1
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Limbu DK, Shakib FA. Real-Time Dynamics and Detailed Balance in Ring Polymer Surface Hopping: The Impact of Frustrated Hops. J Phys Chem Lett 2023; 14:8658-8666. [PMID: 37732811 DOI: 10.1021/acs.jpclett.3c02085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Ring polymer surface hopping (RPSH) has been recently introduced as a well-tailored method for incorporating nuclear quantum effects, such as zero-point energy and tunneling, into nonadiabatic molecular dynamics simulations. The practical widespread usage of RPSH demands a comprehensive benchmarking of different reaction regimes and conditions with equal emphasis on demonstrating both the cons and the pros of the method. Here, we investigate the fundamental questions related to the conservation of energy and detailed balance in the context of RPSH. Using Tully's avoided crossing model as well as a 2-state quantum system coupled to a classical bath undergoing Langevin dynamics, we probe the critical problem of the proper treatment of the classically forbidden transitions stemming from the surface hopping algorithm. We show that proper treatment of these frustrated hops is key to the accurate description of real-time dynamics as well as reproducing the correct quantum Boltzmann populations.
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Affiliation(s)
- Dil K Limbu
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Farnaz A Shakib
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
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2
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Naleem N, Abreu CRA, Warmuz K, Tong M, Kirmizialtin S, Tuckerman ME. An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions. J Chem Phys 2023; 159:034102. [PMID: 37458344 DOI: 10.1063/5.0147597] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
Determining collective variables (CVs) for conformational transitions is crucial to understanding their dynamics and targeting them in enhanced sampling simulations. Often, CVs are proposed based on intuition or prior knowledge of a system. However, the problem of systematically determining a proper reaction coordinate (RC) for a specific process in terms of a set of putative CVs can be achieved using committor analysis (CA). Identifying essential degrees of freedom that govern such transitions using CA remains elusive because of the high dimensionality of the conformational space. Various schemes exist to leverage the power of machine learning (ML) to extract an RC from CA. Here, we extend these studies and compare the ability of 17 different ML schemes to identify accurate RCs associated with conformational transitions. We tested these methods on an alanine dipeptide in vacuum and on a sarcosine dipeptoid in an implicit solvent. Our comparison revealed that the light gradient boosting machine method outperforms other methods. In order to extract key features from the models, we employed Shapley Additive exPlanations analysis and compared its interpretation with the "feature importance" approach. For the alanine dipeptide, our methodology identifies ϕ and θ dihedrals as essential degrees of freedom in the C7ax to C7eq transition. For the sarcosine dipeptoid system, the dihedrals ψ and ω are the most important for the cisαD to transαD transition. We further argue that analysis of the full dynamical pathway, and not just endpoint states, is essential for identifying key degrees of freedom governing transitions.
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Affiliation(s)
- Nawavi Naleem
- Chemistry Program, Science Division, New York University, Abu Dhabi, UAE
| | - Charlles R A Abreu
- Chemical Engineering Department, Escola de Química, Universidade Federal do Rio de Janeiro, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Krzysztof Warmuz
- Computer Science Program, Science Division, New York University, Abu Dhabi, UAE
| | - Muchen Tong
- Department of Chemistry, New York University (NYU), New York, New York 10003, USA
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University, Abu Dhabi, UAE
- Department of Chemistry, New York University (NYU), New York, New York 10003, USA
- Center for Smart Engineering Materials, New York University, Abu Dhabi, UAE
| | - Mark E Tuckerman
- Department of Chemistry, New York University (NYU), New York, New York 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Rd. North, Shanghai 200062, China
- Simons Center for Computational Physical Chemistry at New York University, New York, New York 10003, USA
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3
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Anderson MC, Schile AJ, Limmer DT. Nonadiabatic transition paths from quantum jump trajectories. J Chem Phys 2022; 157:164105. [DOI: 10.1063/5.0102891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a means of studying rare reactive pathways in open quantum systems using transition path theory and ensembles of quantum jump trajectories. This approach allows for the elucidation of reactive paths for dissipative, nonadiabatic dynamics when the system is embedded in a Markovian environment. We detail the dominant pathways and rates of thermally activated processes and the relaxation pathways and photoyields following vertical excitation in a minimal model of a conical intersection. We find that the geometry of the conical intersection affects the electronic character of the transition state as defined through a generalization of a committor function for a thermal barrier crossing event. Similarly, the geometry changes the mechanism of relaxation following a vertical excitation. Relaxation in models resulting from small diabatic coupling proceeds through pathways dominated by pure dephasing, while those with large diabatic coupling proceed through pathways limited by dissipation. The perspective introduced here for the nonadiabatic dynamics of open quantum systems generalizes classical notions of reactive paths to fundamentally quantum mechanical processes.
