1
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Litman Y, Kapil V, Feldman YMY, Tisi D, Begušić T, Fidanyan K, Fraux G, Higer J, Kellner M, Li TE, Pós ES, Stocco E, Trenins G, Hirshberg B, Rossi M, Ceriotti M. i-PI 3.0: A flexible and efficient framework for advanced atomistic simulations. J Chem Phys 2024; 161:062504. [PMID: 39140447 DOI: 10.1063/5.0215869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/11/2024] [Indexed: 08/15/2024] Open
Abstract
Atomic-scale simulations have progressed tremendously over the past decade, largely thanks to the availability of machine-learning interatomic potentials. These potentials combine the accuracy of electronic structure calculations with the ability to reach extensive length and time scales. The i-PI package facilitates integrating the latest developments in this field with advanced modeling techniques thanks to a modular software architecture based on inter-process communication through a socket interface. The choice of Python for implementation facilitates rapid prototyping but can add computational overhead. In this new release, we carefully benchmarked and optimized i-PI for several common simulation scenarios, making such overhead negligible when i-PI is used to model systems up to tens of thousands of atoms using widely adopted machine learning interatomic potentials, such as Behler-Parinello, DeePMD, and MACE neural networks. We also present the implementation of several new features, including an efficient algorithm to model bosonic and fermionic exchange, a framework for uncertainty quantification to be used in conjunction with machine-learning potentials, a communication infrastructure that allows for deeper integration with electronic-driven simulations, and an approach to simulate coupled photon-nuclear dynamics in optical or plasmonic cavities.
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Affiliation(s)
- Yair Litman
- Y. Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Venkat Kapil
- Y. Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Physics and Astronomy, University College London, 17-19 Gordon St, London WC1H 0AH, United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology, 19 Gordon St, London WC1H 0AH, United Kingdom
| | | | - Davide Tisi
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Tomislav Begušić
- Div. of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Karen Fidanyan
- MPI for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Guillaume Fraux
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jacob Higer
- School of Physics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Matthias Kellner
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Tao E Li
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
| | - Eszter S Pós
- MPI for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Elia Stocco
- MPI for the Structure and Dynamics of Matter, Hamburg, Germany
| | - George Trenins
- MPI for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Barak Hirshberg
- School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Mariana Rossi
- MPI for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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2
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Bridge O, Lazzaroni P, Martinazzo R, Rossi M, Althorpe SC, Litman Y. Quantum rates in dissipative systems with spatially varying friction. J Chem Phys 2024; 161:024110. [PMID: 38984959 DOI: 10.1063/5.0216823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/20/2024] [Indexed: 07/11/2024] Open
Abstract
We investigate whether making the friction spatially dependent on the reaction coordinate introduces quantum effects into the thermal reaction rates for dissipative reactions. Quantum rates are calculated using the numerically exact multi-configuration time-dependent Hartree method, as well as the approximate ring-polymer molecular dynamics (RPMD), ring-polymer instanton methods, and classical molecular dynamics. By conducting simulations across a wide range of temperatures and friction strengths, we can identify the various regimes that govern the reactive dynamics. At high temperatures, in addition to the spatial-diffusion and energy-diffusion regimes predicted by Kramer's rate theory, a (coherent) tunneling-dominated regime is identified at low friction. At low temperatures, incoherent tunneling dominates most of Kramer's curve, except at very low friction, when coherent tunneling becomes dominant. Unlike in classical mechanics, the bath's influence changes the equilibrium time-independent properties of the system, leading to a complex interplay between spatially dependent friction and nuclear quantum effects even at high temperatures. More specifically, a realistic friction profile can lead to an increase (or decrease) of the quantum (classical) rates with friction within the spatial-diffusion regime, showing that classical and quantum rates display qualitatively different behaviors. Except at very low frictions, we find that RPMD captures most of the quantum effects in the thermal reaction rates.
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Affiliation(s)
- Oliver Bridge
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Paolo Lazzaroni
- MPI for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Rocco Martinazzo
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Mariana Rossi
- MPI for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Stuart C Althorpe
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Yair Litman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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3
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Pollak E. A personal perspective of the present status and future challenges facing thermal reaction rate theory. J Chem Phys 2024; 160:150902. [PMID: 38639316 DOI: 10.1063/5.0199557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/06/2024] [Indexed: 04/20/2024] Open
Abstract
Reaction rate theory has been at the center of physical chemistry for well over one hundred years. The evolution of the theory is not only of historical interest. Reliable and accurate computation of reaction rates remains a challenge to this very day, especially in view of the development of quantum chemistry methods, which predict the relevant force fields. It is still not possible to compute the numerically exact rate on the fly when the system has more than at most a few dozen anharmonic degrees of freedom, so one must consider various approximate methods, not only from the practical point of view of constructing numerical algorithms but also on conceptual and formal levels. In this Perspective, I present some of the recent analytical results concerning leading order terms in an ℏ2m series expansion of the exact rate and their implications on various approximate theories. A second aspect has to do with the crossover temperature between tunneling and thermal activation. Using a uniform semiclassical transmission probability rather than the "primitive" semiclassical theory leads to the conclusion that there is no divergence problem associated with a "crossover temperature." If one defines a semiclassical crossover temperature as the point at which the tunneling energy of the instanton equals the barrier height, then it is a factor of two higher than its previous estimate based on the "primitive" semiclassical approximation. In the low temperature tunneling regime, the uniform semiclassical theory as well as the "primitive" semiclassical theory were based on the classical Euclidean action of a periodic orbit on the inverted potential. The uniform semiclassical theory wrongly predicts that the "half-point," which is the energy at which the transmission probability equals 1/2, for any barrier potential, is always the barrier energy. We describe here how augmenting the Euclidean action with constant terms of order ℏ2 can significantly improve the accuracy of the semiclassical theory and correct this deficiency. This also leads to a deep connection with and improvement of vibrational perturbation theory. The uniform semiclassical theory also enables an extension of the quantum version of Kramers' turnover theory to temperatures below the "crossover temperature." The implications of these recent advances on various approximate methods used to date are discussed at length, leading to the conclusion that reaction rate theory will continue to challenge us both on conceptual and practical levels for years to come.
