1
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Gupta S, Bull-Vulpe EF, Agnew H, Iyer S, Zhu X, Zhou R, Knight C, Paesani F. MBX V1.2: Accelerating Data-Driven Many-Body Molecular Dynamics Simulations. J Chem Theory Comput 2025; 21:1838-1849. [PMID: 39951328 DOI: 10.1021/acs.jctc.4c01333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2025]
Abstract
The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these potential energy functions integrate physics-based and machine-learned many-body terms trained on electronic structure data calculated at the "gold standard" coupled-cluster level of theory. Recent advancements in MBX have focused on optimizing its performance, resulting in the release of MBX v1.2. While the inherently many-body nature of MB-pol and MB-nrg ensures high accuracy, it poses computational challenges. MBX v1.2 addresses these challenges with significant performance improvements, including enhanced parallelism that fully harnesses the power of modern multicore CPUs. These advancements enable simulations on nanosecond time scales for condensed-phase systems, significantly expanding the scope of high-accuracy, predictive simulations of complex molecular systems powered by data-driven many-body potential energy functions.
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Affiliation(s)
- Shreya Gupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Ethan F Bull-Vulpe
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Henry Agnew
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Shishir Iyer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Xuanyu Zhu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Ruihan Zhou
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Christopher Knight
- University of Chicago, Chicago, Illinois 60637, United States
- Computational Science Division, Argonne National Laboratory, Lemont, Illinois 60439, 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
- Halicioğlu Data Science Institute, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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2
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Palos E, Bull-Vulpe EF, Zhu X, Agnew H, Gupta S, Saha S, Paesani F. Current Status of the MB-pol Data-Driven Many-Body Potential for Predictive Simulations of Water Across Different Phases. J Chem Theory Comput 2024; 20:9269-9289. [PMID: 39401055 DOI: 10.1021/acs.jctc.4c01005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Developing a molecular-level understanding of the properties of water is central to numerous scientific and technological applications. However, accurately modeling water through computer simulations has been a significant challenge due to the complex nature of the hydrogen-bonding network that water molecules form under different thermodynamic conditions. This complexity has led to over five decades of research and many modeling attempts. The introduction of the MB-pol data-driven many-body potential energy function marked a significant advancement toward a universal molecular model capable of predicting the structural, thermodynamic, dynamical, and spectroscopic properties of water across all phases. By integrating physics-based and data-driven (i.e., machine-learned) components, which correctly capture the delicate balance among different many-body interactions, MB-pol achieves chemical and spectroscopic accuracy, enabling realistic molecular simulations of water, from gas-phase clusters to liquid water and ice. In this review, we present a comprehensive overview of the data-driven many-body formalism adopted by MB-pol, highlight the main results and predictions made from computer simulations with MB-pol to date, and discuss the prospects for future extensions to data-driven many-body potentials of generic and reactive molecular systems.
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Affiliation(s)
- Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Ethan F Bull-Vulpe
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Xuanyu Zhu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Henry Agnew
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Shreya Gupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Suman Saha
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- Halicioǧlu Data Science Institute, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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3
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Ho CH, Paesani F. Entropy of Liquid Water as Predicted by the Two-Phase Thermodynamic Model and Data-Driven Many-Body Potentials. J Phys Chem B 2024; 128:6885-6891. [PMID: 38970462 DOI: 10.1021/acs.jpcb.4c03245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
We investigate the entropy of liquid water at ambient conditions using the two-phase thermodynamic (2PT) model, applied to both common pairwise-additive water models and the MB-pol and MB-pol(2023) data-driven many-body potentials. Our simulations demonstrate that the 2PT model yields entropy values in semiquantitative agreement with experimental data when using MB-pol and MB-pol(2023). Additionally, our analyses indicate that the entropy values predicted by pairwise-additive water models may benefit from error compensation between the inherent approximations of the 2PT model and the known limitations of these water models in describing many-body interactions. Despite its approximate nature, the simplicity of the 2PT model makes it a valuable tool for estimating relative entropy changes of liquid water across various environments, especially when combined with water models that provide a consistently robust representation of the structural, thermodynamic, and dynamical properties of liquid water.
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Affiliation(s)
- Ching-Hwa Ho
- 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
- Halicioğlu Data Science Institute, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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4
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Arandhara M, Ramesh SG. Nuclear Quantum Effects in Hydroxide Hydrate Along the H-Bond Bifurcation Pathway. J Phys Chem A 2024; 128:1600-1610. [PMID: 38393819 DOI: 10.1021/acs.jpca.3c08027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Path integral (PI) simulations are used to explore nuclear quantum effects (NQEs) in hydroxide hydrate and its perdeuterated isotopomer along the H-bond bifurcation pathway. Toward this, a new potential energy surface using the symmetric gradient domain machine learning method with ab initio data at the CCSD(T)/aug-cc-pVTZ level is built. From PI umbrella sampling (US) simulations, free energy profiles along the bifurcation coordinate are explored as a function of temperature. At ambient temperature, the bifurcation barrier is increased upon inclusion of NQEs. At low temperatures in the deep tunneling regime, the barrier is strongly decreased and flattened. These trends are examined, and the role of the O-O distance is also investigated through two-dimensional US simulations.
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Affiliation(s)
- Mrinal Arandhara
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sai G Ramesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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5
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Arandhara M, Ramesh SG. Nuclear quantum effects in gas-phase 2-fluoroethanol. Phys Chem Chem Phys 2024; 26:6885-6902. [PMID: 38333949 DOI: 10.1039/d3cp05657k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Torsional motions along the FCCO and HOCC dihedrals lead to the five unique conformations of 2-fluoroethanol, of which the conformer that is gauche along both dihedrals has the lowest energy. In this work, we explore how nuclear quantum effects (NQEs) manifest in the structural parameters of the lowest energy conformer, in the intramolecular free energy landscape along the FCCO and HOCC dihedrals, and also in the infrared spectrum of the title molecule, through the use of path integral simulations. We have first developed a full dimensional potential energy surface using the reaction surface Hamiltonian framework. On this potential, we have carried out path integral molecular dynamics simulations at several temperatures starting from the minimum energy well to explore structural influences of NQEs including geometrical markers of the interaction between the OH and F groups. From the computed free energy landscapes, significant reduction of the torsional barrier is found at low temperature near the cis region of the dihedrals, which can be understood through the trends in the radii of gyration of the atomic ring polymers. We find that the inclusion of NQEs in the computation of infrared spectrum is important to obtain good agreement with the experimental band positions.