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Affiliation(s)
- Michelle C. Anderson
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Addison J. Schile
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - David T. Limmer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Kavli Energy NanoSciences Institute, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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4
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Benson RL, Althorpe SC. On the "Matsubara heating" of overtone intensities and Fermi splittings. J Chem Phys 2021; 155:104107. [PMID: 34525826 DOI: 10.1063/5.0056829] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Classical molecular dynamics (MD) and imaginary-time path-integral dynamics methods underestimate the infrared absorption intensities of overtone and combination bands by typically an order of magnitude. Plé et al. [J. Chem. Phys. 155, 2863 (2021)] have shown that this is because such methods fail to describe the coupling of the centroid to the Matsubara dynamics of the fluctuation modes; classical first-order perturbation theory (PT) applied to the Matsubara dynamics is sufficient to recover most of the lost intensity in simple models and gives identical results to quantum (Rayleigh-Schrödinger) PT. Here, we show numerically that the results of this analysis can be used as post-processing correction factors, which can be applied to realistic (classical MD or path-integral dynamics) simulations of infrared spectra. We find that the correction factors recover most of the lost intensity in the overtone and combination bands of gas-phase water and ammonia and much of it for liquid water. We then re-derive and confirm the earlier PT analysis by applying canonical PT to Matsubara dynamics, which has the advantage of avoiding secular terms and gives a simple picture of the perturbed Matsubara dynamics in terms of action-angle variables. Collectively, these variables "Matsubara heat" the amplitudes of the overtone and combination vibrations of the centroid to what they would be in a classical system with the oscillators (of frequency Ωi) held at their quantum effective temperatures [of ℏΩi coth(βℏΩi/2)/2kB]. Numerical calculations show that a similar neglect of "Matsubara heating" causes path-integral methods to underestimate Fermi resonance splittings.
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Affiliation(s)
- Raz L Benson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Stuart C Althorpe
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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5
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Bhowmick S, Hernández MI, Campos-Martínez J, Suleimanov YV. Isotopic separation of helium through graphyne membranes: a ring polymer molecular dynamics study. Phys Chem Chem Phys 2021; 23:18547-18557. [PMID: 34612392 DOI: 10.1039/d1cp02121d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microscopic-level understanding of the separation mechanism for two-dimensional (2D) membranes is an active area of research due to potential implications of this class of membranes for various technological processes. Helium (He) purification from the natural resources is of particular interest due to the shortfall in its production. In this work, we applied the ring polymer molecular dynamics (RPMD) method to graphdiyne (Gr2) and graphtriyne (Gr3) 2D membranes having variable pore sizes for the separation of He isotopes, and compare for the first time with rigorous quantum calculations. We found that the transmission rate through Gr3 is many orders of magnitude greater than Gr2. The selectivity of either isotope at low temperatures is a consequence of a delicate balance between the zero-point energy effect and tunneling of 4He and 3He. In particular, a remarkable tunneling effect is reported on the Gr2 membrane at 10 K, leading to a much larger permeation of the lighter species as compared to the heavier isotope. RPMD provides an efficient approach for studying the separation of He isotopes, taking into account quantum effects of light nuclei motions at low temperatures, which classical methods fail to capture.