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Affiliation(s)
- Eli Pollak
- Chemical and Biological Physics Department, Weizmann Institute of Science, 76100 Rehovoth, Israel
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4
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Upadhyayula S, Pollak E. Uniform Semiclassical Instanton Rate Theory. J Phys Chem Lett 2023; 14:9892-9899. [PMID: 37906954 PMCID: PMC10641875 DOI: 10.1021/acs.jpclett.3c02779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023]
Abstract
The instanton expression for the thermal transmission probability through a one-dimensional barrier is derived by using the uniform semiclassical energy-dependent transmission coefficient of Kemble. The resulting theory does not diverge at the "crossover temperature" but changes smoothly. The temperature-dependent energy of the instanton is the same as the barrier height when ℏβω‡ = π and not 2π as in the "standard" instanton theory. The concept of a crossover temperature between tunneling and thermal activation, based on the divergence of the instanton rate, is obsolete. The theory is improved by assuring that at high energy when the energy-dependent transmission coefficient approaches unity the integrand decays exponentially as dictated by the Boltzmann factor and not as a Gaussian. This ensures that at sufficiently high temperatures the uniform theory reduces to the classical. Application to Eckart barriers demonstrates that the uniform theory provides a good estimate of the numerically exact result over the whole temperature range.
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Affiliation(s)
- Sameernandan Upadhyayula
- Chemical and Biological Physics
Department Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Eli Pollak
- Chemical and Biological Physics
Department Weizmann Institute of Science, Rehovoth 76100, Israel
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5
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Fang W, Heller ER, Richardson JO. Competing quantum effects in heavy-atom tunnelling through conical intersections. Chem Sci 2023; 14:10777-10785. [PMID: 37829019 PMCID: PMC10566476 DOI: 10.1039/d3sc03706a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/07/2023] [Indexed: 10/14/2023] Open
Abstract
Thermally activated chemical reactions are typically understood in terms of overcoming potential-energy barriers. However, standard rate theories break down in the presence of a conical intersection (CI) because these processes are inherently nonadiabatic, invalidating the Born-Oppenheimer approximation. Moreover, CIs give rise to intricate nuclear quantum effects such as tunnelling and the geometric phase, which are neglected by standard trajectory-based simulations and remain largely unexplored in complex molecular systems. We present new semiclassical transition-state theories based on an extension of golden-rule instanton theory to describe nonadiabatic tunnelling through CIs and thus provide an intuitive picture for the reaction mechanism. We apply the method in conjunction with first-principles electronic-structure calculations to the electron transfer in the bis(methylene)-adamantyl cation. Our study reveals a strong competition between heavy-atom tunnelling and geometric-phase effects.
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Affiliation(s)
- Wei Fang
- Department of Chemistry, Fudan University Shanghai 200438 P. R. China
- Department of Chemistry and Applied Biosciences, ETH Zürich 8093 Zürich Switzerland
| | - Eric R Heller
- Department of Chemistry and Applied Biosciences, ETH Zürich 8093 Zürich Switzerland
| | - Jeremy O Richardson
- Department of Chemistry and Applied Biosciences, ETH Zürich 8093 Zürich Switzerland
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6
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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: 3.5] [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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7
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Lawrence JE, Richardson JO. Improved microcanonical instanton theory. Faraday Discuss 2022; 238:204-235. [PMID: 35929848 DOI: 10.1039/d2fd00063f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Canonical (thermal) instanton theory is now routinely applicable to complex gas-phase reactions and allows for the accurate description of tunnelling in highly non-separable systems. Microcanonical instanton theory is by contrast far less well established. Here, we demonstrate that the best established microcanonical theory [S. Chapman, B. C. Garrett and W. H. Miller, J. Chem. Phys., 1975, 63, 2710-2716], fails to accurately describe the deep-tunnelling regime for systems where the frequencies of the orthogonal modes change rapidly along the instanton path. By taking a first principles approach to the derivation of microcanonical instanton theory, we obtain an improved method, which accurately recovers the thermal instanton rate when integrated over energy. The resulting theory also correctly recovers the separable limit and can be thought of as an instanton generalisation of Rice-Ramsperger-Kassel-Marcus (RRKM) theory. When combined with the density-of-states approach [W. Fang, P. Winter and J. O. Richardson, J. Chem. Theory Comput., 2021, 17, 40-55], this new method can be straightforwardly applied to real molecular systems.