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Affiliation(s)
- Mrinal Arandhara
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
| | - Sai G Ramesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
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6
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Xiao T, Yang JL, Zhang B, Wu J, Li J, Mai W, Fan HJ. All-Round Ionic Liquids for Shuttle-Free Zinc-Iodine Battery. Angew Chem Int Ed Engl 2024; 63:e202318470. [PMID: 38179860 DOI: 10.1002/anie.202318470] [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: 12/02/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/06/2024]
Abstract
The practical implementation of aqueous zinc-iodine batteries (ZIBs) is hindered by the rampant Zn dendrites growth, parasite corrosion, and polyiodide shuttling. In this work, ionic liquid EMIM[OAc] is employed as an all-round solution to mitigate challenges on both the Zn anode and the iodine cathode side. First, the EMIM+ embedded lean-water inner Helmholtz plane (IHP) and inert solvation sheath modulated by OAc- effectively repels H2 O molecules away from the Zn anode surface. The preferential adsorption of EMIM+ on Zn metal facilitates uniform Zn nucleation via a steric hindrance effect. Second, EMIM+ can reduce the polyiodide shuttling by hindering the iodine dissolution and forming an EMIM+ -I3 - dominated phase. These effects holistically enhance the cycle life, which is manifested by both Zn || Zn symmetric cells and Zn-I2 full cells. ZIBs with EAc deliver a capacity decay rate of merely 0.01 ‰ per cycle after over 18,000 cycles at 4 A g-1 , and lower self-discharge and better calendar life than the ZIBs without ionic liquid EAc additive.
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Affiliation(s)
- Tao Xiao
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Jin-Lin Yang
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Bao Zhang
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Jiawen Wu
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
- Institute of Flexible Electronics Technology, Tsinghua University, Jiaxing, 314000, China
| | - Jinliang Li
- Department of Physics, Jinan University, Guangzhou, 510632, China
| | - Wenjie Mai
- Department of Physics, Jinan University, Guangzhou, 510632, China
| | - Hong Jin Fan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
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7
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Palos E, Caruso A, Paesani F. Consistent density functional theory-based description of ion hydration through density-corrected many-body representations. J Chem Phys 2023; 159:181101. [PMID: 37947509 DOI: 10.1063/5.0174577] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
Delocalization error constrains the accuracy of density functional theory in describing molecular interactions in ion-water systems. Using Na+ and Cl- in water as model systems, we calculate the effects of delocalization error in the SCAN functional for describing ion-water and water-water interactions in hydrated ions, and demonstrate that density-corrected SCAN (DC-SCAN) predicts n-body and interaction energies with an accuracy approaching coupled cluster theory. The performance of DC-SCAN is size-consistent, maintaining an accurate description of molecular interactions well beyond the first solvation shell. Molecular dynamics simulations at ambient conditions with many-body MB-SCAN(DC) potentials, derived from the many-body expansion, predict the solvation structure of Na+ and Cl- in quantitative agreement with reference data, while simultaneously reproducing the structure of liquid water. Beyond rationalizing the accuracy of density-corrected models of ion hydration, our findings suggest that our unified density-corrected MB formalism holds great promise for efficient DFT-based simulations of condensed-phase systems with chemical accuracy.
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Affiliation(s)
- Etienne Palos
- Department of Chemistry and Biochemistry, 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
| | - 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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8
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Yang X, Liu R, Xu R, Wang Z. Sequential flipping: the donor-acceptor exchange mechanism in water trimers. Phys Chem Chem Phys 2023; 25:21957-21963. [PMID: 37553960 DOI: 10.1039/d3cp02666c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The donor-acceptor exchange (DAE) is a significant hydrogen bond network rearrangement (HBNR) mechanism because it can lead to the change of the hydrogen bond direction. In this work, we report a new DAE mechanism found in water trimers that is realized by sequential flipping (SF) of all molecules rather than the well-known proton transfer (PT) process. Meanwhile, the SF process has a much smaller potential barrier (0.262 eV) than the previously predicted collective rotation process (about 1.7 eV), implying that the SF process is the main flipping process that can lead to DAE. Importantly, high-precision ab initio calculations show that SF-DAE can make the water ring to show a clear chiral difference from PT-DAE, which brings the prospect of distinguishing the two confusing processes based on circular dichroism spectra. The reaction rate analysis including quantum tunneling indicates an obvious temperature-dependent competitive relationship between the SF and PT processes; specifically, the SF process dominates above 65 K, while the PT process dominates below 65 K. Therefore, in most cases, the contribution for DAE mainly comes from the flipping process, rather than the PT process as previously thought. Our work enriches the understanding of the DAE mechanism in water trimers and provides a piece of the jigsaw that has been sought for the HBNR mechanism.
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Affiliation(s)
- Xinrui Yang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China.
| | - Rui Liu
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China.
| | - Ruiqi Xu
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China.
| | - Zhigang Wang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China.
- International Center for Computational Method & Software, College of Physics, Jilin University, Changchun 130012, China
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9
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Riera M, Knight C, Bull-Vulpe EF, Zhu X, Agnew H, Smith DGA, Simmonett AC, Paesani F. MBX: A many-body energy and force calculator for data-driven many-body simulations. J Chem Phys 2023; 159:054802. [PMID: 37526156 PMCID: PMC10550339 DOI: 10.1063/5.0156036] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
Many-Body eXpansion (MBX) is a C++ library that implements many-body potential energy functions (PEFs) within the "many-body energy" (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of many-body interactions to achieve chemical accuracy from the gas to the condensed phases. MBX can be employed either as a stand-alone package or as an energy/force engine that can be integrated with generic software for molecular dynamics and Monte Carlo simulations. MBX is parallelized internally using Open Multi-Processing and can utilize Message Passing Interface when available in interfaced molecular simulation software. MBX enables classical and quantum molecular simulations with MB-nrg PEFs, as well as hybrid simulations that combine conventional force fields and MB-nrg PEFs, for diverse systems ranging from small gas-phase clusters to aqueous solutions and molecular fluids to biomolecular systems and metal-organic frameworks.