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Affiliation(s)
- Somnath Bhowmick
- Computation-based Science and Technology Research Center, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
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6
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Li X, Huo P. Investigating Tunneling-Controlled Chemical Reactions through Ab Initio Ring Polymer Molecular Dynamics. J Phys Chem Lett 2021; 12:6714-6721. [PMID: 34261316 DOI: 10.1021/acs.jpclett.1c01630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We use the ab initio ring polymer molecular dynamics (RPMD) approach to investigate tunneling-controlled reactions in methylhydroxycarbene. Nuclear tunneling effects enable molecules to overcome the barriers which cannot be overcome classically. Under low-temperature conditions, intrinsic quantum tunneling effects can facilitate the chemical reaction in a pathway that is favored neither thermodynamically nor kinetically. This behavior is referred to as the tunneling-controlled chemical reaction and is regarded as the third paradigm of chemical reaction controls. In this work, we use the ab initio RPMD approach to incorporate the tunneling effects in our quantum dynamics simulations and investigate the reaction kinetics of two competitive reaction pathways at various temperatures. The reaction rate constants obtained here agree extremely well with the experimentally measured rates. We demonstrate the feasibility of using ab initio RPMD rate calculations in a realistic molecular system and provide an interesting and important example for future investigations of reaction mechanisms dominated by quantum tunneling effects.
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Affiliation(s)
- Xinyang Li
- 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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7
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Chowdhury SN, Huo P. Non-adiabatic Matsubara dynamics and non-adiabatic ring-polymer molecular dynamics. J Chem Phys 2021; 154:124124. [PMID: 33810665 DOI: 10.1063/5.0042136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We present the non-adiabatic Matsubara dynamics, a general framework for computing the time-correlation function (TCF) of electronically non-adiabatic systems. This new formalism is derived based on the generalized Kubo-transformed TCF using the Wigner representation for both the nuclear degrees of freedom and the electronic mapping variables. By dropping the non-Matsubara nuclear normal modes in the quantum Liouvillian and explicitly integrating these modes out from the expression of the TCF, we derived the non-adiabatic Matsubara dynamics approach. Further making the approximation to drop the imaginary part of the Matsubara Liouvillian and enforce the nuclear momentum integral to be real, we arrived at the non-adiabatic ring-polymer molecular dynamics (NRPMD) approach. We have further justified the capability of NRPMD for simulating the non-equilibrium TCF. This work provides the rigorous theoretical foundation for several recently proposed state-dependent RPMD approaches and offers a general framework for developing new non-adiabatic quantum dynamics methods in the future.
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Affiliation(s)
- Sutirtha N Chowdhury
- 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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8
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Jiang H, Tao X, Kammler M, Ding F, Wodtke AM, Kandratsenka A, Miller TF, Bünermann O. Small Nuclear Quantum Effects in Scattering of H and D from Graphene. J Phys Chem Lett 2021; 12:1991-1996. [PMID: 33596383 DOI: 10.1021/acs.jpclett.0c02933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We study nuclear quantum effects in H/D sticking to graphene, comparing scattering experiments at near-zero coverage with classical, quantized, and transition-state calculations. The experiment shows H/D sticking probabilities that are indistinguishable from one another and markedly smaller than those expected from a consideration of zero-point energy shifts of the chemisorption transition state. Inclusion of dynamical effects and vibrational anharmonicity via ring-polymer molecular dynamics (RPMD) yields results that are in good agreement with the experimental results. RPMD also reveals that nuclear quantum effects, while modest, arise primarily from carbon and not from H/D motion, confirming the importance of a C atom rehybridization mechanism associated with H/D sticking on graphene.