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8
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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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9
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Litman Y, Pós ES, Box CL, Martinazzo R, Maurer RJ, Rossi M. Dissipative tunneling rates through the incorporation of first-principles electronic friction in instanton rate theory. II. Benchmarks and applications. J Chem Phys 2022; 156:194107. [PMID: 35597654 DOI: 10.1063/5.0088400] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], we presented the ring-polymer instanton with explicit friction (RPI-EF) method and showed how it can be connected to the ab initio electronic friction formalism. This framework allows for the calculation of tunneling reaction rates that incorporate the quantum nature of the nuclei and certain types of non-adiabatic effects (NAEs) present in metals. In this paper, we analyze the performance of RPI-EF on model potentials and apply it to realistic systems. For a 1D double-well model, we benchmark the method against numerically exact results obtained from multi-layer multi-configuration time-dependent Hartree calculations. We demonstrate that RPI-EF is accurate for medium and high friction strengths and less accurate for extremely low friction values. We also show quantitatively how the inclusion of NAEs lowers the crossover temperature into the deep tunneling regime, reduces the tunneling rates, and, in certain regimes, steers the quantum dynamics by modifying the tunneling pathways. As a showcase of the efficiency of this method, we present a study of hydrogen and deuterium hopping between neighboring interstitial sites in selected bulk metals. The results show that multidimensional vibrational coupling and nuclear quantum effects have a larger impact than NAEs on the tunneling rates of diffusion in metals. Together with Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], these results advance the calculations of dissipative tunneling rates from first principles.
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Affiliation(s)
- Y Litman
- MPI for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - E S Pós
- MPI for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - C L Box
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - R Martinazzo
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - R J Maurer
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - M Rossi
- MPI for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
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10
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Han E, Fang W, Stamatakis M, Richardson JO, Chen J. Quantum Tunnelling Driven H 2 Formation on Graphene. J Phys Chem Lett 2022; 13:3173-3181. [PMID: 35362977 DOI: 10.1021/acs.jpclett.2c00520] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
It is commonly believed that it is unfavorable for adsorbed H atoms on carbonaceous surfaces to form H2 without the help of incident H atoms. Using ring-polymer instanton theory to describe multidimensional tunnelling effects, combined with ab initio electronic structure calculations, we find that these quantum-mechanical simulations reveal a qualitatively different picture. Recombination of adsorbed H atoms, which was believed to be irrelevant at low temperature due to high barriers, is enabled by deep tunnelling, with reaction rates enhanced by tens of orders of magnitude. Furthermore, we identify a new path for H recombination that proceeds via multidimensional tunnelling but would have been predicted to be unfeasible by a simple one-dimensional description of the reaction. The results suggest that hydrogen molecule formation at low temperatures are rather fast processes that should not be ignored in experimental settings and natural environments with graphene, graphite, and other planar carbon segments.
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Affiliation(s)
- Erxun Han
- School of Physics, Peking University, Beijing 100871, China
- Interdisciplinary Institute of Light-Element Quantum Materials and Research Center for Light-Element Advanced Materials, Peking University, Beijing 100871, People's Republic of China
| | - Wei Fang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- Department of Chemistry, Fudan University, Shanghai 200438, China
- Laboratory of Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Michail Stamatakis
- Thomas Young Centre and Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom
| | | | - Ji Chen
- School of Physics, Peking University, Beijing 100871, China
- Interdisciplinary Institute of Light-Element Quantum Materials and Research Center for Light-Element Advanced Materials, Peking University, Beijing 100871, People's Republic of China
- Frontiers Science Center for Nano-Optoelectronics, Peking University, Beijing 100871, People's Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100871, People's Republic of China
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11
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Trenins G, Richardson JO. Nonadiabatic instanton rate theory beyond the golden-rule limit. J Chem Phys 2022; 156:174115. [DOI: 10.1063/5.0088518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fermi's golden rule describes the leading-order behaviour of the reaction rate as a function of the diabatic coupling. Its asymptotic (ℏ →0) limit is the semiclassical golden-rule instanton rate theory, which rigorously approximates nuclear quantum effects, lends itself to efficient numerical computation and gives physical insight into reaction mechanisms. However the golden rule by itself becomes insufficient as the strength of the diabatic coupling increases, so higher-order terms must be additionally considered. In this work we give a first-principles derivation of the next-order term beyond the golden rule, represented as a sum of three components. Two of them lead to new instanton pathways that extend the golden-rule case and, among other factors, account for the effects of recrossing on the full rate. The remaining component derives from the equilibrium partition function and accounts for changes in potential energy around the reactant and product wells due to diabatic coupling. The new semiclassical theory demands little computational effort beyond a golden-rule instanton calculation. It makes it possible to rigorously assess the accuracy of the golden-rule approximation and sets the stage for future work on general semiclassical nonadiabatic rate theories.