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Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Christopher Knight
- Argonne National Laboratory, Computational Science Division, Lemont, Illinois 60439, USA
| | - Ethan F. Bull-Vulpe
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Xuanyu Zhu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Henry Agnew
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | | | - Andrew C. Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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10
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Goutham S, Keerthi A, Ismail A, Bhardwaj A, Jalali H, You Y, Li Y, Hassani N, Peng H, Martins MVS, Wang F, Neek-Amal M, Radha B. Beyond steric selectivity of ions using ångström-scale capillaries. NATURE NANOTECHNOLOGY 2023; 18:596-601. [PMID: 36997753 DOI: 10.1038/s41565-023-01337-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Ion-selective channels play a key role in physiological processes and are used in many technologies. Although biological channels can efficiently separate same-charge ions with similar hydration shells, it remains a challenge to mimic such exquisite selectivity using artificial solid-state channels. Although there are several nanoporous membranes that show high selectivity with respect to certain ions, the underlying mechanisms are based on the hydrated ion size and/or charge. There is a need to rationalize the design of artificial channels to make them capable of selecting between similar-sized same-charge ions, which, in turn, requires an understanding of why and how such selectivity can occur. Here we study ångström-scale artificial channels made by van der Waals assembly, which are comparable in size with typical ions and carry little residual charge on the channel walls. This allows us to exclude the first-order effects of steric- and Coulomb-based exclusion. We show that the studied two-dimensional ångström-scale capillaries can distinguish between same-charge ions with similar hydrated diameters. The selectivity is attributed to different positions occupied by ions within the layered structure of nanoconfined water, which depend on the ion-core size and differ for anions and cations. The revealed mechanism points at the possibilities of ion separation beyond simple steric sieving.
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Affiliation(s)
- Solleti Goutham
- Department of Physics and Astronomy, School of Natural Sciences, The University of Manchester, Manchester, UK
- National Graphene Institute, The University of Manchester, Manchester, UK
| | - Ashok Keerthi
- National Graphene Institute, The University of Manchester, Manchester, UK
- Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Abdulghani Ismail
- Department of Physics and Astronomy, School of Natural Sciences, The University of Manchester, Manchester, UK
- National Graphene Institute, The University of Manchester, Manchester, UK
| | - Ankit Bhardwaj
- Department of Physics and Astronomy, School of Natural Sciences, The University of Manchester, Manchester, UK
- National Graphene Institute, The University of Manchester, Manchester, UK
| | - Hossein Jalali
- Department of Physics, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Yi You
- Department of Physics and Astronomy, School of Natural Sciences, The University of Manchester, Manchester, UK
- National Graphene Institute, The University of Manchester, Manchester, UK
| | - Yiheng Li
- Chinese Academy of Sciences Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China
| | - Nasim Hassani
- Department of Physics, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Haoke Peng
- Chinese Academy of Sciences Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China
| | - Marcos Vinicius Surmani Martins
- Department of Physics and Astronomy, School of Natural Sciences, The University of Manchester, Manchester, UK
- National Graphene Institute, The University of Manchester, Manchester, UK
| | - Fengchao Wang
- Chinese Academy of Sciences Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China
| | - Mehdi Neek-Amal
- Department of Physics, Shahid Rajaee Teacher Training University, Tehran, Iran
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | - Boya Radha
- Department of Physics and Astronomy, School of Natural Sciences, The University of Manchester, Manchester, UK.
- National Graphene Institute, The University of Manchester, Manchester, UK.
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11
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Park BW, Kim J, Shin TJ, Kim YS, Kim MG, Seok SI. Stabilization of the Alkylammonium Cations in Halide Perovskite Thin Films by Water-Mediated Proton Transfer. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211386. [PMID: 36646632 DOI: 10.1002/adma.202211386] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The development of alkylammonium lead trihalide perovskite (ALHP) photovoltaics has grown rapidly over the past decade. However, there are remaining critical challenges, such as proton defects, which can lead to the material instability of ALHPs. Although specific strategies, including the use of halide additives, have significantly reduced the defects, a fundamental understanding of the defect passivation mechanism remains elusive. Herein, an approach and mechanism for minimizing proton defects in ALHP crystals by adding ionized halides to the perovskite precursor solution are reported. This work clarifies that the ionized halides induced proton transfer from H2 O to the alkylammonium cation in the precursor solution, stabilizing the ALHP crystals. The fundamental characteristics of ALHP and its precursors are examined by X-ray diffraction, transmittance electron microscopy, in situ extended X-ray absorption fine structure, Fourier transform NMR spectroscopy, and Fourier transform infrared spectroscopy. The findings from this work will guide the development of highly stable ALHP crystals, enabling efficient and stable optoelectronic ALHP devices.
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Affiliation(s)
- Byung-Wook Park
- Department of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Jincheol Kim
- New & Renewable Energy Research Centre, Korea Electronics Technology Institute, Seong-Nam, 13509, Republic of Korea
- School of Engineering, Macquarie University Sustainable Energy Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Tae Joo Shin
- UNIST Central Research Facilities & School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Yung Sam Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Min Gyu Kim
- Beamline Research Division, Pohang Accelerator Laboratory (PAL), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Sang Il Seok
- Department of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
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12
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Stephens AD, Kölbel J, Moons R, Chung CW, Ruggiero MT, Mahmoudi N, Shmool TA, McCoy TM, Nietlispach D, Routh AF, Sobott F, Zeitler JA, Kaminski Schierle GS. Decreased Water Mobility Contributes To Increased α-Synuclein Aggregation. Angew Chem Int Ed Engl 2023; 62:e202212063. [PMID: 36316279 PMCID: PMC10107867 DOI: 10.1002/anie.202212063] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 01/13/2023]
Abstract
The solvation shell is essential for the folding and function of proteins, but how it contributes to protein misfolding and aggregation has still to be elucidated. We show that the mobility of solvation shell H2 O molecules influences the aggregation rate of the amyloid protein α-synuclein (αSyn), a protein associated with Parkinson's disease. When the mobility of H2 O within the solvation shell is reduced by the presence of NaCl, αSyn aggregation rate increases. Conversely, in the presence CsI the mobility of the solvation shell is increased and αSyn aggregation is reduced. Changing the solvent from H2 O to D2 O leads to increased aggregation rates, indicating a solvent driven effect. We show the increased aggregation rate is not directly due to a change in the structural conformations of αSyn, it is also influenced by a reduction in both the H2 O mobility and αSyn mobility. We propose that reduced mobility of αSyn contributes to increased aggregation by promoting intermolecular interactions.
