculation of the 3-body energy, was found to be small but not quite negligible. The model represents a practical, efficient, and transferable approach for obtaining accurate nonadditive interactions for multicomponent systems without the need to perform tens of thousands of high level electronic structure calculations and fitting them with PIPs.
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Affiliation(s)
- Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, Washington 98185, United States
| | - Anthony J Stone
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98185, United States
- Advanced Computing Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN J7-10, Richland, Washington 99352, United States
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4
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Yu Q, Qu C, Houston PL, Nandi A, Pandey P, Conte R, Bowman JM. A Status Report on "Gold Standard" Machine-Learned Potentials for Water. J Phys Chem Lett 2023; 14:8077-8087. [PMID: 37656898 PMCID: PMC10510435 DOI: 10.1021/acs.jpclett.3c01791] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
Owing to the central importance of water to life as well as its unusual properties, potentials for water have been the subject of extensive research over the past 50 years. Recently, five potentials based on different machine learning approaches have been reported that are at or near the "gold standard" CCSD(T) level of theory. The development of such high-level potentials enables efficient and accurate simulations of water systems using classical and quantum dynamical approaches. This Perspective serves as a status report of these potentials, focusing on their methodology and applications to water systems across different phases. Their performances on the energies of gas phase water clusters, as well as condensed phase structural and dynamical properties, are discussed.
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Affiliation(s)
- Qi Yu
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Independent
Researcher, Toronto, Ontario M9B 0E3, Canada
| | - Paul L. Houston
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
- Department of Chemistry
and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Apurba Nandi
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - Priyanka Pandey
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Riccardo Conte
- Dipartimento
di Chimica, Università degli Studi
di Milano, via Golgi 19, 20133 Milano, Italy
| | - Joel M. Bowman
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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5
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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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6
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Bore SL, Paesani F. Realistic phase diagram of water from "first principles" data-driven quantum simulations. Nat Commun 2023; 14:3349. [PMID: 37291095 DOI: 10.1038/s41467-023-38855-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/12/2023] [Indexed: 06/10/2023] Open
Abstract
Since the experimental characterization of the low-pressure region of water's phase diagram in the early 1900s, scientists have been on a quest to understand the thermodynamic stability of ice polymorphs on the molecular level. In this study, we demonstrate that combining the MB-pol data-driven many-body potential for water, which was rigorously derived from "first principles" and exhibits chemical accuracy, with advanced enhanced-sampling algorithms, which correctly describe the quantum nature of molecular motion and thermodynamic equilibria, enables computer simulations of water's phase diagram with an unprecedented level of realism. Besides providing fundamental insights into how enthalpic, entropic, and nuclear quantum effects shape the free-energy landscape of water, we demonstrate that recent progress in "first principles" data-driven simulations, which rigorously encode many-body molecular interactions, has opened the door to realistic computational studies of complex molecular systems, bridging the gap between experiments and simulations.
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Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
- Materials Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
- Halicioğlu Data Science Institute, University of California San Diego, La Jolla, CA, 92093, USA.
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 92093, USA.
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7
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Zhai Y, Caruso A, Bore SL, Luo Z, Paesani F. A "short blanket" dilemma for a state-of-the-art neural network potential for water: Reproducing experimental properties or the physics of the underlying many-body interactions? J Chem Phys 2023; 158:084111. [PMID: 36859071 DOI: 10.1063/5.0142843] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Deep neural network (DNN) potentials have recently gained popularity in computer simulations of a wide range of molecular systems, from liquids to materials. In this study, we explore the possibility of combining the computational efficiency of the DeePMD framework and the demonstrated accuracy of the MB-pol data-driven, many-body potential to train a DNN potential for large-scale simulations of water across its phase diagram. We find that the DNN potential is able to reliably reproduce the MB-pol results for liquid water, but provides a less accurate description of the vapor-liquid equilibrium properties. This shortcoming is traced back to the inability of the DNN potential to correctly represent many-body interactions. An attempt to explicitly include information about many-body effects results in a new DNN potential that exhibits the opposite performance, being able to correctly reproduce the MB-pol vapor-liquid equilibrium properties, but losing accuracy in the description of the liquid properties. These results suggest that DeePMD-based DNN potentials are not able to correctly "learn" and, consequently, represent many-body interactions, which implies that DNN potentials may have limited ability to predict the properties for state points that are not explicitly included in the training process. The computational efficiency of the DeePMD framework can still be exploited to train DNN potentials on data-driven many-body potentials, which can thus enable large-scale, "chemically accurate" simulations of various molecular systems, with the caveat that the target state points must have been adequately sampled by the reference data-driven many-body potential in order to guarantee a faithful representation of the associated properties.
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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
| | - Sigbjørn Løland Bore
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Zhishang Luo
- 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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8
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Jónsson EÖ, Rasti S, Galynska M, Meyer J, Jónsson H. Transferable Potential Function for Flexible H 2O Molecules Based on the Single-Center Multipole Expansion. J Chem Theory Comput 2022; 18:7528-7543. [PMID: 36395502 DOI: 10.1021/acs.jctc.2c00598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A potential function is presented for describing a system of flexible H2O molecules based on the single-center multipole expansion (SCME) of the electrostatic interaction. The model, referred to as SCME/f, includes the variation of the molecular quadrupole moment as well as the dipole moment with changes in bond length and angle so as to reproduce results of high-level electronic structure calculations. The multipole expansion also includes fixed octupole and hexadecapole moments, as well as anisotropic dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole polarizability tensors. The model contains five adjustable parameters related to the repulsive interaction and damping functions in the electrostatic and dispersion interactions. Their values are adjusted to reproduce the lowest energy isomers of small clusters, (H2O)n with n = 2-6, as well as measured properties of the ice Ih crystal. Subsequent calculations of the energy difference between the various isomer configurations of the clusters show that SCME/f gives good agreement with results of electronic structure calculations and represents a significant improvement over the previously presented rigid SCME potential function. Analysis of the vibrational frequencies of the clusters and structural properties of ice Ih crystal show the importance of accurately describing the variation of the quadrupole moment with molecular structures.