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Affiliation(s)
- George Trenins
- ETH Zurich Department of Chemistry and Applied Biosciences, Switzerland
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12
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Nagahata Y, Hernandez R, Komatsuzaki T. Phase space geometry of isolated to condensed chemical reactions. J Chem Phys 2021; 155:210901. [PMID: 34879678 DOI: 10.1063/5.0059618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The complexity of gas and condensed phase chemical reactions has generally been uncovered either approximately through transition state theories or exactly through (analytic or computational) integration of trajectories. These approaches can be improved by recognizing that the dynamics and associated geometric structures exist in phase space, ensuring that the propagator is symplectic as in velocity-Verlet integrators and by extending the space of dividing surfaces to optimize the rate variationally, respectively. The dividing surface can be analytically or variationally optimized in phase space, not just over configuration space, to obtain more accurate rates. Thus, a phase space perspective is of primary importance in creating a deeper understanding of the geometric structure of chemical reactions. A key contribution from dynamical systems theory is the generalization of the transition state (TS) in terms of the normally hyperbolic invariant manifold (NHIM) whose geometric phase-space structure persists under perturbation. The NHIM can be regarded as an anchor of a dividing surface in phase space and it gives rise to an exact non-recrossing TS theory rate in reactions that are dominated by a single bottleneck. Here, we review recent advances of phase space geometrical structures of particular relevance to chemical reactions in the condensed phase. We also provide conjectures on the promise of these techniques toward the design and control of chemical reactions.
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Affiliation(s)
- Yutaka Nagahata
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Tamiki Komatsuzaki
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0 020, Japan
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13
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Georgievskii Y, Klippenstein SJ. Entanglement Effect and Angular Momentum Conservation in a Nonseparable Tunneling Treatment. J Chem Theory Comput 2021; 17:3863-3885. [PMID: 34196562 DOI: 10.1021/acs.jctc.1c00386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The important, and often dominant, role of tunneling in low temperature kinetics has resulted in numerous theoretical explorations into the methodology for predicting it. Nevertheless, there are still key aspects of the derivations that are lacking, particularly for nonseparable systems in the low temperature regime, and further explorations of the physical factors affecting the tunneling rate are warranted. In this work we obtain a closed-form rate expression for the tunneling rate constant that is a direct analog of the rigid-rotor-harmonic-oscillator expression. This expression introduces a novel "entanglement factor" that modulates the reaction rate. Furthermore, we are able to extend this expression, which is valid for nonseparable systems at low temperatures, to properly account for the conservation of angular momentum. In contrast, previous calculations have considered only vibrational transverse modes and so effectively employ a decoupled rotational partition function for the orientational modes. We also suggest a simple theoretical model to describe the tunneling effects in the vicinity of the crossover temperature (the temperature where tunneling becomes the dominating mechanism). This model allows one to naturally classify, interpret, and predict experimental data. Among other things, it quantitatively explains in simple terms the so-called "quantum bobsled" effect, also known as the negative centrifugal effect, which is related to curvature of the reaction path. Taken together, the expressions obtained here allow one to predict the thermal and E-resolved rate constants over broad ranges of temperatures and energies.
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Affiliation(s)
- Yuri Georgievskii
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Stephen J Klippenstein
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
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14
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Brian D, Sun X. Linear-Response and Nonlinear-Response Formulations of the Instantaneous Marcus Theory for Nonequilibrium Photoinduced Charge Transfer. J Chem Theory Comput 2021; 17:2065-2079. [PMID: 33687212 DOI: 10.1021/acs.jctc.0c01250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Instantaneous Marcus theory (IMT) offers a way for capturing the time-dependent charge transfer (CT) rate coefficient in nonequilibrium photoinduced CT processes, where the system was photoexcited from its equilibrated ground state vertically to the excitonic state, followed by an electronic transition to the CT state. As derived from the linearized semiclassical nonequilibrium Fermi's golden rule (LSC NE-FGR), the original IMT requires expensive all-atom nonequilibrium molecular dynamics (NEMD) simulations. In this work, we propose computationally efficient linear-response and nonlinear-response formulations for IMT rate calculations, which only require equilibrium molecular dynamics simulations. The linear- and nonlinear-response IMT methods were tested to predict the transient behavior in the photoinduced CT dynamics of the carotenoid-porphyrin-C60 molecular triad solvated in explicit tetrahydrofuran. Our result demonstrated that the nonlinear-response IMT is in excellent agreement with the benchmark NEMD for all cases investigated here, whereas the linear-response IMT predicts the correct trend for all cases but overestimates the transient CT rate in one case involving a significant nonequilibrium relaxation. This mild breakdown of linear-response IMT is due to neglecting the higher-order terms in the exact nonlinear-response IMT. Taking advantage of time translational symmetry, the linear- and nonlinear-response approaches were demonstrated to be able to reduce the computational cost by 80% and 60% compared with NEMD simulations, respectively. Thus, we highly recommend the readily applicable and accurate nonlinear-response IMT approach for simulating nonequilibrium CT processes in complex molecular systems in the condensed phase.