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Affiliation(s)
| | - Johanna Kölbel
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Rani Moons
- Department of ChemistryUniversity of AntwerpBelgium
| | - Chyi Wei Chung
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Michael T. Ruggiero
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
- Department of ChemistryUniversity of VermontUSA
| | | | - Talia A. Shmool
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Thomas M. McCoy
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | | | - Alexander F. Routh
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Frank Sobott
- Department of ChemistryUniversity of AntwerpBelgium
- The Astbury Centre for Structural Molecular BiologyUniversity of LeedsUK
| | - J. Axel Zeitler
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
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13
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Ge J, Zhang XD, Peng Y, Bai XL. Unraveling the effect of solvents on the excited state dynamics of C540A by experimental and theoretical study. RSC Adv 2023; 13:4924-4931. [PMID: 36762085 PMCID: PMC9906279 DOI: 10.1039/d3ra00259d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
In this work, the excited-state dynamics including intramolecular charge transfer (ICT) and the redshift of C540A have been investigated in a series of solvents on the basis of the Kamlet-Taft solvatochromic parameters (π*, α, β) using femtosecond transient absorption spectra and systematic theoretical calculation. We demonstrate that the redshift of the emission peak has a linear relationship with the α and π* scales and the effect of the π* scale is slightly stronger than that of the α scale. Meanwhile, the ICT rates can be suggested as relevant to not only the α scale but also the π* scale. Additionally, C540A-AN has proved that the excited state molecules have a unique inactivation mechanism because of the dark feature of the S1 (CT) state. The valuable mechanistic information gleaned from the excited-state dynamics by the experimental and theoretical study would facilitate the design of organic materials for prospective applications in photochemistry and photobiology.
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Affiliation(s)
- Jing Ge
- School of Physics and Information Engineering, Key Laboratory of Spectral Measurement and Analysis of Shanxi Province, Shanxi Normal University Taiyuan 030031 China
| | - Xue-Dong Zhang
- School of Physics and Information Engineering, Key Laboratory of Spectral Measurement and Analysis of Shanxi Province, Shanxi Normal University Taiyuan 030031 China
| | - Yue Peng
- School of Physics and Information Engineering, Key Laboratory of Spectral Measurement and Analysis of Shanxi Province, Shanxi Normal University Taiyuan 030031 China
| | - Xi-Lin Bai
- School of Physics and Information Engineering, Key Laboratory of Spectral Measurement and Analysis of Shanxi Province, Shanxi Normal University Taiyuan 030031 China
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14
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Stephens AD, Kölbel J, Moons R, Chung CW, Ruggiero MT, Mahmoudi N, Shmool TA, McCoy TM, Nietlispach D, Routh AF, Sobott F, Zeitler JA, Kaminski Schierle GS. Decreased Water Mobility Contributes To Increased α-Synuclein Aggregation. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202212063. [PMID: 38516046 PMCID: PMC10952249 DOI: 10.1002/ange.202212063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Indexed: 03/23/2024]
Abstract
The solvation shell is essential for the folding and function of proteins, but how it contributes to protein misfolding and aggregation has still to be elucidated. We show that the mobility of solvation shell H2O molecules influences the aggregation rate of the amyloid protein α-synuclein (αSyn), a protein associated with Parkinson's disease. When the mobility of H2O within the solvation shell is reduced by the presence of NaCl, αSyn aggregation rate increases. Conversely, in the presence CsI the mobility of the solvation shell is increased and αSyn aggregation is reduced. Changing the solvent from H2O to D2O leads to increased aggregation rates, indicating a solvent driven effect. We show the increased aggregation rate is not directly due to a change in the structural conformations of αSyn, it is also influenced by a reduction in both the H2O mobility and αSyn mobility. We propose that reduced mobility of αSyn contributes to increased aggregation by promoting intermolecular interactions.
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Affiliation(s)
| | - Johanna Kölbel
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Rani Moons
- Department of ChemistryUniversity of AntwerpBelgium
| | - Chyi Wei Chung
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Michael T. Ruggiero
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
- Department of ChemistryUniversity of VermontUSA
| | | | - Talia A. Shmool
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Thomas M. McCoy
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | | | - Alexander F. Routh
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Frank Sobott
- Department of ChemistryUniversity of AntwerpBelgium
- The Astbury Centre for Structural Molecular BiologyUniversity of LeedsUK
| | - J. Axel Zeitler
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
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15
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Li X, Lu B, Jiang J, Wang L, Trabelsi T, Francisco JS, Fang W, Zhou M, Zeng X. Water Complex of Imidogen. J Am Chem Soc 2023; 145:1982-1987. [PMID: 36633923 DOI: 10.1021/jacs.2c12808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Imidogen (NH) is the simplest nitrogen hydride that plays an important role in combustion and interstellar chemistry, and its combination with H2O is the prototypical amidation reaction of O-H bonds involving a nitrene intermediate. Herein, we report the observation of the elusive water complex of NH, a prereaction complex associated with the amidation reaction in a solid N2 matrix at 10 K. The hydrogen-bonded structure of NH···OH2 (versus HN···HOH) is confirmed via IR spectroscopy with comprehensive isotope labeling (D, 18O, and 15N) and quantum chemical calculations at the UCCSD(T)/aug-cc-pVQZ level of theory. In line with the observed absorption at 350 nm, irradiation of the complex at 365 nm leads to O-H bond insertion, yielding hydroxylamine NH2OH.
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Affiliation(s)
- Xiaolong Li
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, 200433 Shanghai, China
| | - Bo Lu
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, 200433 Shanghai, China
| | - Junjie Jiang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, 200433 Shanghai, China
| | - Lina Wang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, 200433 Shanghai, China
| | - Tarek Trabelsi
- Department of Earth and Environment Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6243, United States
| | - Joseph S Francisco
- Department of Earth and Environment Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6243, United States
| | - Wei Fang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, 200433 Shanghai, China
| | - Mingfei Zhou
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, 200433 Shanghai, China
| | - Xiaoqing Zeng
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, 200433 Shanghai, China
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16
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Bull-Vulpe EF, Riera M, Bore SL, Paesani F. Data-Driven Many-Body Potential Energy Functions for Generic Molecules: Linear Alkanes as a Proof-of-Concept Application. J Chem Theory Comput 2022. [PMID: 36113028 DOI: 10.1021/acs.jctc.2c00645] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a generalization of the many-body energy (MB-nrg) theoretical/computational framework that enables the development of data-driven potential energy functions (PEFs) for generic covalently bonded molecules, with arbitrary quantum mechanical accuracy. The "nearsightedness of electronic matter" is exploited to define monomers as "natural building blocks" on the basis of their distinct chemical identity. The energy of generic molecules is then expressed as a sum of individual many-body energies of incrementally larger subsystems. The MB-nrg PEFs represent the low-order n-body energies, with n = 1-4, using permutationally invariant polynomials derived from electronic structure data carried out at an arbitrary quantum mechanical level of theory, while all higher-order n-body terms (n > 4) are represented by a classical many-body polarization term. As a proof-of-concept application of the general MB-nrg framework, we present MB-nrg PEFs for linear alkanes. The MB-nrg PEFs are shown to accurately reproduce reference energies, harmonic frequencies, and potential energy scans of alkanes, independently of their length. Since, by construction, the MB-nrg framework introduced here can be applied to generic covalently bonded molecules, we envision future computer simulations of complex molecular systems using data-driven MB-nrg PEFs, with arbitrary quantum mechanical accuracy.
