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Brown SE, Shakib FA. Recent progress in approximate quantum dynamics methods for the study of proton-coupled electron transfer reactions. Phys Chem Chem Phys 2021; 23:2535-2556. [PMID: 33367437 DOI: 10.1039/d0cp05166g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Proton-coupled electron transfer (PCET) reactions are ubiquitous natural processes at the heart of energy conversion reactions in photosynthesis and respiration, DNA repair, and diverse enzymatic reactions. Theoretical formulation and computational method developments have eyed modeling of thermal and photoinduced PCET for the last three decades. The accumulation of these studies, collected in dozens of reviews, accounts, and perspectives, has firmly established the influence of quantum effects, including non-adiabatic electronic transitions, vibrational relaxation, zero-point energy, and proton tunneling, on the rate and mechanism of PCET reactions. Here, we focus on some recently-developed methods, spanning the last eight years, that can quantitatively capture these effects in the PCET context and provide efficient means for their qualitative description in complex systems. The theoretical background of each method and their accuracy with respect to exact results are discussed and the results of relevant PCET simulations based on each method are presented.
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Affiliation(s)
- Sandra E Brown
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Farnaz A Shakib
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA.
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2
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Mandal A, Sandoval C. JS, Shakib FA, Huo P. Quasi-Diabatic Propagation Scheme for Direct Simulation of Proton-Coupled Electron Transfer Reaction. J Phys Chem A 2019; 123:2470-2482. [DOI: 10.1021/acs.jpca.9b00077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Arkajit Mandal
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, United States
| | - Juan S. Sandoval C.
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, United States
| | - Farnaz A. Shakib
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, United States
| | - Pengfei Huo
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, United States
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3
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Schile AJ, Limmer DT. Studying rare nonadiabatic dynamics with transition path sampling quantum jump trajectories. J Chem Phys 2018; 149:214109. [DOI: 10.1063/1.5058281] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Addison J. Schile
- Department of Chemistry, University of California, Berkeley, California 94618, USA
- Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94618, USA
| | - David T. Limmer
- Department of Chemistry, University of California, Berkeley, California 94618, USA
- Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94618, USA
- Kavli Energy NanoSciences Institute, University of California, Berkeley, California 94618, USA
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4
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Mandal A, Shakib FA, Huo P. Investigating photoinduced proton coupled electron transfer reaction using quasi diabatic dynamics propagation. J Chem Phys 2018; 148:244102. [DOI: 10.1063/1.5030634] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Arkajit Mandal
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
| | - Farnaz A. Shakib
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
| | - Pengfei Huo
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
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5
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Kananenka AA, Hsieh CY, Cao J, Geva E. Nonadiabatic Dynamics via the Symmetrical Quasi-Classical Method in the Presence of Anharmonicity. J Phys Chem Lett 2018; 9:319-326. [PMID: 29239614 DOI: 10.1021/acs.jpclett.7b03002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The symmetrical quasi-classical (SQC) method recently proposed by Miller and Cotton allows one to simulate nonadiabatic dynamics based on an algorithm with classical-like scaling with respect to system size. This is made possible by casting the electronic degrees of freedom in terms of mapping variables that can be propagated in a classical-like manner. While SQC was shown to be rather accurate when applied to benchmark models with harmonic electronic potential energy surfaces, it was also found to become inaccurate and to suffer numerical instabilities when applied to anharmonic systems. In this paper, we propose an extended SQC (E-SQC) methodology for overcoming those discrepancies by describing the anharmonic nuclear modes, which are coupled to the electronic degrees of freedom, in terms of classical-like mapping variables. The accuracy of E-SQC relative to standard SQC is demonstrated on benchmark models with quartic and Morse potential energy surfaces.
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Affiliation(s)
- Alexei A Kananenka
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Chang-Yu Hsieh
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02319, United States
- Singapore-MIT Alliance for Research and Technology (SMART) Center , Singapore 487373
| | - Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02319, United States
- Singapore-MIT Alliance for Research and Technology (SMART) Center , Singapore 487373
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Pierre S, Duke JR, Hele TJH, Ananth N. A mapping variable ring polymer molecular dynamics study of condensed phase proton-coupled electron transfer. J Chem Phys 2017; 147:234103. [DOI: 10.1063/1.4986517] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Sadrach Pierre
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jessica R. Duke
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Timothy J. H. Hele
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Nandini Ananth
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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7
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Song K, Shi Q. Theoretical study of photoinduced proton coupled electron transfer reaction using the non-perturbative hierarchical equations of motion method. J Chem Phys 2017. [DOI: 10.1063/1.4982928] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Kai Song
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Seki Y, Takayanagi T, Shiga M. Photoexcited Ag ejection from a low-temperature He cluster: a simulation study by nonadiabatic Ehrenfest ring-polymer molecular dynamics. Phys Chem Chem Phys 2017; 19:13798-13806. [DOI: 10.1039/c7cp00888k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nonadiabatic ring-polymer molecular dynamics simulations were performed to understand the photoexcitation dynamics of a low-temperature Ag·He500 cluster.