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Affiliation(s)
- Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107Reykjavík, Iceland
| | - Soroush Rasti
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RALeiden, The Netherlands
| | - Marta Galynska
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107Reykjavík, Iceland
| | - Jörg Meyer
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RALeiden, The Netherlands
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107Reykjavík, Iceland
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9
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Zhu YC, Yang S, Zeng JX, Fang W, Jiang L, Zhang DH, Li XZ. Torsional Tunneling Splitting in a Water Trimer. J Am Chem Soc 2022; 144:21356-21362. [DOI: 10.1021/jacs.2c09909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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, Beijing100871, 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, Beijing100871, People’s Republic of China
| | - Shuo Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100871, 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, Beijing100871, 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, Beijing100871, People’s Republic of China
| | - Wei Fang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, People’s Republic of China
- Department of Chemistry, Fudan University, Shanghai200438, People’s Republic of China
| | - Ling Jiang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, People’s Republic of China
| | - Dong H. Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, 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, Beijing100871, 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, Beijing100871, People’s Republic of China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, People’s Republic of China
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10
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Effect of Orientational Isomerism in Neutral Water Hexamers on Their Thermodynamic Properties and Concentrations in the Gas Phase. J CLUST SCI 2022. [DOI: 10.1007/s10876-022-02365-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Witek J, Heindel JP, Guan X, Leven I, Hao H, Naullage P, LaCour A, Sami S, Menger MFSJ, Cofer-Shabica DV, Berquist E, Faraji S, Epifanovsky E, Head-Gordon T. M-Chem: a Modular Software Package for Molecular Simulation that Spans Scientific Domains. Mol Phys 2022; 121:e2129500. [PMID: 37470065 PMCID: PMC10353727 DOI: 10.1080/00268976.2022.2129500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/06/2022] [Indexed: 10/10/2022]
Abstract
We present a new software package called M-Chem that is designed from scratch in C++ and parallelized on shared-memory multi-core architectures to facilitate efficient molecular simulations. Currently, M-Chem is a fast molecular dynamics (MD) engine that supports the evaluation of energies and forces from two-body to many-body all-atom potentials, reactive force fields, coarse-grained models, combined quantum mechanics molecular mechanics (QM/MM) models, and external force drivers from machine learning, augmented by algorithms that are focused on gains in computational simulation times. M-Chem also includes a range of standard simulation capabilities including thermostats, barostats, multi-timestepping, and periodic cells, as well as newer methods such as fast extended Lagrangians and high quality electrostatic potential generation. At present M-Chem is a developer friendly environment in which we encourage new software contributors from diverse fields to build their algorithms, models, and methods in our modular framework. The long-term objective of M-Chem is to create an interdisciplinary platform for computational methods with applications ranging from biomolecular simulations, reactive chemistry, to materials research.
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Affiliation(s)
- Jagna Witek
- Kenneth S. Pitzer Theory Center and Department of Chemistry
| | - Joseph P Heindel
- Kenneth S. Pitzer Theory Center and Department of Chemistry
- Chemical Sciences Division, Lawrence Berkeley National Laboratory
| | - Xingyi Guan
- Kenneth S. Pitzer Theory Center and Department of Chemistry
- Chemical Sciences Division, Lawrence Berkeley National Laboratory
| | - Itai Leven
- Kenneth S. Pitzer Theory Center and Department of Chemistry
| | - Hongxia Hao
- Kenneth S. Pitzer Theory Center and Department of Chemistry
| | | | - Allen LaCour
- Kenneth S. Pitzer Theory Center and Department of Chemistry
- Chemical Sciences Division, Lawrence Berkeley National Laboratory
| | - Selim Sami
- Kenneth S. Pitzer Theory Center and Department of Chemistry
| | - M F S J Menger
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - D Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19128 USA
| | - Eric Berquist
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Shirin Faraji
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry
- Chemical Sciences Division, Lawrence Berkeley National Laboratory
- Department of Bioengineering and Chemical and Biomolecular Engineering University of California, Berkeley, CA, USA
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12
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Heindel JP, Kirov MV, Xantheas SS. Hydrogen Bond Arrangements in (H2O)20, 24, 28 Clathrate Hydrate Cages: Optimization and Many-Body Analysis. J Chem Phys 2022; 157:094301. [DOI: 10.1063/5.0095335] [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] Open
Abstract
We provide a detailed study of the hydrogen bonding arrangements, relative stability, residual entropy and an analysis of the many-body effects in the (H2O)20 (D-cage), (H2O)24 (T-cage) and (H2O)28 (H-cage) hollow cages making up structures I (sI) and II (sII) of clathrate hydrate lattices. Based on the enumeration of the possible hydrogen bonding networks for a fixed oxygen atom scaffold, the residual entropy () of these three gas phase cages was estimated at 0.75482, 0.7544 and 0.75417, where is the number of molecules and is Boltzmann's constant. A previously identified descriptor of enhanced stability based on the relative arrangement and connectivity of nearest-neighbor fragments on the polyhedral water cluster (Strong-Weak-Effective-Bond (SWEB) model), also applies to the larger hollow cages. The three cages contain a maximum of 7, 9 and 11 such preferable arrangements of trans nearest dimer pairs with one "free" OH bond on the donor molecule ( t1d dimers). The Many-Body Expansion (MBE) up to the 4-body suggests that the many-body terms vary nearly linearly with the cluster binding energy. Using a hierarchical approach of screening the relative stability of networks starting from optimizations with the TIP4P, TTM2.1-F and MB-pol classical potentials, subsequently refining at more accurate levels of electronic structure theory (DFT and MP2) and finally correcting for zero-point energy, we were able to identify a group of 4 low-lying isomers of the (H2O)24 T-cage, two of which are antisymmetric and the other two form a pair of antipode configurations.