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Affiliation(s)
- Ethan F. Bull-Vulpe
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Sigbjørn L. Bore
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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17
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Heller ER, Richardson JO. Heavy-Atom Quantum Tunnelling in Spin Crossovers of Nitrenes. Angew Chem Int Ed Engl 2022; 61:e202206314. [PMID: 35698730 PMCID: PMC9540336 DOI: 10.1002/anie.202206314] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Indexed: 01/01/2023]
Abstract
We simulate two recent matrix-isolation experiments at cryogenic temperatures, in which a nitrene undergoes spin crossover from its triplet state to a singlet state via quantum tunnelling. We detail the failure of the commonly applied weak-coupling method (based on a linear approximation of the potentials) in describing these deep-tunnelling reactions. The more rigorous approach of semiclassical golden-rule instanton theory in conjunction with double-hybrid density-functional theory and multireference perturbation theory does, however, provide rate constants and kinetic isotope effects in good agreement with experiment. In addition, these calculations locate the optimal tunnelling pathways, which provide a molecular picture of the reaction mechanism. The reactions involve substantial heavy-atom quantum tunnelling of carbon, nitrogen and oxygen atoms, which unexpectedly even continues to play a role at room temperature.
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Affiliation(s)
- Eric R. Heller
- Laboratory of Physical ChemistryETH Zürich8093ZürichSwitzerland
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18
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Liu J, Lan J, He X. Toward High-level Machine Learning Potential for Water Based on Quantum Fragmentation and Neural Networks. J Phys Chem A 2022; 126:3926-3936. [PMID: 35679610 DOI: 10.1021/acs.jpca.2c00601] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate and efficient simulation of liquids, such as water and salt solutions, using high-level wave function theories is still a formidable task for computational chemists owing to the high computational costs. In this study, we develop a deep machine learning potential based on fragment-based second-order Møller-Plesset perturbation theory (DP-MP2) for water through neural networks. We show that the DP-MP2 potential predicts the structural, dynamical, and thermodynamic properties of liquid water in better agreement with the experimental data than previous studies based on density functional theory (DFT). The nuclear quantum effects (NQEs) on the properties of liquid water are also examined, which are noticeable in affecting the structural and dynamical properties of liquid water under ambient conditions. This work provides a general framework for quantitative predictions of the properties of condensed-phase systems with the accuracy of high-level wave function theory while achieving significant computational savings compared to ab initio simulations.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Jinggang Lan
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,New York University-East China Normal University Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
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19
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Heller ER, Richardson JO. Heavy‐Atom Quantum Tunnelling in Spin Crossovers of Nitrenes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Eric R Heller
- Eidgenossische Technische Hochschule Zurich Lab. Physical Chemistry SWITZERLAND
| | - Jeremy O Richardson
- Eidgenössische Technische Hochschule Zürich Lab. Physical Chemistry Vladimir-Prelog-Weg 2 8093 Zurich SWITZERLAND
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20
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Robinson VN, Ghosh R, Egan CK, Riera M, Knight C, Paesani F, Hassanali A. The behavior of methane-water mixtures under elevated pressures from simulations using many-body potentials. J Chem Phys 2022; 156:194504. [PMID: 35597630 DOI: 10.1063/5.0089773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Non-polarizable empirical potentials have been proven to be incapable of capturing the mixing of methane-water mixtures at elevated pressures. Although density functional theory-based ab initio simulations may circumvent this discrepancy, they are limited in terms of the relevant time and length scales associated with mixing phenomena. Here, we show that the many-body MB-nrg potential, designed to reproduce methane-water interactions with coupled cluster accuracy, successfully captures this phenomenon up to 3 GPa and 500 K with varying methane concentrations. Two-phase simulations and long time scales that are required to fully capture the mixing, affordable due to the speed and accuracy of the MBX software, are assessed. Constructing the methane-water equation of state across the phase diagram shows that the stable mixtures are denser than the sum of their parts at a given pressure and temperature. We find that many-body polarization plays a central role, enhancing the induced dipole moments of methane by 0.20 D during mixing under pressure. Overall, the mixed system adopts a denser state, which involves a significant enthalpic driving force as elucidated by a systematic many-body energy decomposition analysis.
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Affiliation(s)
- Victor Naden Robinson
- The 'Abdus Salam' International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Raja Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Colin K Egan
- The 'Abdus Salam' International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Christopher Knight
- Computational Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Ali Hassanali
- The 'Abdus Salam' International Centre for Theoretical Physics, I-34151 Trieste, Italy
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21
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Ansari IM, Heller ER, Trenins G, Richardson JO. Instanton theory for Fermi's golden rule and beyond. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200378. [PMID: 35341312 PMCID: PMC8958279 DOI: 10.1098/rsta.2020.0378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/22/2021] [Indexed: 05/29/2023]
Abstract
Instanton theory provides a semiclassical approximation for computing quantum tunnelling effects in complex molecular systems. It is typically applied to proton-transfer reactions for which the Born-Oppenheimer approximation is valid. However, many processes in physics, chemistry and biology, such as electron transfers, are non-adiabatic and are correctly described instead using Fermi's golden rule. In this work, we discuss how instanton theory can be generalized to treat these reactions in the golden-rule limit. We then extend the theory to treat fourth-order processes such as bridge-mediated electron transfer and apply the method to simulate an electron moving through a model system of three coupled quantum dots. By comparison with benchmark quantum calculations, we demonstrate that the instanton results are much more reliable than alternative approximations based on superexchange-mediated effective coupling or a classical sequential mechanism. This article is part of the theme issue 'Chemistry without the Born-Oppenheimer approximation'.
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Affiliation(s)
| | - Eric R. Heller
- Laboratory of Physical Chemistry, ETH, Zürich, Switzerland
| | - George Trenins
- Laboratory of Physical Chemistry, ETH, Zürich, Switzerland
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22
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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: 1.0] [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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23
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Bull-Vulpe EF, Riera M, Götz AW, Paesani F. MB-Fit: Software infrastructure for data-driven many-body potential energy functions. J Chem Phys 2021; 155:124801. [PMID: 34598567 DOI: 10.1063/5.0063198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.