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Affiliation(s)
- Hongyan Jiang
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
| | - Xuecheng Tao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Marvin Kammler
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
| | - Feizhi Ding
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Alec M Wodtke
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
- Institut für Physikalische Chemie, Georg-Georg-August-Universität Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
- International Center for Advanced Studies of Energy Conversion, Georg-August University of Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
| | - Alexander Kandratsenka
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Oliver Bünermann
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
- Institut für Physikalische Chemie, Georg-Georg-August-Universität Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
- International Center for Advanced Studies of Energy Conversion, Georg-August University of Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
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9
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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: 0.7] [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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10
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Chowdhury SN, Mandal A, Huo P. Ring polymer quantization of the photon field in polariton chemistry. J Chem Phys 2021; 154:044109. [PMID: 33514102 DOI: 10.1063/5.0038330] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We use the ring polymer (RP) representation to quantize the radiation field inside an optical cavity to investigate polariton quantum dynamics. Using a charge transfer model coupled to an optical cavity, we demonstrate that the RP quantization of the photon field provides accurate rate constants of the polariton mediated electron transfer reaction compared to Fermi's golden rule. Because RP quantization uses extended phase space to describe the photon field, it significantly reduces the computational costs compared to the commonly used Fock state description of the radiation field. Compared to the other quasi-classical descriptions of the photon field, such as the classical Wigner based mean-field Ehrenfest model, the RP representation provides a much more accurate description of the polaritonic quantum dynamics because it alleviates the potential quantum distribution leakage problem associated with the photonic degrees of freedom (DOF). This work demonstrates the possibility of using the ring polymer description to treat the quantized radiation field in polariton chemistry, offering an accurate and efficient approach for future investigations in cavity quantum electrodynamics.
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Affiliation(s)
- Sutirtha N Chowdhury
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
| | - Arkajit Mandal
- 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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11
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Kellett CW, Berlinguette CP. Defining Direct Orbital Pathways for Intermolecular Electron Transfer Using Sensitized Semiconducting Surfaces. Inorg Chem 2020; 59:14696-14705. [PMID: 32997937 DOI: 10.1021/acs.inorgchem.0c02251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-performance electronic materials and redox catalysts often rely on fast rates of intermolecular electron transfer (IET). Maximizing IET rates requires strong electronic coupling (HDA) between the electron donor and acceptor, yet universal structure-property relationships governing HDA in outer-sphere IET reactions have yet to be developed. For ground-state IET reactions, HDA is reasonably approximated by the extent of overlap between the frontier donor and acceptor orbitals involved in the electron-transfer reaction. Intermolecular interactions that encourage overlap between these orbitals, thereby creating a direct orbital pathway for IET, have a strong impact on HDA and, by extension, the IET rates. In this Forum Article, we present a set of intuitive molecular design strategies employing this direct orbital pathway principle to maximize HDA for IET reactions. We highlight how the careful design of redox-active molecules anchored to solid semiconducting substrates provides a powerful experimental platform for elucidating how electronic structure and specific intermolecular interactions affect IET reactions.
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Affiliation(s)
- Cameron W Kellett
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Curtis P Berlinguette
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada.,Department of Chemical and Biological Engineering, The University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Stewart Blusson Quantum Matter Institute, The University of British Columbia, 2355 East Mall, Vancouver, British Columbia V6T 1Z4, Canada.,Canadian Institute for Advanced Research, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
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12
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Leitold C, Mundy CJ, Baer MD, Schenter GK, Peters B. Solvent reaction coordinate for an SN2 reaction. J Chem Phys 2020; 153:024103. [DOI: 10.1063/5.0002766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Christian Leitold
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Christopher J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Marcel D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Gregory K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Baron Peters
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Chemistry and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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13
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Heller ER, Richardson JO. Semiclassical instanton formulation of Marcus–Levich–Jortner theory. J Chem Phys 2020; 152:244117. [DOI: 10.1063/5.0013521] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Eric R. Heller
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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14
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Tao X, Shushkov P, Miller TF. Microcanonical rates from ring-polymer molecular dynamics: Direct-shooting, stationary-phase, and maximum-entropy approaches. J Chem Phys 2020; 152:124117. [DOI: 10.1063/1.5144307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Xuecheng Tao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Philip Shushkov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Thomas F. Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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15
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Sakaushi K, Kumeda T, Hammes-Schiffer S, Melander MM, Sugino O. Advances and challenges for experiment and theory for multi-electron multi-proton transfer at electrified solid–liquid interfaces. Phys Chem Chem Phys 2020; 22:19401-19442. [DOI: 10.1039/d0cp02741c] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Understanding microscopic mechanism of multi-electron multi-proton transfer reactions at complexed systems is important for advancing electrochemistry-oriented science in the 21st century.