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Affiliation(s)
- Dominikus Brian
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
| | - Xiang Sun
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
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15
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Sahu N, Richardson JO, Berger R. Instanton calculations of tunneling splittings in chiral molecules. J Comput Chem 2021; 42:210-221. [PMID: 33259074 DOI: 10.1002/jcc.26447] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 11/11/2022]
Abstract
We report the ground state tunneling splittings (ΔE± ) of a number of axially chiral molecules using the ring-polymer instanton (RPI) method (J. Chem. Phys., 2011, 134, 054109). The list includes isotopomers of hydrogen dichalcogenides H2 X2 (X = O, S, Se, Te, and Po), hydrogen thioperoxide HSOH and dichlorodisulfane S2 Cl2 . Ab initio electronic-structure calculations have been performed on the level of second-order Møller-Plesset perturbation (MP2) theory either with split-valance basis sets or augmented correlation-consistent basis sets on H, O, S, and Cl atoms. Energy-consistent pseudopotential and corresponding triple zeta basis sets of the Stuttgart group are used on Se, Te, and Po atoms. The results are further improved using single point calculations performed at the coupled cluster level with iterative singles and doubles and perturbative triples amplitudes. When available for comparison, our computed values of ΔE± are found to lie within the same order of magnitude as values reported in the literature, although RPI also provides predictions for H2 Po2 and S2 Cl2 , which have not previously been directly calculated. Since RPI is a single-shot method which does not require detailed prior knowledge of the optimal tunneling path, it offers an effective way for estimating the tunneling dynamics of more complex chiral molecules, and especially those with small tunneling splittings.
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Affiliation(s)
- Nityananda Sahu
- Fachbereich Chemie, Theoretische Chemie, Philipps Universität Marburg, Marburg, Germany
| | | | - Robert Berger
- Fachbereich Chemie, Theoretische Chemie, Philipps Universität Marburg, Marburg, Germany
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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: 1.3] [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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Litman Y, Rossi M. Multidimensional Hydrogen Tunneling in Supported Molecular Switches: The Role of Surface Interactions. PHYSICAL REVIEW LETTERS 2020; 125:216001. [PMID: 33275002 DOI: 10.1103/physrevlett.125.216001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/08/2020] [Indexed: 06/12/2023]
Abstract
The nuclear tunneling crossover temperature (T_{c}) of hydrogen transfer reactions in supported molecular-switch architectures can lie close to room temperature. This calls for the inclusion of nuclear quantum effects (NQEs) in the calculation of reaction rates even at high temperatures. However, computations of NQEs relying on standard parametrized dimensionality-reduced models quickly become inadequate in these environments. In this Letter, we study the paradigmatic molecular switch based on porphycene molecules adsorbed on metallic surfaces with full-dimensional calculations that combine density-functional theory for the electrons with the semiclassical ring-polymer instanton approximation for the nuclei. We show that the double intramolecular hydrogen transfer (DHT) rate can be enhanced by orders of magnitude due to surface fluctuations in the deep-tunneling regime. We also explain the origin of an Arrhenius temperature dependence of the rate below T_{c} and why this dependence differs at different surfaces. We propose a simple model to rationalize the temperature dependence of DHT rates spanning diverse fcc [110] surfaces.
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Affiliation(s)
- Yair Litman
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany and Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Mariana Rossi
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany and MPI for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
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18
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Hu Z, Tong Z, Cheung MS, Dunietz BD, Geva E, Sun X. Photoinduced Charge Transfer Dynamics in the Carotenoid–Porphyrin–C60 Triad via the Linearized Semiclassical Nonequilibrium Fermi’s Golden Rule. J Phys Chem B 2020; 124:9579-9591. [DOI: 10.1021/acs.jpcb.0c06306] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Zhubin Hu
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
| | - Zhengqing Tong
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
| | - Margaret S. Cheung
- Department of Physics, University of Houston, Houston, Texas 77204, United States
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, United States
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xiang Sun
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
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19
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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: 1.8] [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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20
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Affiliation(s)
- Sason Shaik
- Institute of Chemistry The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram Jerusalem 9090401 Israel
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21
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Munar I, Fındık V, Degirmenci I, Aviyente V. Solvent Effects on Thiol–Ene Kinetics and Reactivity of Carbon and Sulfur Radicals. J Phys Chem A 2020; 124:2580-2590. [DOI: 10.1021/acs.jpca.9b10165] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ipek Munar
- Department of Chemistry, Faculty of Arts and Sciences, Bogazici University, Bebek, 34342, Istanbul, Turkey
| | - Volkan Fındık
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722 Istanbul, Turkey
| | - Isa Degirmenci
- Chemical Engineering Department, Ondokuz Mayıs University, 55139 Samsun, Turkey
| | - Viktorya Aviyente
- Department of Chemistry, Faculty of Arts and Sciences, Bogazici University, Bebek, 34342, Istanbul, Turkey
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22