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Affiliation(s)
- Ethan F Bull-Vulpe
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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24
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Lambros E, Dasgupta S, Palos E, Swee S, Hu J, Paesani F. General Many-Body Framework for Data-Driven Potentials with Arbitrary Quantum Mechanical Accuracy: Water as a Case Study. J Chem Theory Comput 2021; 17:5635-5650. [PMID: 34370954 DOI: 10.1021/acs.jctc.1c00541] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a general framework for the development of data-driven many-body (MB) potential energy functions (MB-QM PEFs) that represent the interactions between small molecules at an arbitrary quantum-mechanical (QM) level of theory. As a demonstration, a family of MB-QM PEFs for water is rigorously derived from density functionals belonging to different rungs across Jacob's ladder of approximations within density functional theory (MB-DFT) and from Møller-Plesset perturbation theory (MB-MP2). Through a systematic analysis of individual MB contributions to the interaction energies of water clusters, we demonstrate that all MB-QM PEFs preserve the same accuracy as the corresponding ab initio calculations, with the exception of those derived from density functionals within the generalized gradient approximation (GGA). The differences between the DFT and MB-DFT results are traced back to density-driven errors that prevent GGA functionals from accurately representing the underlying molecular interactions for different cluster sizes and hydrogen-bonding arrangements. We show that this shortcoming may be overcome, within the MB formalism, by using density-corrected functionals (DC-DFT) that provide a more consistent representation of each individual MB contribution. This is demonstrated through the development of a MB-DFT PEF derived from DC-PBE-D3 data, which more accurately reproduce the corresponding ab initio results.
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Affiliation(s)
- Eleftherios Lambros
- 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
| | - Etienne Palos
- 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
| | - 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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25
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Caruso A, Paesani F. Data-driven many-body models enable a quantitative description of chloride hydration from clusters to bulk. J Chem Phys 2021; 155:064502. [PMID: 34391363 DOI: 10.1063/5.0059445] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We present a new data-driven potential energy function (PEF) describing chloride-water interactions, which is developed within the many-body-energy (MB-nrg) theoretical framework. Besides quantitatively reproducing low-order many-body energy contributions, the new MB-nrg PEF is able to correctly predict the interaction energies of small chloride-water clusters calculated at the coupled cluster level of theory. Importantly, classical and quantum molecular dynamics simulations of a single chloride ion in water demonstrate that the new MB-nrg PEF predicts x-ray spectra in close agreement with the experimental results. Comparisons with an popular empirical model and a polarizable PEF emphasize the importance of an accurate representation of short-range many-body effect while demonstrating that pairwise additive representations of chloride-water and water-water interactions are inadequate for correctly representing the hydration structure of chloride in both gas-phase clusters and solution. We believe that the analyses presented in this study provide additional evidence for the accuracy and predictive ability of the MB-nrg PEFs, which can then enable more realistic simulations of ionic aqueous systems in different environments.
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Affiliation(s)
- Alessandro Caruso
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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26
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Cruzeiro VWD, Lambros E, Riera M, Roy R, Paesani F, Götz AW. Highly Accurate Many-Body Potentials for Simulations of N 2O 5 in Water: Benchmarks, Development, and Validation. J Chem Theory Comput 2021; 17:3931-3945. [PMID: 34029079 DOI: 10.1021/acs.jctc.1c00069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Dinitrogen pentoxide (N2O5) is an important intermediate in the atmospheric chemistry of nitrogen oxides. Although there has been much research, the processes that govern the physical interactions between N2O5 and water are still not fully understood at a molecular level. Gaining a quantitative insight from computer simulations requires going beyond the accuracy of classical force fields while accessing length scales and time scales that are out of reach for high-level quantum-chemical approaches. To this end, we present the development of MB-nrg many-body potential energy functions for nonreactive simulations of N2O5 in water. This MB-nrg model is based on electronic structure calculations at the coupled cluster level of theory and is compatible with the successful MB-pol model for water. It provides a physically correct description of long-range many-body interactions in combination with an explicit representation of up to three-body short-range interactions in terms of multidimensional permutationally invariant polynomials. In order to further investigate the importance of the underlying interactions in the model, a TTM-nrg model was also devised. TTM-nrg is a more simplistic representation that contains only two-body short-range interactions represented through Born-Mayer functions. In this work, an active learning approach was employed to efficiently build representative training sets of monomer, dimer, and trimer structures, and benchmarks are presented to determine the accuracy of our new models in comparison to a range of density functional theory methods. By assessing the binding curves, distortion energies of N2O5, and interaction energies in clusters of N2O5 and water, we evaluate the importance of two-body and three-body short-range potentials. The results demonstrate that our MB-nrg model has high accuracy with respect to the coupled cluster reference, outperforms current density functional theory models, and thus enables highly accurate simulations of N2O5 in aqueous environments.
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Affiliation(s)
- Vinícius Wilian D Cruzeiro
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States.,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
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Ronak Roy
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States.,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
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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27
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Sahu N, Richardson JO, Berger R. Instanton calculations of tunneling splittings in chiral molecules. J Comput Chem 2021; 42:210-221. [PMID: 33259074 DOI: 10.1002/jcc.26447] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 11/11/2022]
Abstract
We report the ground state tunneling splittings (ΔE± ) of a number of axially chiral molecules using the ring-polymer instanton (RPI) method (J. Chem. Phys., 2011, 134, 054109). The list includes isotopomers of hydrogen dichalcogenides H2 X2 (X = O, S, Se, Te, and Po), hydrogen thioperoxide HSOH and dichlorodisulfane S2 Cl2 . Ab initio electronic-structure calculations have been performed on the level of second-order Møller-Plesset perturbation (MP2) theory either with split-valance basis sets or augmented correlation-consistent basis sets on H, O, S, and Cl atoms. Energy-consistent pseudopotential and corresponding triple zeta basis sets of the Stuttgart group are used on Se, Te, and Po atoms. The results are further improved using single point calculations performed at the coupled cluster level with iterative singles and doubles and perturbative triples amplitudes. When available for comparison, our computed values of ΔE± are found to lie within the same order of magnitude as values reported in the literature, although RPI also provides predictions for H2 Po2 and S2 Cl2 , which have not previously been directly calculated. Since RPI is a single-shot method which does not require detailed prior knowledge of the optimal tunneling path, it offers an effective way for estimating the tunneling dynamics of more complex chiral molecules, and especially those with small tunneling splittings.