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Affiliation(s)
| | - Mikhail V. Kirov
- Tyumen Scientific Center, Earth Cryosphere Institute Tyumen Scientific Centre of the Siberian Branch of the Russian Academy of Sciences, Russia
| | - Sotiris S. Xantheas
- Pacific Northwest National Laboratory, United States of America
- University of Washington
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13
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Palos E, Lambros E, Swee S, Hu J, Dasgupta S, Paesani F. Assessing the Interplay between Functional-Driven and Density-Driven Errors in DFT Models of Water. J Chem Theory Comput 2022; 18:3410-3426. [PMID: 35506889 DOI: 10.1021/acs.jctc.2c00050] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the interplay between functional-driven and density-driven errors in different density functional approximations within density functional theory (DFT) and the implications of these errors for simulations of water with DFT-based data-driven potentials. Specifically, we quantify density-driven errors in two widely used dispersion-corrected functionals derived within the generalized gradient approximation (GGA), namely BLYP-D3 and revPBE-D3, and two modern meta-GGA functionals, namely strongly constrained and appropriately normed (SCAN) and B97M-rV. The effects of functional-driven and density-driven errors on the interaction energies are first assessed for the water clusters of the BEGDB dataset. Further insights into the nature of functional-driven errors are gained from applying the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) to the interaction energies, which demonstrates that functional-driven errors are strongly correlated with the nature of the interactions. We discuss cases where density-corrected DFT (DC-DFT) models display higher accuracy than the original DFT models and cases where reducing the density-driven errors leads to larger deviations from the reference energies due to the presence of large functional-driven errors. Finally, molecular dynamics simulations are performed with data-driven many-body potentials derived from DFT and DC-DFT data to determine the effect that minimizing density-driven errors has on the description of liquid water. Besides rationalizing the performance of widely used DFT models of water, we believe that our findings unveil fundamental relations between the shortcomings of some common DFT approximations and the requirements for accurate descriptions of molecular interactions, which will aid the development of a consistent, DFT-based framework for the development of data-driven and machine-learned potentials for simulations of condensed-phase systems.
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Affiliation(s)
- Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Steven Swee
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Jie Hu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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14
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Zaverkin V, Holzmüller D, Schuldt R, Kästner J. Predicting properties of periodic systems from cluster data: A case study of liquid water. J Chem Phys 2022; 156:114103. [DOI: 10.1063/5.0078983] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The accuracy of the training data limits the accuracy of bulk properties from machine-learned potentials. For example, hybrid functionals or wave-function-based quantum chemical methods are readily available for cluster data but effectively out of scope for periodic structures. We show that local, atom-centered descriptors for machine-learned potentials enable the prediction of bulk properties from cluster model training data, agreeing reasonably well with predictions from bulk training data. We demonstrate such transferability by studying structural and dynamical properties of bulk liquid water with density functional theory and have found an excellent agreement with experimental and theoretical counterparts.
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Affiliation(s)
- Viktor Zaverkin
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - David Holzmüller
- Institute for Stochastics and Applications, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Robin Schuldt
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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15
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Yue S, Riera M, Ghosh R, Panagiotopoulos AZ, Paesani F. Transferability of data-driven, many-body models for CO2 simulations in the vapor and liquid phases. J Chem Phys 2022; 156:104503. [DOI: 10.1063/5.0080061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Shuwen Yue
- Princeton University, United States of America
| | - Marc Riera
- Chemistry and Biochemistry, University of California San Diego Department of Chemistry and Biochemistry, United States of America
| | - Raja Ghosh
- University of California San Diego, United States of America
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16
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Theoretical Description of Water from Single-Molecule to Condensed Phase: a Review of Recent Progress on Potential Energy Surfaces and Molecular Dynamics. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2201005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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17
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Naseem-Khan S, Piquemal JP, Cisneros GA. Improvement of the Gaussian Electrostatic Model by separate fitting of Coulomb and exchange-repulsion densities and implementation of a new dispersion term. J Chem Phys 2021; 155:194103. [PMID: 34800949 PMCID: PMC8598263 DOI: 10.1063/5.0072380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/28/2021] [Indexed: 11/15/2022] Open
Abstract
The description of each separable contribution of the intermolecular interaction is a useful approach to develop polarizable force fields (polFFs). The Gaussian Electrostatic Model (GEM) is based on this approach, coupled with the use of density fitting techniques. In this work, we present the implementation and testing of two improvements of GEM: the Coulomb and exchange-repulsion energies are now computed with separate frozen molecular densities and a new dispersion formulation inspired by the Sum of Interactions Between Fragments Ab initio Computed polFF, which has been implemented to describe the dispersion and charge-transfer interactions. Thanks to the combination of GEM characteristics and these new features, we demonstrate a better agreement of the computed structural and condensed properties for water with experimental results, as well as binding energies in the gas phase with the ab initio reference compared with the previous GEM* potential. This work provides further improvements to GEM and the items that remain to be improved and the importance of the accurate reproduction for each separate contribution.