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Sanches-Neto FO, Coutinho ND, Palazzetti F, Carvalho-Silva VH. Temperature dependence of rate constants for the H(D) + CH4 reaction in gas and aqueous phase: deformed Transition-State Theory study including quantum tunneling and diffusion effects. Struct Chem 2019. [DOI: 10.1007/s11224-019-01437-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Xie W, Sapunar M, Došlić N, Sala M, Domcke W. Assessing the performance of trajectory surface hopping methods: Ultrafast internal conversion in pyrazine. J Chem Phys 2019; 150:154119. [DOI: 10.1063/1.5084961] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Weiwei Xie
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Marin Sapunar
- Department of Physical Chemistry, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia
| | - Matthieu Sala
- Laboratoire Interdisciplinaire Carnot de Bourgogne UMR 6303 CNRS, Université de Bourgogne, BP 47870, F-21078 Dijon, France and Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
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24
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Shan X, Burd TAH, Clary DC. New Developments in Semiclassical Transition-State Theory. J Phys Chem A 2019; 123:4639-4657. [DOI: 10.1021/acs.jpca.9b01987] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiao Shan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Timothy A. H. Burd
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David C. Clary
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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25
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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: 1.4] [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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26
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Thapa MJ, Fang W, Richardson JO. Nonadiabatic quantum transition-state theory in the golden-rule limit. I. Theory and application to model systems. J Chem Phys 2019; 150:104107. [DOI: 10.1063/1.5081108] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Manish J. Thapa
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Wei Fang
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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27
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Aieta C, Gabas F, Ceotto M. Parallel Implementation of Semiclassical Transition State Theory. J Chem Theory Comput 2019; 15:2142-2153. [PMID: 30822385 DOI: 10.1021/acs.jctc.8b01286] [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
This paper presents the parsctst code, an efficient parallel implementation of the semiclassical transition state theory (SCTST) for reaction rate constant calculations. Parsctst is developed starting from a previously presented approach for the computation of the vibrational density of states of fully coupled anharmonic molecules ( Nguyen et al. Chem. Phys. Lett. 2010 , 499 , 915 ). The parallel implementation makes it practical to tackle reactions involving more than 100 fully coupled anharmonic vibrational degrees of freedom and also includes multidimensional tunneling effects. After describing the pseudocode and demonstrating its computational efficiency, we apply the new code for estimating the rate constant of the proton transfer isomerization reaction of the 2,4,6-tri- tert-butylphenyl to 3,5-di- tert-butylneophyl. Comparison with both theoretical and experimental results is presented. Parsctst code is user-friendly and provides a significant computational time saving compared to serial calculations. We believe that parsctst can boost the application of SCTST as an alternative to the basic transition state theory for accurate kinetics modeling not only in combustion or atmospheric chemistry, but also in organic synthesis, where bigger reactive systems are encountered.
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Affiliation(s)
- Chiara Aieta
- Dipartimento di Chimica , Università degli Studi di Milano , via C. Golgi 19 , 20133 Milano , Italy
| | - Fabio Gabas
- Dipartimento di Chimica , Università degli Studi di Milano , via C. Golgi 19 , 20133 Milano , Italy
| | - Michele Ceotto
- Dipartimento di Chimica , Università degli Studi di Milano , via C. Golgi 19 , 20133 Milano , Italy
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28
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Meisner J, Hallmen PP, Kästner J, Rauhut G. Vibrational analysis of methyl cation—Rare gas atom complexes: CH3+—Rg (Rg = He, Ne, Ar, Kr). J Chem Phys 2019; 150:084306. [DOI: 10.1063/1.5084100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jan Meisner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Philipp P. Hallmen
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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29
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Watson NAI, Black JA, Stonelake TM, Knowles PJ, Beames JM. An Extended Computational Study of Criegee Intermediate-Alcohol Reactions. J Phys Chem A 2018; 123:218-229. [PMID: 30507197 DOI: 10.1021/acs.jpca.8b09349] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
High-level ab initio calculations (DF-LCCSD(T)-F12a//B3LYP/aug-cc-pVTZ) are performed on a range of stabilized Criegee intermediate (sCI)-alcohol reactions, computing reaction coordinate energies, leading to the formation of α-alkoxyalkyl hydroperoxides (AAAHs). These potential energy surfaces are used to model bimolecular reaction kinetics over a range of temperatures. The calculations performed in this work reproduce the complicated temperature-dependent reaction rates of CH2OO and (CH3)2COO with methanol, which have previously been experimentally determined. This methodology is then extended to compute reaction rates of 22 different Criegee intermediates with methanol, including several intermediates derived from isoprene ozonolysis. In some cases, sCI-alcohol reaction rates approach those of sCI-(H2O)2. This suggests that in regions with elevated alcohol concentrations, such as urban Brazil, these reactions may generate significant quantities of AAAHs and may begin to compete with sCI reactions with other trace tropospheric pollutants such as SO2. This work also demonstrates the ability of alcohols to catalyze the 1,4-H transfer unimolecular decomposition of α-methyl substituted sCIs.