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Affiliation(s)
- Ken Sakaushi
- Center for Green Research on Energy and Environmental Materials
- National Institute for Materials Science
- Ibaraki 305-0044
- Japan
| | - Tomoaki Kumeda
- Center for Green Research on Energy and Environmental Materials
- National Institute for Materials Science
- Ibaraki 305-0044
- Japan
| | | | - Marko M. Melander
- Nanoscience Center
- Department of Chemistry
- University of Jyväskylä
- Jyväskylä
- Finland
| | - Osamu Sugino
- The Institute of Solid State Physics
- the University of Tokyo
- Chiba 277-8581
- Japan
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16
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Fang W, Thapa MJ, Richardson JO. Nonadiabatic quantum transition-state theory in the golden-rule limit. II. Overcoming the pitfalls of the saddle-point and semiclassical approximations. J Chem Phys 2019; 151:214101. [DOI: 10.1063/1.5131092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Wei Fang
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Manish J. Thapa
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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17
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Lawrence JE, Fletcher T, Lindoy LP, Manolopoulos DE. On the calculation of quantum mechanical electron transfer rates. J Chem Phys 2019; 151:114119. [DOI: 10.1063/1.5116800] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Joseph E. Lawrence
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Theo Fletcher
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Lachlan P. Lindoy
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - David E. Manolopoulos
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, United Kingdom
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18
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Trenins G, Willatt MJ, Althorpe SC. Path-integral dynamics of water using curvilinear centroids. J Chem Phys 2019. [DOI: 10.1063/1.5100587] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- George Trenins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Michael J. Willatt
- Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Stuart C. Althorpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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19
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Chowdhury SN, Huo P. State dependent ring polymer molecular dynamics for investigating excited nonadiabatic dynamics. J Chem Phys 2019; 150:244102. [DOI: 10.1063/1.5096276] [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)
- Sutirtha N. Chowdhury
- 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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20
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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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21
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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: 2.0] [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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22
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Tao X, Shushkov P, Miller TF. Simple Flux-Side Formulation of State-Resolved Thermal Reaction Rates for Ring-Polymer Surface Hopping. J Phys Chem A 2019; 123:3013-3020. [DOI: 10.1021/acs.jpca.9b00877] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Xuecheng Tao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Philip Shushkov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Thomas F. Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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23
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Soudackov AV, Hammes-Schiffer S. Proton-coupled electron transfer reactions: analytical rate constants and case study of kinetic isotope effects in lipoxygenase. Faraday Discuss 2018; 195:171-189. [PMID: 27735009 DOI: 10.1039/c6fd00122j] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A general theory has been developed for proton-coupled electron transfer (PCET), which is vital to a wide range of chemical and biological processes. This theory describes PCET reactions in terms of nonadiabatic transitions between reactant and product electron-proton vibronic states and includes the effects of thermal fluctuations of the solvent or protein environment, as well as the proton donor-acceptor motion. Within the framework of this general PCET theory, a series of analytical rate constant expressions has been derived for PCET reactions in well-defined regimes. Herein, the application of this theory to PCET in the enzyme soybean lipoxygenase illustrates the regimes of validity for the various rate constant expressions and elucidates the fundamental physical principles dictating PCET reactions. Such theoretical studies provide significant physical insights that guide the interpretation of experimental data and lead to experimentally testable predictions. A combination of theoretical treatments with atomic-level simulations is essential to understanding PCET.