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Affiliation(s)
- Nityananda Sahu
- Fachbereich Chemie, Theoretische Chemie, Philipps Universität Marburg, Marburg, Germany
| | | | - Robert Berger
- Fachbereich Chemie, Theoretische Chemie, Philipps Universität Marburg, Marburg, Germany
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28
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Fang W, Winter P, Richardson JO. Microcanonical Tunneling Rates from Density-of-States Instanton Theory. J Chem Theory Comput 2020; 17:40-55. [PMID: 33351621 DOI: 10.1021/acs.jctc.0c01118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Semiclassical instanton theory is a form of quantum transition-state theory which can be applied to the computation of thermal reaction rates in complex molecular systems including quantum tunneling effects. There have been a number of attempts to extend the theory to treat microcanonical rates. However, the previous formulations are either computationally unfeasible for large systems due to an explicit sum over states or they involve extra approximations, which make them less reliable. We propose a robust and practical microcanonical formulation called density-of-states instanton theory, which avoids the sum over states altogether. In line with the semiclassical approximations inherent to the instanton approach, we employ the stationary-phase approximation to the inverse Laplace transform to obtain the densities of states. This can be evaluated using only post-processing of the data available from a small set of instanton calculations, such that our approach remains computationally efficient. We show that the new formulation predicts results that agree well with quantum scattering theory for an atom-diatom reaction and with experiments for a photoexcited unimolecular hydrogen transfer in a Criegee intermediate. When the thermal rate is evaluated from a Boltzmann average over our new microcanonical formalism, it can overcome some problems of conventional instanton theory. In particular, it predicts a smooth transition at the crossover temperature and is able to describe bimolecular reactions with pre-reactive complexes such as CH3OH + OH.
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Affiliation(s)
- Wei Fang
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Pierre Winter
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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29
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Riera M, Hirales A, Ghosh R, Paesani F. Data-Driven Many-Body Models with Chemical Accuracy for CH4/H2O Mixtures. J Phys Chem B 2020; 124:11207-11221. [DOI: 10.1021/acs.jpcb.0c08728] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Alan Hirales
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Raja Ghosh
- 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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30
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Abdelbassit MS, Curnow OJ, Libowitzky E, Piltz RO, Polson MIJ. A Discrete Chloride Monohydrate: A Solid-State Structural and Spectroscopic Characterization. J Phys Chem A 2020; 124:9244-9251. [PMID: 33119304 DOI: 10.1021/acs.jpca.0c07589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solid-state structure of a discrete chloride monohydrate species, [Cl(H2O)]-, is reported for the first time. It was isolated as a salt of the tris(dipropylamino)cyclopropenium cation and has been structurally characterized by X-ray and neutron diffraction. Infrared (IR), far-infrared, and Raman spectroscopic studies were also carried out. Additionally, the D2O and HDO isotopomers were investigated. Of the six fundamental vibrational modes, only the out-of-plane bend ν3 was not observed as it forms an IR- and Raman-inactive local mode phonon.
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Affiliation(s)
- Mohammed S Abdelbassit
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Owen J Curnow
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Eugen Libowitzky
- Institut für Mineralogie und Kristallographie, Universität Wien, Geozentrum, Althanstraße 14, A-1090 Vienna, Austria
| | - Ross O Piltz
- Australian Centre for Neutron Scattering, Lucas Heights, NSW 2234, Australia
| | - Matthew I J Polson
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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31
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Mapping the temperature-dependent and network site-specific onset of spectral diffusion at the surface of a water cluster cage. Proc Natl Acad Sci U S A 2020; 117:26047-26052. [PMID: 33024015 DOI: 10.1073/pnas.2017150117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We explore the kinetic processes that sustain equilibrium in a microscopic, finite system. This is accomplished by monitoring the spontaneous, time-dependent frequency evolution (the frequency autocorrelation) of a single OH oscillator, embedded in a water cluster held in a temperature-controlled ion trap. The measurements are carried out by applying two-color, infrared-infrared photodissociation mass spectrometry to the D3O+·(HDO)(D2O)19 isotopologue of the "magic number" protonated water cluster, H+·(H2O)21 The OH group can occupy any one of the five spectroscopically distinct sites in the distorted pentagonal dodecahedron cage structure. The OH frequency is observed to evolve over tens of milliseconds in the temperature range (90 to 120 K). Starting at 100 K, large "jumps" are observed between two OH frequencies separated by ∼300 cm-1, indicating migration of the OH group from the bound OH site at 3,350 cm-1 to the free position at 3,686 cm-1 Increasing the temperature to 110 K leads to partial interconversion among many sites. All sites are observed to interconvert at 120 K such that the distribution of the unique OH group among them adopts the form one would expect for a canonical ensemble. The spectral dynamics displayed by the clusters thus offer an unprecedented view into the molecular-level processes that drive spectral diffusion in an extended network of water molecules.
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32
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Hydrogen-bonded host-guest systems are stable in ionic liquids. Sci Rep 2020; 10:15414. [PMID: 32963260 PMCID: PMC7508985 DOI: 10.1038/s41598-020-71803-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/17/2020] [Indexed: 11/08/2022] Open
Abstract
We show that H-bonded host–guest systems associate in ionic liquids (ILs), pure salts with melting point below room temperature, in which dipole–dipole electrostatic interactions should be negligible in comparison with dipole-charge interactions. Binding constants (Ka) obtained from titrations of four H-bonded host–guest systems in two organic solvents and two ionic liquids yield smaller yet comparable Ka values in ionic liquids than in organic solvents. We also detect the association event using force spectroscopy, which confirms that the binding is not solely due to (de)solvation processes. Our results indicate that classic H-bonded host–guest supramolecular chemistry takes place in ILs. This implies that strong H-bonds are only moderately affected by surroundings composed entirely of charges, which can be interpreted as an indication that the balance of Coulombic to covalent forces in strong H-bonds is not tipped towards the former.
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33
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Jahr E, Laude G, Richardson JO. Instanton theory of tunneling in molecules with asymmetric isotopic substitutions. J Chem Phys 2020; 153:094101. [PMID: 32891112 DOI: 10.1063/5.0021831] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We consider quantum tunneling in asymmetric double-well systems for which the local minima in the two wells have the same energy, but the frequencies differ slightly. In a molecular context, this situation can arise if the symmetry is broken by isotopic substitutions. We derive a generalization of instanton theory for these asymmetric systems, leading to a semiclassical expression for the tunneling matrix element and hence the energy-level splitting. We benchmark the method using a set of one- and two-dimensional models, for which the results compare favorably with numerically exact quantum calculations. Using the ring-polymer instanton approach, we apply the method to compute the level splittings in various isotopomers of malonaldehyde in full dimensionality and analyze the relative contributions from the zero-point energy difference and tunneling effects.