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Affiliation(s)
- Nathan A I Watson
- School of Chemistry , Cardiff University , Main Building, Park Pl , Cardiff CF10 3AT , United Kingdom
| | - Joshua A Black
- School of Chemistry , Cardiff University , Main Building, Park Pl , Cardiff CF10 3AT , United Kingdom
| | - Thomas M Stonelake
- School of Chemistry , Cardiff University , Main Building, Park Pl , Cardiff CF10 3AT , United Kingdom
| | - Peter J Knowles
- School of Chemistry , Cardiff University , Main Building, Park Pl , Cardiff CF10 3AT , United Kingdom
| | - Joseph M Beames
- School of Chemistry , Cardiff University , Main Building, Park Pl , Cardiff CF10 3AT , United Kingdom
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30
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Meuwly M. Reactive molecular dynamics: From small molecules to proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1386] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Markus Meuwly
- Department of Chemistry University of Basel Basel Switzerland
- Department of Chemistry Brown University Providence Rhode Island
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31
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32
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33
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Ásgeirsson V, Arnaldsson A, Jónsson H. Efficient evaluation of atom tunneling combined with electronic structure calculations. J Chem Phys 2018; 148:102334. [DOI: 10.1063/1.5007180] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vilhjálmur Ásgeirsson
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107 Reykjavík, Iceland
| | - Andri Arnaldsson
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107 Reykjavík, Iceland
- Vatnaskil, Sídumúli 28, 108 Reykjavík, Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107 Reykjavík, Iceland
- Center for Nonlinear Studies, Los Alamos, New Mexico 87545, USA
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34
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Mattiat J, Richardson JO. Effects of tunnelling and asymmetry for system-bath models of electron transfer. J Chem Phys 2018; 148:102311. [PMID: 29544261 DOI: 10.1063/1.5001116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We apply the newly derived nonadiabatic golden-rule instanton theory to asymmetric models describing electron-transfer in solution. The models go beyond the usual spin-boson description and have anharmonic free-energy surfaces with different values for the reactant and product reorganization energies. The instanton method gives an excellent description of the behaviour of the rate constant with respect to asymmetry for the whole range studied. We derive a general formula for an asymmetric version of the Marcus theory based on the classical limit of the instanton and find that this gives significant corrections to the standard Marcus theory. A scheme is given to compute this rate based only on equilibrium simulations. We also compare the rate constants obtained by the instanton method with its classical limit to study the effect of tunnelling and other quantum nuclear effects. These quantum effects can increase the rate constant by orders of magnitude.
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Affiliation(s)
- Johann Mattiat
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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35
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Affiliation(s)
- Jan Meisner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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36
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Clary DC. Spiers Memorial Lecture : Introductory lecture: quantum dynamics of chemical reactions. Faraday Discuss 2018; 212:9-32. [DOI: 10.1039/c8fd00131f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This Spiers Memorial Lecture discusses quantum effects that can be calculated and observed in the chemical reactions of small molecules.
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Affiliation(s)
- David C. Clary
- Physical and Theoretical Chemistry Laboratory
- Department of Chemistry
- University of Oxford
- Oxford
- UK
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37
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Laude G, Calderini D, Tew DP, Richardson JO. Ab initio instanton rate theory made efficient using Gaussian process regression. Faraday Discuss 2018; 212:237-258. [PMID: 30230495 DOI: 10.1039/c8fd00085a] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ab initio instanton rate theory is a computational method for rigorously including tunnelling effects into the calculations of chemical reaction rates based on a potential-energy surface computed on the fly from electronic-structure theory. This approach is necessary to extend conventional transition-state theory into the deep-tunnelling regime, but it is also more computationally expensive as it requires many more ab initio calculations. We propose an approach which uses Gaussian process regression to fit the potential-energy surface locally around the dominant tunnelling pathway. The method can be converged to give the same result as from an on-the-fly ab initio instanton calculation but it requires far fewer electronic-structure calculations. This makes it a practical approach for obtaining accurate rate constants based on high-level electronic-structure methods. We show fast convergence to reproduce benchmark H + CH4 results and evaluate new low-temperature rates of H + C2H6 in full dimensionality at a UCCSD(T)-F12b/cc-pVTZ-F12 level.
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Affiliation(s)
- Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland. and On exchange from School of Chemistry, University of Edinburgh, UK
| | | | - David P Tew
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, 70569 Stuttgart, Germany
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38
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Karandashev K, Xu ZH, Meuwly M, Vaníček J, Richardson JO. Kinetic isotope effects and how to describe them. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061501. [PMID: 29282447 PMCID: PMC5729036 DOI: 10.1063/1.4996339] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 08/23/2017] [Indexed: 06/01/2023]
Abstract
We review several methods for computing kinetic isotope effects in chemical reactions including semiclassical and quantum instanton theory. These methods describe both the quantization of vibrational modes as well as tunneling and are applied to the ⋅H + H2 and ⋅H + CH4 reactions. The absolute rate constants computed with the semiclassical instanton method both using on-the-fly electronic structure calculations and fitted potential-energy surfaces are also compared directly with exact quantum dynamics results. The error inherent in the instanton approximation is found to be relatively small and similar in magnitude to that introduced by using fitted surfaces. The kinetic isotope effect computed by the quantum instanton is even more accurate, and although it is computationally more expensive, the efficiency can be improved by path-integral acceleration techniques. We also test a simple approach for designing potential-energy surfaces for the example of proton transfer in malonaldehyde. The tunneling splittings are computed, and although they are found to deviate from experimental results, the ratio of the splitting to that of an isotopically substituted form is in much better agreement. We discuss the strengths and limitations of the potential-energy surface and based on our findings suggest ways in which it can be improved.