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Affiliation(s)
- Sehr Naseem-Khan
- Department of Chemistry, University of North Texas, Denton, Texas 76201, USA
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 75005 Paris, France
| | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, USA
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18
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Heindel JP, Xantheas SS. Molecular Dynamics Driven by the Many-Body Expansion (MBE-MD). J Chem Theory Comput 2021; 17:7341-7352. [PMID: 34723531 DOI: 10.1021/acs.jctc.1c00780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a protocol for classical and nuclear quantum dynamics, in which the energies and forces are generated by the many-body expansion (MBE), and apply it to water clusters using the TTM2.1-F and MB-Pol interaction potentials at various temperatures. We carry out MBE-molecular dynamics (MD) classical and nuclear quantum dynamical simulations, in which the energies and forces of the full system are approximated by the two-, three-, and four-body terms of the MBE, and compare the average potential and the vibrational density of states with the full simulation, i.e., the one for which no MBE is used. Our results indicate that the thermally averaged potential energy from the MBE up to the four-body term converges with near-identical behavior to the one from the full simulation. The three-body makes a substantial contribution (∼20%) to the energy, whereas the four-body is necessary for obtaining quantitatively accurate energetics and forces, albeit making a small contribution to each (∼2%). We further show that the harmonic frequencies are reproduced to within a few wavenumbers (cm-1) at the four-body level and that the slowest modes to converge with the MBE rank are those involving the strongest hydrogen bonds. Anharmonicity exacerbates this effect, so that a four-body description of the energies and forces is needed to achieve accurate anharmonic vibrational frequencies in the hydrogen-bonded OH-stretching region. We also discuss the asymptotic scaling of the MBE-MD protocol with respect to the cost of the underlying potential energy evaluation, suggesting that electronic structure methods that scale at least as N4, N being the size of the system, are needed to result in savings over the traditional full MD simulation. We anticipate that the MBE-MD protocol can evolve into a powerful and practical method, which will allow for highly accurate ab initio MD simulations on a much broader range of molecular systems than can be currently handled.
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Affiliation(s)
- Joseph P Heindel
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.,Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
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19
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Chedid J, Jocelyn N, Eshuis H. Energies, structures, and harmonic frequencies of small water clusters from the direct random phase approximation. J Chem Phys 2021; 155:084303. [PMID: 34470345 DOI: 10.1063/5.0059343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The binding energies, structures, and vibrational frequencies of water clusters up to 20 molecules are computed at the direct random phase approximation (RPA) level of theory and compared to theoretical benchmarks. Binding energies of the WATER27 set, which includes neutral and positively and negatively charged clusters, are predicted to be too low in the complete basis set limit by an average of 7 kcal/mol (9%) and are worse than the results from the best density functional theory methods or from the Møller-Plesset theory. The RPA shows significant basis set size dependence for binding energies. The order of the relative energies of the water hexamer and dodecamer isomers is predicted correctly by the RPA. The mean absolute deviation for angles and distances for neutral clusters up to the water hexamer are 0.2° and 0.6 pm, respectively, using quintuple-ζ basis sets. The relative energetic order of the hexamer isomers is preserved upon optimization. Vibrational frequencies for these systems are underestimated by several tens of wavenumbers for large basis sets, and deviations increase with the basis set size. Overall, the direct RPA method yields accurate structural parameters but systematically underestimates binding energies and shows strong basis set size dependence.
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Affiliation(s)
- Julianna Chedid
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, USA
| | - Nedjie Jocelyn
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, USA
| | - Henk Eshuis
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, USA
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20
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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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21
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Herman KM, Heindel JP, Xantheas SS. The many-body expansion for aqueous systems revisited: III. Hofmeister ion-water interactions. Phys Chem Chem Phys 2021; 23:11196-11210. [PMID: 33899854 DOI: 10.1039/d1cp00409c] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a Many Body Energy (MBE) analysis of aqueous ionic clusters containing anions and cations at the two opposite ends of the Hofmeister series, viz. the kosmotropes Ca2+ and SO42- and the chaotropes NH4+ and ClO4-, with 9 water molecules to quantify how these ions alter the interaction between the water molecules in their immediate surroundings. We specifically aim at quantifying how various ions (depending on their position in the Hofmeister series) affect the interaction between the surrounding water molecules and probe whether there is a qualitatively different behavior between kosmotropic vs. chaotropic ions. The current results when compared to the ones reported earlier for water clusters [J. P. Heindel and S. S. Xantheas, J. Chem. Theor. Comput., 2020, 16, 6843-6855] as well as for alkali metal and halide ion aqueous clusters of the same size [J. P. Heindel and S. S. Xantheas, J. Chem. Theor. Comput., 2021, 17, 2200-2216], which lie in the middle of the Hofmeister series, offer a complete account of the effect an ion across the Hofmeister series from "kosmotropes" to "chaotropes" has on the interaction between the neighboring water molecules. Through this analysis, noteworthy differences between the MBE of kosmotropes and chaotropes were identified. The MBE of kosmotropes is dominated by ion-water interactions that extend beyond the 4-body term, the rank at which the MBE of pure water converges. The percentage contribution of the 2-B term to the total cluster binding energy is noticeably larger. The disruption of the hydrogen bonded network due to the dominant ion-water interactions results in weak, unfavorable water-water interactions. The MBE for chaotropes, on the other hand, was found to converge more quickly as it more closely resembles that of pure water clusters. Chaotropes exhibit weaker overall binding energies and weaker ion-water interactions in favor of water-water interactions, somewhat recovering the pattern of the 2-4 body terms exemplified by pure water clusters. A remarkable anti-correlation between the 2-B ion-water (I-W) and water-water (W-W) interactions as well as between the 3-B (I-W-W) and (I-W) interactions was found for both kosmotropic and chaotropic ions. This anti-correlation is linear for both monatomic anions and monatomic cations, suggesting the existence of underlying physical mechanisms that were previously unexplored. The consideration of two different structural arrangements (ion inside and outside of a water cluster) suggests that fully solvated (ion inside) chaotropes disrupt the hydrogen bonding network in a similar manner to partially solvated (ion outside) kosmotropes and offers useful insights into the modeling requirements of bulk vs. interfacial ion solvation. It is noteworthy that the 2-B contribution to the total Basis Set Superposition Error (BSSE) correction for both kosmotropic and chaotropic ions follows the universal erf profile vs. intermolecular distance previously reported for pure water, halide ion-water and alkali metal ion-water clusters. When scaled for the corresponding dimer energies and distances, a single profile fits the current results together with all previously reported ones for pure water and halide water clusters. This finding lends further support to schemes for accurately estimating the 2-B BSSE correction in condensed environments.