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Affiliation(s)
- Elena Jahr
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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34
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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: 3.8] [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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35
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Riera M, Talbot JJ, Steele RP, Paesani F. Infrared signatures of isomer selectivity and symmetry breaking in the Cs+(H2O)3 complex using many-body potential energy functions. J Chem Phys 2020; 153:044306. [DOI: 10.1063/5.0013101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Justin J. Talbot
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Ryan P. Steele
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, 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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36
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Laude G, Calderini D, Welsch R, Richardson JO. Calculations of quantum tunnelling rates for muonium reactions with methane, ethane and propane. Phys Chem Chem Phys 2020; 22:16843-16854. [PMID: 32666960 DOI: 10.1039/d0cp01346c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermal rate constants for Mu + CH4, Mu + C2H6 and Mu + C3H8 and their equivalent reactions with H were evaluated with ab initio instanton rate theory. The potential-energy surfaces are fitted using Gaussian process regression to high-level electronic-structure calculations evaluated around the tunnelling pathway. This method was able to successfully reproduce various experimental measurements for the rate constant of these reactions. However, it was not able to reproduce the faster-than-expected rate of Mu + C3H8 at 300 K reported by Fleming et al. [Phys. Chem. Chem. Phys., 2015, 17, 19901 and Phys. Chem. Chem. Phys., 2020, 22, 6326]. Analysis of our results indicates that the kinetic isotope effect at this temperature is not significantly influenced by quantum tunnelling. We consider many possible factors for the discrepancy between theory and experiment but conclude that in each case, the instanton approximation is unlikely to be the cause of the error. This is in part based on the good agreement we find between the instanton predictions and new multiconfigurational time-dependent Hartree (MCTDH) calculations for Mu + CH4 using the same potential-energy surface. Further experiments will therefore be needed to resolve this issue.
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Affiliation(s)
- Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zürich, Switzerland.
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37
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He H, Liu Z, Chen S, He X, Wang X, Wang X. Active Role of Water in the Hydration of Macromolecules with Ionic End Group for Hydrophobic Effect-Caused Assembly. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00683] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Huiwen He
- College of Materials Science and Engineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, China
| | - Zhen Liu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Si Chen
- College of Materials Science and Engineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, China
| | - Xiaohua He
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xu Wang
- College of Materials Science and Engineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, China
| | - Xiaosong Wang
- Waterloo Institute for Nanotechnology and Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
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38
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Lan J, Rybkin VV, Iannuzzi M. Ionization of Water as an Effect of Quantum Delocalization at Aqueous Electrode Interfaces. J Phys Chem Lett 2020; 11:3724-3730. [PMID: 32315196 DOI: 10.1021/acs.jpclett.0c01025] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The enhanced probability of water dissociation at the aqueous electrode interfaces is predicted by path-integral ab initio molecular dynamics. The ionization process is observed at the aqueous platinum interface when nuclear quantum effects are introduced in the statistical sampling, while minor effects have been observed at the gold interface. We characterize the dissociation mechanism of the formed water ions. In spite of the fact that the concentration and lifetime of the ions might be challenging to experimentally detect, they may serve as a guide to future experiments. Our observation might have a significant impact on the understanding of electrochemical processes occurring at the metal electrode surface.
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Affiliation(s)
- Jinggang Lan
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
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39
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Riera M, Yeh EP, Paesani F. Data-Driven Many-Body Models for Molecular Fluids: CO2/H2O Mixtures as a Case Study. J Chem Theory Comput 2020; 16:2246-2257. [DOI: 10.1021/acs.jctc.9b01175] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eric P. Yeh
- 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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40
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Heller ER, Richardson JO. Instanton formulation of Fermi’s golden rule in the Marcus inverted regime. J Chem Phys 2020; 152:034106. [DOI: 10.1063/1.5137823] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Eric R. Heller
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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41
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Yuan R, Fayer MD. Dynamics of Water Molecules and Ions in Concentrated Lithium Chloride Solutions Probed with Ultrafast 2D IR Spectroscopy. J Phys Chem B 2019; 123:7628-7639. [DOI: 10.1021/acs.jpcb.9b06038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Rongfeng Yuan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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42
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Egan CK, Paesani F. Assessing Many-Body Effects of Water Self-Ions. II: H3O+(H2O)n Clusters. J Chem Theory Comput 2019; 15:4816-4833. [DOI: 10.1021/acs.jctc.9b00418] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Colin K. Egan
- 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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43
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Xu M, Zhu T, Zhang JZH. Molecular Dynamics Simulation of Zinc Ion in Water with an ab Initio Based Neural Network Potential. J Phys Chem A 2019; 123:6587-6595. [DOI: 10.1021/acs.jpca.9b04087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mingyuan Xu
- State Key Lab of Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Tong Zhu
- State Key Lab of Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - John Z. H. Zhang
- State Key Lab of Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York City, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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44
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Bajaj P, Zhuang D, Paesani F. Specific Ion Effects on Hydrogen-Bond Rearrangements in the Halide-Dihydrate Complexes. J Phys Chem Lett 2019; 10:2823-2828. [PMID: 31082245 DOI: 10.1021/acs.jpclett.9b00899] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Small aqueous ionic clusters represent ideal systems to investigate the microscopic hydrogen-bonding structure and dynamics in ion hydration shells. In this context, halide-dihydrate complexes are the smallest systems where the interplay between halide-water and water-water interactions can be studied simultaneously. Here, quantum molecular dynamics simulations unravel specific ion effects on the temperature-dependent structural transition in X-(H2O)2 complexes (X = Cl, Br, and I), which is induced by the breaking of the water-water hydrogen bond. A systematic analysis of the hydrogen-bonding rearrangements at low temperature provides fundamental insights into the competition between halide-water and water-water interactions depending on the properties of the halide ion. While the halide-water hydrogen-bond strength decreases going from Cl-(H2O)2 to I-(H2O)2, the opposite trend in observed in the strength of the water-water hydrogen-bond, suggesting that nontrivial many-body effects may also be at play in the hydration shells of halide ions in solution, especially in frustrated systems (e.g., interfaces) where the water molecules can have dangling OH bonds.
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Affiliation(s)
- Pushp Bajaj
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Debbie Zhuang
- 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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45
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Laage D, Stirnemann G. Effect of Ions on Water Dynamics in Dilute and Concentrated Aqueous Salt Solutions. J Phys Chem B 2019; 123:3312-3324. [DOI: 10.1021/acs.jpcb.9b01053] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Damien Laage
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
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46
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Winter P, Richardson JO. Divide-and-Conquer Method for Instanton Rate Theory. J Chem Theory Comput 2019; 15:2816-2825. [DOI: 10.1021/acs.jctc.8b01267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pierre Winter
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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