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Affiliation(s)
- Konstantin Karandashev
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Zhen-Hao Xu
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jeremy O Richardson
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich (ETHZ), CH-8093 Zürich, Switzerland
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39
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Fang W, Richardson JO, Chen J, Li XZ, Michaelides A. Simultaneous Deep Tunneling and Classical Hopping for Hydrogen Diffusion on Metals. PHYSICAL REVIEW LETTERS 2017; 119:126001. [PMID: 29341641 DOI: 10.1103/physrevlett.119.126001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Indexed: 06/07/2023]
Abstract
Hydrogen diffusion on metals exhibits rich quantum behavior, which is not yet fully understood. Using simulations, we show that many hydrogen diffusion barriers can be categorized into those with parabolic tops and those with broad tops. With parabolic-top barriers, hydrogen diffusion evolves gradually from classical hopping, to shallow tunneling, to deep tunneling as the temperature (T) decreases, and noticeable quantum effects persist at moderate T. In contrast, with broad-top barriers quantum effects become important only at low T and the classical-to-quantum transition is sharp, at which classical hopping and deep tunneling both occur. This coexistence indicates that more than one mechanism contributes to the quantum reaction rate. The conventional definition of the classical-to-quantum crossover T is invalid for the broad tops, and we give a new definition. Extending this, we propose a model to predict the transition T for broad-top diffusion, providing a general guide for theory and experiment.
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Affiliation(s)
- Wei Fang
- Thomas Young Centre, London Centre for Nanotechnology and Department of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | | | - Ji Chen
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Xin-Zheng Li
- School of Physics and the Collaborative Innovation Center of Quantum Matters, Peking University, Beijing 100871, People's Republic of China
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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40
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Wang W, Zhao Y. The dissociation and recombination rates of CH 4 through the Ni(111) surface: The effect of lattice motion. J Chem Phys 2017; 147:044703. [PMID: 28764359 DOI: 10.1063/1.4995299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Methane dissociation is a prototypical system for the study of surface reaction dynamics. The dissociation and recombination rates of CH4 through the Ni(111) surface are calculated by using the quantum instanton method with an analytical potential energy surface. The Ni(111) lattice is treated rigidly, classically, and quantum mechanically so as to reveal the effect of lattice motion. The results demonstrate that it is the lateral displacements rather than the upward and downward movements of the surface nickel atoms that affect the rates a lot. Compared with the rigid lattice, the classical relaxation of the lattice can increase the rates by lowering the free energy barriers. For instance, at 300 K, the dissociation and recombination rates with the classical lattice exceed the ones with the rigid lattice by 6 and 10 orders of magnitude, respectively. Compared with the classical lattice, the quantum delocalization rather than the zero-point energy of the Ni atoms further enhances the rates by widening the reaction path. For instance, the dissociation rate with the quantum lattice is about 10 times larger than that with the classical lattice at 300 K. On the rigid lattice, due to the zero-point energy difference between CH4 and CD4, the kinetic isotope effects are larger than 1 for the dissociation process, while they are smaller than 1 for the recombination process. The increasing kinetic isotope effect with decreasing temperature demonstrates that the quantum tunneling effect is remarkable for the dissociation process.
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Affiliation(s)
- Wenji Wang
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100 Shaanxi Province, People's Republic of China
| | - Yi Zhao
- State Key Laboratory for Physical Chemistry of Solid Surfaces and Fujian Provincial Key Lab of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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Hochlaf M. Advances in spectroscopy and dynamics of small and medium sized molecules and clusters. Phys Chem Chem Phys 2017; 19:21236-21261. [DOI: 10.1039/c7cp01980g] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Investigations of the spectroscopy and dynamics of small- and medium-sized molecules and clusters represent a hot topic in atmospheric chemistry, biology, physics, atto- and femto-chemistry and astrophysics.
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Affiliation(s)
- Majdi Hochlaf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
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42
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Sun J, Shao Y, Wu W, Tang Y, Zhang Y, Hu Y, Liu J, Yi H, Chen F, Cheng Y. A quantum chemical study on ˙Cl-initiated atmospheric degradation of acrylonitrile. RSC Adv 2017. [DOI: 10.1039/c7ra01521f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Degradation of acrylonitrile (CH2CHCN) by reaction with atomic chlorine was studied using quantum chemical methods.
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Richardson JO. Full- and reduced-dimensionality instanton calculations of the tunnelling splitting in the formic acid dimer. Phys Chem Chem Phys 2017; 19:966-970. [DOI: 10.1039/c6cp07808g] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nearly all degrees of freedom need to be included for accurate theoretical predictions of quantum dynamics.
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