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Affiliation(s)
- Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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22
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Allen AEA, Dusson G, Ortner C, Csányi G. Atomic permutationally invariant polynomials for fitting molecular force fields. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abd51e] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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23
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Leven I, Hao H, Das AK, Head-Gordon T. A Reactive Force Field with Coarse-Grained Electrons for Liquid Water. J Phys Chem Lett 2020; 11:9240-9247. [PMID: 33073998 DOI: 10.1021/acs.jpclett.0c02516] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nonreactive force fields are defined by perturbations of electron density that are relatively small, whereas chemical reactivity involves wholesale electronic rearrangements that make and break bonds. Thus, reactive force fields are incredibly difficult to develop compared to nonreactive force fields, yet at the same time, they fill a critical need when ab initio molecular dynamics methods are not affordable. We introduce a new reactive force field model for water that combines modified nonbonded terms of the ReaxFF model and its embedding in the electrostatic interactions described by our recently introduced coarse-grained electron model (C-GeM). The ReaxFF/C-GeM force field is characterized for many energetic and dissociative water properties for water clusters, structure, and dynamical properties under ambient conditions in the condensed phase, as well as the temperature dependence of density and water diffusion, with very good agreement with experiment. The ReaxFF/C-GeM force field should be more transferable and more broadly applicable to a range of reactive systems involving both proton and electron transfer in the condensed phase.
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Affiliation(s)
- Itai Leven
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hongxia Hao
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | - Teresa Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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24
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Heindel JP, Xantheas SS. The Many-Body Expansion for Aqueous Systems Revisited: I. Water–Water Interactions. J Chem Theory Comput 2020; 16:6843-6855. [DOI: 10.1021/acs.jctc.9b00749] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Joseph P. Heindel
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sotiris S. Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box
999, MS K1-83, Richland, Washington 99352, United States
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25
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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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26
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Lee VGM, Vetterli NJ, Boyer MA, McCoy AB. Diffusion Monte Carlo Studies on the Detection of Structural Changes in the Water Hexamer upon Isotopic Substitution. J Phys Chem A 2020; 124:6903-6912. [DOI: 10.1021/acs.jpca.0c05686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victor G. M. Lee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas J. Vetterli
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mark A. Boyer
- 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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27
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Pan C, Liu C, Peng J, Ren P, Huang X. Three-site and five-site fixed-charge water models compatible with AMOEBA force field. J Comput Chem 2020; 41:1034-1044. [PMID: 31976572 DOI: 10.1002/jcc.26151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/01/2020] [Indexed: 11/06/2022]
Abstract
In a typical biomolecular simulation using Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field, the vast majority molecules in the simulation box consist of water, and these water molecules consume the most CPU power due to the explicit mutual induction effect. To improve the computational efficiency, we here develop two new nonpolarizable water models (with flexible bonds and fixed charges) that are compatible with AMOEBA solute: the 3-site AW3C and 5-site AW5C. To derive the force-field parameters for AW3C and AW5C, we fit to six experimental liquid thermodynamic properties: liquid density, enthalpy of vaporization, dielectric constant, isobaric heat capacity, isothermal compressibility and thermal expansion coefficient, at a broad range of temperatures from 261.15 to 353.15 K under 1.0 atm pressure. We further validate our AW3C and AW5C water models by showing that they can well reproduce the radial distribution function g(r), self-diffusion constant D, and hydration free energy from the AMOEBA03 water model and the experimental observations. Furthermore, we show that our AW3C and AW5C water models can greatly accelerate (>5 times) the bulk water as well as biomolecular simulations when compared to AMOEBA water. Specifically, we demonstrate that the applications of AW3C and AW5C water models to simulate a DNA duplex lead to a threefold acceleration, and in the meanwhile well maintain the structural properties as the fully polarizable AMOEBA water. We expect that our AW3C and AW5C water models hold great promise to be widely applied to simulate complex bio-molecules using the AMOEBA force field.