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Affiliation(s)
- Alexander V Soudackov
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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24
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Gillet N, Elstner M, Kubař T. Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer. J Chem Phys 2018; 149:072328. [PMID: 30134697 DOI: 10.1063/1.5027100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a new concept of free energy calculations of chemical reactions by means of extended sampling molecular dynamics simulations. Biasing potentials are applied on partial atomic charges, which may be combined with atomic coordinates either in a single collective variable or in multi-dimensional biasing simulations. The necessary additional gradients are obtained by solving coupled-perturbed equations within the approximative density-functional tight-binding method. The new computational scheme was implemented in a combination of Gromacs and Plumed. As a prospective application, proton-coupled electron transfer in a model molecular system is studied. Two collective variables are introduced naturally, one for the proton transfer and the other for the electron transfer. The results are in qualitative agreement with the extended free simulations performed for reference. Free energy minima as well as the mechanism of the process are identified correctly, while the topology of the transition region and the height of the energy barrier are only reproduced qualitatively. The application also illustrates possible difficulties with the new methodology. These may be inefficient sampling of spatial coordinates when atomic charges are biased exclusively and a decreased stability of the simulations. Still, the new approach represents a viable alternative for free energy calculations of a certain class of chemical reactions, for instance a proton-coupled electron transfer in proteins.
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Affiliation(s)
- Natacha Gillet
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
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25
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Sandoval C. JS, Mandal A, Huo P. Symmetric quasi-classical dynamics with quasi-diabatic propagation scheme. J Chem Phys 2018; 149:044115. [DOI: 10.1063/1.5036787] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
| | - Arkajit Mandal
- 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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26
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Trenins G, Althorpe SC. Mean-field Matsubara dynamics: Analysis of path-integral curvature effects in rovibrational spectra. J Chem Phys 2018; 149:014102. [DOI: 10.1063/1.5038616] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- George Trenins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Stuart C. Althorpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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27
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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: 2.5] [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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28
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Han Y, Jin J, Wagner JW, Voth GA. Quantum theory of multiscale coarse-graining. J Chem Phys 2018; 148:102335. [PMID: 29544317 DOI: 10.1063/1.5010270] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals. It identifies the optimal choice of CG action functional and effective quantum CG (qCG) force field to generate a quantum MS-CG (qMS-CG) description of the equilibrium system that is consistent with the quantum fine-grained model projected onto the CG variables. A variational principle then provides a class of algorithms for optimally approximating the qMS-CG force fields. Specifically, a variational method based on force matching, which was also adopted in the classical MS-CG theory, is generalized to quantum Boltzmann statistics. The qMS-CG numerical algorithms and practical issues in implementing this variational minimization procedure are also discussed. Then, two numerical examples are presented to demonstrate the method. Finally, as an alternative strategy, a quasi-classical approximation for the thermal density matrix expressed in the CG variables is derived. This approach provides an interesting physical picture for coarse-graining in quantum Boltzmann statistical mechanics in which the consistency with the quantum particle delocalization is obviously manifest, and it opens up an avenue for using path integral centroid-based effective classical force fields in a coarse-graining methodology.