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Affiliation(s)
- Yusuke Seki
- Department of Chemistry
- Saitama University
- Saitama City
- Japan
| | | | - Motoyuki Shiga
- Center for Computational Science and E-Systems
- Japan Atomic Energy Agency
- Kashiwa
- Japan
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9
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Shakib F, Hanna G. Mixed Quantum-Classical Liouville Approach for Calculating Proton-Coupled Electron-Transfer Rate Constants. J Chem Theory Comput 2016; 12:3020-9. [DOI: 10.1021/acs.jctc.6b00362] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Farnaz Shakib
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gabriel Hanna
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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10
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Minoshima Y, Seki Y, Takayanagi T, Shiga M. Effects of temperature and isotopic substitution on electron attachment dynamics of guanine–cytosine base pair: Ring-polymer and classical molecular dynamics simulations. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kretchmer JS, Miller III TF. Kinetically-constrained ring-polymer molecular dynamics for non-adiabatic chemistries involving solvent and donor–acceptor dynamical effects. Faraday Discuss 2016; 195:191-214. [DOI: 10.1039/c6fd00143b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the performance of the recently developed kinetically-constrained ring polymer molecular dynamics (KC-RPMD) method for the description of model condensed-phase electron transfer (ET) reactions in which solvent and donor–acceptor dynamics play an important role. Comparison of KC-RPMD with results from Golden-Rule rate theories and numerically exact quantum dynamics calculations demonstrates that KC-RPMD accurately captures the combination of electronic- and nuclear-dynamical effects throughout the Marcus (intermediate solvent friction) and Zusman (large solvent friction) regimes of ET. It is also demonstrated that KC-RPMD accurately describes systems in which the magnitude of the diabatic coupling depends on the position of a dynamical donor–acceptor mode. In addition to these successes, however, we present an unsurprising failure of KC-RPMD to capture the enhancement of the ET rate in the low solvent friction regime associated with nuclear coherence effects. In this analysis, we re-visit several aspects of the original KC-RPMD formulation, including the form of the kinetic constraint and the choice of the mass of the auxiliary electronic variable. In particular, we introduce a Langevin bath for the auxiliary electronic variable to correct for its unphysically low coupling with the nuclear degrees of freedom. This work demonstrates that the KC-RPMD method is well suited for the direct simulation of non-adiabatic donor–acceptor chemistries associated with many complex systems, including those for which solvent dynamics plays an important role in the reaction mechanism.
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Affiliation(s)
- Joshua S. Kretchmer
- Division of Chemistry and Chemical Engineering
- California Institute of Technology
- Pasadena
- USA
| | - Thomas F. Miller III
- Division of Chemistry and Chemical Engineering
- California Institute of Technology
- Pasadena
- USA
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12
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Richardson JO. Ring-polymer instanton theory of electron transfer in the nonadiabatic limit. J Chem Phys 2015; 143:134116. [DOI: 10.1063/1.4932362] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jeremy O. Richardson
- Institut für Theoretische Physik und Interdisziplinäres Zentrum für Molekulare Materialien, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Staudtstraße 7/B2, 91058 Erlangen, Germany
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13
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Kretchmer JS, Miller TF. Tipping the Balance between Concerted versus Sequential Proton-Coupled Electron Transfer. Inorg Chem 2015; 55:1022-31. [PMID: 26440812 DOI: 10.1021/acs.inorgchem.5b01821] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joshua S. Kretchmer
- Department of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Thomas F. Miller
- Department of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
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Zeng T, Roy PN. Microscopic molecular superfluid response: theory and simulations. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2014; 77:046601. [PMID: 24647079 DOI: 10.1088/0034-4885/77/4/046601] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Since its discovery in 1938, superfluidity has been the subject of much investigation because it provides a unique example of a macroscopic manifestation of quantum mechanics. About 60 years later, scientists successfully observed this phenomenon in the microscopic world though the spectroscopic Andronikashvili experiment in helium nano-droplets. This reduction of scale suggests that not only helium but also para-H2 (pH2) can be a candidate for superfluidity. This expectation is based on the fact that the smaller number of neighbours and surface effects of a finite-size cluster may hinder solidification and promote a liquid-like phase. The first prediction of superfluidity in pH2 clusters was reported in 1991 based on quantum Monte Carlo simulations. The possible superfluidity of pH2 was later indirectly observed in a spectroscopic Andronikashvili experiment in 2000. Since then, a growing number of studies have appeared, and theoretical simulations have been playing a special role because they help guide and interpret experiments. In this review, we go over the theoretical studies of pH2 superfluid clusters since the experiment of 2000. We provide a historical perspective and introduce the basic theoretical formalism along with key experimental advances. We then present illustrative results of the theoretical studies and comment on the possible future developments in the field. We include sufficient theoretical details such that the review can serve as a guide for newcomers to the field.
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Affiliation(s)
- Tao Zeng
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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15
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Kretchmer JS, Miller TF. Direct simulation of proton-coupled electron transfer across multiple regimes. J Chem Phys 2013; 138:134109. [DOI: 10.1063/1.4797462] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Habershon S, Manolopoulos DE, Markland TE, Miller TF. Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space. Annu Rev Phys Chem 2013; 64:387-413. [DOI: 10.1146/annurev-physchem-040412-110122] [Citation(s) in RCA: 448] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Scott Habershon
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom;
| | - David E. Manolopoulos
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Thomas E. Markland
- Department of Chemistry, Stanford University, Stanford, California 94305;
| | - Thomas F. Miller
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125;
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