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Affiliation(s)
- Cong Pan
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
| | - Junhui Peng
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong.,Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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28
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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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29
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Metz MP, Szalewicz K. Automatic Generation of Flexible-Monomer Intermolecular Potential Energy Surfaces. J Chem Theory Comput 2020; 16:2317-2339. [PMID: 32240593 DOI: 10.1021/acs.jctc.9b01241] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A method is developed for automatic generation of nonreactive intermolecular two-body potential energy surfaces (PESs) including intramonomer degrees of freedom. This method, called flex-autoPES, is an extension of the autoPES method developed earlier, which assumes rigid monomers. In both cases, the whole PES development proceeds without any human intervention. The functional form used is a sum of products of site-site functions (both atomic and off-atomic sites can be used). The leading terms with sites involving different monomers are of physically motivated form. The long-range part of a PES is computed from monomer properties without using any dimer information. The close-range part is fitted to dimer interaction energies computed using electronic structure methods. Virtually any method can be used in such calculations, but the use of symmetry-adapted perturbation theory provides a seamless connection to the long-range part of the PES. The performance of the flex-autoPES code was tested by developing a full-dimensional PES for the water dimer and PESs including only some soft intramonomer degrees of freedom for the ethylene glycol dimer and for the ethylene glycol-water dimer. In the case of the water dimer, the root-mean-square error (RMSE) of the PES from the data points with negative total energies is 0.03 kcal/mol, and we expect this PES to be more accurate than any previously published PES of this type. For the ethylene glycol dimer and the ethylene glycol-water dimers, the analogous RMSEs are 0.25 and 0.1 kcal/mol, respectively.
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Affiliation(s)
- Michael P Metz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
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30
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Ansari N, Onat B, Sosso GC, Hassanali A. Insights into the Emerging Networks of Voids in Simulated Supercooled Water. J Phys Chem B 2020; 124:2180-2190. [PMID: 32032486 DOI: 10.1021/acs.jpcb.9b10144] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural evolution of supercooled liquid water as we approach the glass transition temperature continues to be an active area of research. Here, we use molecular dynamics simulations of TIP4P/ice water to study the changes in the connected regions of empty space within the liquid, which we investigate using the Voronoi-voids network. We observe two important features: supercooling enhances the fraction of nonspherical voids and different sizes of voids tend to cluster forming a percolating network. By examining order parameters such as the local structure index (LSI), tetrahedrality and topological defects, we show that water molecules near large void clusters tend to be slightly more tetrahedral than those near small voids, with a lower population of under- and overcoordinated defects. We show further that the distribution of closed rings of water molecules around small and large void clusters maintain a balance between 6 and 7 membered rings. Our results highlight the changes of the dual voids and water network as a structural hallmark of supercooling and provide insights into the molecular origins of cooperative effects underlying density fluctuations on the subnanometer and nanometer length scale. In addition, the percolation of the voids and the hydrogen bond network around the voids may serve as useful order parameters to investigate density fluctuations in supercooled water.
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Affiliation(s)
- Narjes Ansari
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Berk Onat
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom.,School of Engineering, University of Warwick, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Ali Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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31
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Honda K. A coarse-grained potential for liquid water by spherically projected hydrogen-bonding interactions. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Jana S, Constantin LA, Samal P. Accurate Water Properties from an Efficient ab Initio Method. J Chem Theory Comput 2020; 16:974-987. [DOI: 10.1021/acs.jctc.9b01018] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Subrata Jana
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Lucian A. Constantin
- Center for Biomolecular Nanotechnologies @UNILE, Istituto Italiano di Tecnologia, Via Barsanti, I-73010 Arnesano, Italy
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
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33
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Rakshit A, Bandyopadhyay P, Heindel JP, Xantheas SS. Atlas of putative minima and low-lying energy networks of water clusters n = 3-25. J Chem Phys 2019; 151:214307. [PMID: 31822087 DOI: 10.1063/1.5128378] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report a database consisting of the putative minima and ∼3.2 × 106 local minima lying within 5 kcal/mol from the putative minima for water clusters of sizes n = 3-25 using an improved version of the Monte Carlo temperature basin paving (MCTBP) global optimization procedure in conjunction with the ab initio based, flexible, polarizable Thole-Type Model (TTM2.1-F, version 2.1) interaction potential for water. Several of the low-lying structures, as well as low-lying penta-coordinated water networks obtained with the TTM2.1-F potential, were further refined at the Møller-Plesset second order perturbation (MP2)/aug-cc-pVTZ level of theory. In total, we have identified 3 138 303 networks corresponding to local minima of the clusters n = 3-25, whose Cartesian coordinates and relative energies can be obtained from the webpage https://sites.uw.edu/wdbase/. Networks containing penta-coordinated water molecules start to appear at n = 11 and, quite surprisingly, are energetically close (within 1-3 kcal/mol) to the putative minima, a fact that has been confirmed from the MP2 calculations. This large database of water cluster minima spanning quite dissimilar hydrogen bonding networks is expected to influence the development and assessment of the accuracy of interaction potentials for water as well as lower scaling electronic structure methods (such as different density functionals). Furthermore, it can also be used in conjunction with data science approaches (including but not limited to neural networks and machine and deep learning) to understand the properties of water, nature's most important substance.
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Affiliation(s)
- Avijit Rakshit
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Joseph P Heindel
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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34
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Schran C, Behler J, Marx D. Automated Fitting of Neural Network Potentials at Coupled Cluster Accuracy: Protonated Water Clusters as Testing Ground. J Chem Theory Comput 2019; 16:88-99. [DOI: 10.1021/acs.jctc.9b00805] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christoph Schran
- Lehrstuhl für Theoretische Chemie, Ruhr−Universität Bochum, 44780 Bochum, Germany
| | - Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr−Universität Bochum, 44780 Bochum, Germany
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35
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Duke RE, Cisneros GA. Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM. J Mol Model 2019; 25:307. [PMID: 31501946 DOI: 10.1007/s00894-019-4194-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/28/2019] [Indexed: 10/26/2022]
Abstract
The development of accurate potentials for computational simulations has been an active area of research. Our group has been involved in the development of the Gaussian electrostatic model (GEM), a force field based on molecular densities. The philosophy of GEM is based on the pioneering work of N. Gresh and co-workers of the reproduction of individual inter-molecular interaction components obtained from quantum mechanical (QM) energy decomposition analysis (EDA). The molecular densities used in GEM are represented by fitting accurate QM molecular densities using auxiliary basis sets (comprised of Hermite Gaussians). The use of these molecular densities results in the need to evaluate a large number of Gaussian integrals. We have previously shown that the particle-mesh Ewald (PME), and fast Fourier Poisson (FFP) methods can be used for efficiently evaluating these types of integrals. Here, we present the latest parameterization of GEM* and its application for an extensive study of PME and FFP for molecular dynamics (MD) simulations using a hybrid version of our potential, GEM*. The temperature dependence of various bulk properties is presented and discussed, as well as the effect of various parameters affecting the performance/accuracy of both methods.