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Affiliation(s)
- Yining Han
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jaehyeok Jin
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jacob W Wagner
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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29
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30
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Tao X, Shushkov P, Miller TF. Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics. J Chem Phys 2018; 148:102327. [DOI: 10.1063/1.5005544] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xuecheng Tao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Philip Shushkov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Thomas F. Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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31
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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: 3.1] [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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32
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Chowdhury SN, Huo P. Coherent state mapping ring polymer molecular dynamics for non-adiabatic quantum propagations. J Chem Phys 2017; 147:214109. [DOI: 10.1063/1.4995616] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sutirtha N. Chowdhury
- 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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33
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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: 1.4] [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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34
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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: 1.1] [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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35
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An analysis of nonadiabatic ring-polymer molecular dynamics and its application to vibronic spectra. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.09.036] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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36
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Welsch R, Song K, Shi Q, Althorpe SC, Miller TF. Non-equilibrium dynamics from RPMD and CMD. J Chem Phys 2016; 145:204118. [DOI: 10.1063/1.4967958] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Ralph Welsch
- Division of Chemistry and Chemical Engineering, California Institute of Technology,1200 E. California Blvd., Pasadena, California 91125, USA
| | - Kai Song
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Stuart C. Althorpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Thomas F. Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology,1200 E. California Blvd., Pasadena, California 91125, USA
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37
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Suleimanov YV, Aoiz FJ, Guo H. Chemical Reaction Rate Coefficients from Ring Polymer Molecular Dynamics: Theory and Practical Applications. J Phys Chem A 2016; 120:8488-8502. [DOI: 10.1021/acs.jpca.6b07140] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yury V. Suleimanov
- Computation-based Science
and Technology Research Center, Cyprus Institute, 20 Kavafi Street, Nicosia 2121, Cyprus
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - F. Javier Aoiz
- Departamento de Química
Física I, Facultad de CC. Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Hua Guo
- Department of Chemistry and
Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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38
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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: 0.8] [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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39
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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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40
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Hele TJH, Althorpe SC. An alternative derivation of ring-polymer molecular dynamics transition-state theory. J Chem Phys 2016; 144:174107. [DOI: 10.1063/1.4947589] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Timothy J. H. Hele
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Stuart C. Althorpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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41
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Hele TJH. On the relation between thermostatted ring-polymer molecular dynamics and exact quantum dynamics. Mol Phys 2016. [DOI: 10.1080/00268976.2015.1136003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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42
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Kim I, Warshel A. A Microscopic Capacitor Model of Voltage Coupling in Membrane Proteins: Gating Charge Fluctuations in Ci-VSD. J Phys Chem B 2016; 120:418-32. [PMID: 26716721 DOI: 10.1021/acs.jpcb.5b10956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The voltage sensitivity of membrane proteins is reflected in the response of the voltage sensing domains (VSDs) to the changes in membrane potential. This response is implicated in the displacement of positively charged residues, associated with the conformational changes of VSDs. The displaced charges generate nonlinear (i.e., voltage-dependent) capacitance current called the gating current (and its corresponding gating charge), which is a key experimental quantity that characterizes voltage activation in VSMP. However, the relevant theoretical/computational approaches, aimed to correlate the structural information on VSMP to electrophysiological measurements, have been rather limited, posing a broad challenge in computer simulations of VSMP. Concomitant with the development of our coarse-graining (CG) model of voltage coupling, we apply our theoretical framework for the treatments of voltage effects in membrane proteins to modeling the VSMP activation, taking the VSDs (Ci-VSD) derived from the Ciona intestinalis voltage sensitive phosphatase (Ci-VSP) as a model system. Our CG model reproduces the observed gating charge of Ci-VSD activation in several different perspectives. In particular, a new closed-form expression of the gating charge is evaluated in both nonequilibrium and equilibrium ways, while considering the fluctuation-dissipation relation that connects a nonequilibrium measurement of the gating charge to an equilibrium measurement of charge fluctuations (i.e., the voltage-independent linear component of membrane capacitance). In turn, the expression uncovers a novel link that connects an equilibrium measurement of the voltage-independent linear capacitance to a nonequilibrium measurement of the voltage-dependent nonlinear capacitance (whose integral over voltage is equal to the gating charge). In addition, our CG model yields capacitor-like voltage dependent free energy parabolas, resulting in the free energy difference and the free energy barrier for the Ci-VSD activation at "zero" (depolarization) membrane potential. Significantly, the resultant voltage dependent energetics enables a direct evaluation of capacitance-voltage relationship (C-V curve) as well as charge-voltage relationship (Q-V curve) that is in a good agreement with the observed measurement of Ci-VSD voltage activation. Importantly, an extension of our kinetic/thermodynamic model of voltage dependent activation in VSMP allows for novel derivations of voltage-dependent rate constants, whose parameters are expressed by the intrinsic properties of VSMP. These novel closed-form expressions offer a physicochemical foundation for the semiempirical Eyring-type voltage dependent rate equations that have been the cornerstone for the phenomenological (kinetic) descriptions of gating and membrane currents in the mechanistic study of ion channels and transporters. Our extended theoretical framework developed in the present study has potential implications on the roles played by gating charge fluctuations for the spike generations in nerve cells within the framework of the Hodgkin-Huxley-type model.