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Affiliation(s)
- Robert E Duke
- Department of Chemistry, University of North Texas, Denton, TX, 76202, USA
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX, 76202, USA.
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36
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Das AK, Urban L, Leven I, Loipersberger M, Aldossary A, Head-Gordon M, Head-Gordon T. Development of an Advanced Force Field for Water Using Variational Energy Decomposition Analysis. J Chem Theory Comput 2019; 15:5001-5013. [DOI: 10.1021/acs.jctc.9b00478] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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37
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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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38
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Watanabe HC, Cui Q. Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations. J Chem Theory Comput 2019; 15:3917-3928. [DOI: 10.1021/acs.jctc.9b00180] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hiroshi C. Watanabe
- Quantum Computing Center, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- Japan Science and Technology Agency, PRESTO, 4-18, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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39
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Réal F, Vallet V, Masella M. Improving the description of solvent pairwise interactions using local solute/solvent three-body functions. The case of halides and carboxylates in aqueous environment. J Comput Chem 2019; 40:1209-1218. [PMID: 30702761 DOI: 10.1002/jcc.25779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 11/07/2022]
Abstract
We propose a general strategy to remediate force-field artifacts in describing pairwise interactions among similar molecules M in the vicinity of another chemical species, C, like water molecules interacting at short distance from a monoatomic ion. This strategy is based on introducing a three-body potential energy term that alters the pairwise interactions among M-type molecules when they lie at short range from the species C. In other words the species C is the center of a space domain where the pairwise interactions among the molecules M is altered. Here, we apply it to improve the description of the water interactions provided by the polarizable water model TCPE/2013 in the vicinity of halides, from F- to At- , and of the prototypical carboxylate anion CH3 COO- . We show the accuracy and the transferability of such an approach to investigate not only the hydration process of single anions but also of a salt solution NH 4 + / Cl - in aqueous phase. This strategy can be used to remediate the drawbacks of any kind of force fields. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Florent Réal
- CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, Université de Lille, F-59000 Lille, France
| | - Valérie Vallet
- CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, Université de Lille, F-59000 Lille, France
| | - Michel Masella
- Laboratoire de Biologie Structurale et Radiobiologie, Service de Bioénergétique, Biologie Structurale et Mécanismes, Institut Joliot, CEA Saclay, F-91191 Gif sur Yvette Cedex, France
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40
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Bizzarro BB, Egan CK, Paesani F. Nature of Halide–Water Interactions: Insights from Many-Body Representations and Density Functional Theory. J Chem Theory Comput 2019; 15:2983-2995. [DOI: 10.1021/acs.jctc.9b00064] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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41
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Saá JM, Lillo VJ, Mansilla J. Catalysis by Networks of Cooperative Hydrogen Bonds. NONCOVALENT INTERACTIONS IN CATALYSIS 2019. [DOI: 10.1039/9781788016490-00066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The main paradigm of today's chemistry is sustainability. In pursuing sustainability, we need to learn from chemical processes carried out by Nature and realize that Nature does not use either strong acids, or strong bases or fancy reagents to achieve outstanding chemical processes. Instead, enzyme activity leans on the cooperation of several chemical entities to avoid strong acids or bases or to achieve such an apparently simple goal as transferring a proton from an NuH unit to an E unit (NuH + E → Nu–EH). Hydrogen bond catalysis emerged strongly two decades ago in trying to imitate Nature and avoid metal catalysis. Now to mount another step in pursuing the goal of sustainability, the focus is upon cooperativity between the different players involved in catalysis. This chapter looks at the concept of cooperativity and, more specifically, (a) examines the role of cooperative hydrogen bonded arrays of the general type NuH⋯(NuH)n⋯NuH (i.e. intermolecular cooperativity) to facilitate general acid–base catalysis, not only in the solution phase but also under solvent-free and catalyst-free conditions, and, most important, (b) analyzes the capacity of designer chiral organocatalysts displaying intramolecular networks of cooperative hydrogen bonds (NCHBs) to facilitate enantioselective synthesis by bringing conformational rigidity to the catalyst in addition to simultaneously increasing the acidity of key hydrogen atoms so to achieve better complementarity in the highly polarized transition states.
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Affiliation(s)
- José M. Saá
- Department de Química, Universitat de les Illes Balears Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Illes Balears Spain
| | - Victor J. Lillo
- Department de Química, Universitat de les Illes Balears Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Illes Balears Spain
| | - Javier Mansilla
- Department de Química, Universitat de les Illes Balears Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Illes Balears Spain
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42
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Zhuang D, Riera M, Schenter GK, Fulton JL, Paesani F. Many-Body Effects Determine the Local Hydration Structure of Cs + in Solution. J Phys Chem Lett 2019; 10:406-412. [PMID: 30629438 DOI: 10.1021/acs.jpclett.8b03829] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A systematic analysis of the hydration structure of Cs+ ions in solution is derived from simulations carried out using a series of molecular models built upon a hierarchy of approximate representations of many-body effects in ion-water interactions. It is found that a pairwise-additive model, commonly used in biomolecular simulations, provides poor agreement with experimental X-ray spectra, indicating an incorrect description of the underlying hydration structure. Although the agreement with experiment improves in simulations with a polarizable model, the predicted hydration structure is found to lack the correct sequence of water shells. Progressive inclusion of explicit many-body effects in the representation of Cs+-water interactions as well as accounting for nuclear quantum effects is shown to be necessary for quantitatively reproducing the experimental X-ray spectra. Besides emphasizing the importance of many-body effects, these results suggest that molecular models rigorously derived from many-body expansions hold promise for realistic simulations of aqueous solutions.
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Affiliation(s)
- Debbie Zhuang
- 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
| | - Gregory K Schenter
- Physical and Computational Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - John L Fulton
- Physical and Computational Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99352 , 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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43
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Metz MP, Szalewicz K, Sarka J, Tóbiás R, Császár AG, Mátyus E. Molecular dimers of methane clathrates: ab initio potential energy surfaces and variational vibrational states. Phys Chem Chem Phys 2019; 21:13504-13525. [DOI: 10.1039/c9cp00993k] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Motivated by the energetic and environmental relevance of methane clathrates, highly accurate ab initio potential energy surfaces (PESs) have been developed for the three possible dimers of the methane and water molecules: (H2O)2, CH4·H2O, and (CH4)2.
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Affiliation(s)
- Michael P. Metz
- Department of Physics and Astronomy
- University of Delaware
- Newark
- USA
| | | | - János Sarka
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
| | - Roland Tóbiás
- Institute of Chemistry
- ELTE Eötvös Loránd University
- Budapest
- Hungary
- MTA-ELTE Complex Chemical Systems Research Group
| | - Attila G. Császár
- Institute of Chemistry
- ELTE Eötvös Loránd University
- Budapest
- Hungary
- MTA-ELTE Complex Chemical Systems Research Group
| | - Edit Mátyus
- Institute of Chemistry
- ELTE Eötvös Loránd University
- Budapest
- Hungary
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44
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Ansari N, Dandekar R, Caravati S, Sosso GC, Hassanali A. High and low density patches in simulated liquid water. J Chem Phys 2018; 149:204507. [PMID: 30501251 DOI: 10.1063/1.5053559] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We present insights into the nature of structural heterogeneities in liquid water by characterizing the empty space within the hydrogen bond network. Using molecular dynamics simulations, we show that density fluctuations create regions of empty space characterized by a diverse morphology - from spherical to fractal-like voids. These voids allow for the identification of low and high density patches of the liquid, encompassing short (0.3-0.5 nm) as well as long (1-2 nm) length-scales. In addition, we show that the formation of these patches is coupled to collective fluctuations involving the topology of hydrogen-bonded rings of water molecules. In particular, water molecules in the high density patches tend to be slightly more tetrahedral - which is consistent with the predictions of the hydrophobic effect.
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Affiliation(s)
- N Ansari
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - R Dandekar
- The Institute of Mathematical Sciences-HBNI, 4th Cross Street, CIT Campus, Tharamani, Chennai, India
| | - S Caravati
- Department of Chemistry, University of Zurich, Winterhurerstrasse 190, Zurich CH-8057, Switzerland
| | - G C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - A Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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45
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Sexton TM, Tschumper GS. 2-body:Many-body QM:QM study of structures, energetics, and vibrational frequencies for microhydrated halide ions. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1554827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Thomas More Sexton
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA
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46
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Hunter KM, Shakib FA, Paesani F. Disentangling Coupling Effects in the Infrared Spectra of Liquid Water. J Phys Chem B 2018; 122:10754-10761. [DOI: 10.1021/acs.jpcb.8b09910] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Kelly M. Hunter
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, California 92093, United States
| | - Farnaz A. Shakib
- 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
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47
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Tsimpanogiannis IN, Moultos OA, Franco LFM, Spera MBDM, Erdős M, Economou IG. Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1511903] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ioannis N. Tsimpanogiannis
- Environmental Research Laboratory, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
| | - Othonas A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Luís F. M. Franco
- School of Chemical Engineering, University of Campinas, Campinas, Brazil
| | | | - Máté Erdős
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Ioannis G. Economou
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Chemical Engineering Program, Texas A&M University at Qatar, Doha, Qatar
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48
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Nguyen TT, Székely E, Imbalzano G, Behler J, Csányi G, Ceriotti M, Götz AW, Paesani F. Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions. J Chem Phys 2018; 148:241725. [DOI: 10.1063/1.5024577] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Thuong T. Nguyen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Eszter Székely
- Engineering Department, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, United Kingdom
| | - Giulio Imbalzano
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstr. 6, 37077 Göttingen, Germany
| | - Gábor Csányi
- Engineering Department, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, United Kingdom
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - 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
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
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49
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Sidler D, Meuwly M, Hamm P. An efficient water force field calibrated against intermolecular THz and Raman spectra. J Chem Phys 2018; 148:244504. [DOI: 10.1063/1.5037062] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David Sidler
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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50
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Riera M, Brown SE, Paesani F. Isomeric Equilibria, Nuclear Quantum Effects, and Vibrational Spectra of M+(H2O)n=1–3 Clusters, with M = Li, Na, K, Rb, and Cs, through Many-Body Representations. J Phys Chem A 2018; 122:5811-5821. [DOI: 10.1021/acs.jpca.8b04106] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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