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Affiliation(s)
- Ilsoo Kim
- Department of Chemistry, University of Southern California , SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California , SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States
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43
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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: 2.6] [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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44
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Benabbas A, Salna B, Sage JT, Champion PM. Deep proton tunneling in the electronically adiabatic and non-adiabatic limits: comparison of the quantum and classical treatment of donor-acceptor motion in a protein environment. J Chem Phys 2015; 142:114101. [PMID: 25796225 DOI: 10.1063/1.4913591] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Analytical models describing the temperature dependence of the deep tunneling rate, useful for proton, hydrogen, or hydride transfer in proteins, are developed and compared. Electronically adiabatic and non-adiabatic expressions are presented where the donor-acceptor (D-A) motion is treated either as a quantized vibration or as a classical "gating" distribution. We stress the importance of fitting experimental data on an absolute scale in the electronically adiabatic limit, which normally applies to these reactions, and find that vibrationally enhanced deep tunneling takes place on sub-ns timescales at room temperature for typical H-bonding distances. As noted previously, a small room temperature kinetic isotope effect (KIE) does not eliminate deep tunneling as a major transport channel. The quantum approach focuses on the vibrational sub-space composed of the D-A and hydrogen atom motions, where hydrogen bonding and protein restoring forces quantize the D-A vibration. A Duschinsky rotation is mandated between the normal modes of the reactant and product states and the rotation angle depends on the tunneling particle mass. This tunnel-mass dependent rotation contributes substantially to the KIE and its temperature dependence. The effect of the Duschinsky rotation is solved exactly to find the rate in the electronically non-adiabatic limit and compared to the Born-Oppenheimer (B-O) approximation approach. The B-O approximation is employed to find the rate in the electronically adiabatic limit, where we explore both harmonic and quartic double-well potentials for the hydrogen atom bound states. Both the electronically adiabatic and non-adiabatic rates are found to diverge at high temperature unless the proton coupling includes the often neglected quadratic term in the D-A displacement from equilibrium. A new expression is presented for the electronically adiabatic tunnel rate in the classical limit for D-A motion that should be useful to experimentalists working near room temperature. This expression also holds when a broad protein conformational distribution of D-A equilibrium distances dominates the spread of the D-A vibrational wavefunction.
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Affiliation(s)
- Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems,Northeastern University, Boston, Massachusetts 02115, USA
| | - Bridget Salna
- Department of Physics and Center for Interdisciplinary Research on Complex Systems,Northeastern University, Boston, Massachusetts 02115, USA
| | - J Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems,Northeastern University, Boston, Massachusetts 02115, USA
| | - Paul M Champion
- Department of Physics and Center for Interdisciplinary Research on Complex Systems,Northeastern University, Boston, Massachusetts 02115, USA
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45
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Sarsa A, Alcaraz-Pelegrina JM, Le Sech C. Isotopic Effects on Covalent Bond Confined in a Penetrable Sphere. J Phys Chem B 2015; 119:14364-72. [PMID: 26484576 DOI: 10.1021/acs.jpcb.5b06758] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A model of confinement of the covalent bond by a finite potential beyond the Born-Oppenheimer approximation is presented. A two-electron molecule is located at the center of a penetrable spherical cavity. The Schrödinger equation has been solved by using the diffusion Monte Carlo method. Total energies, internuclear distances, and vibrational frequencies of the confined molecular system have been obtained. Even for confining potentials of a few electronvolts, a noticeable increase in the bond energy and the nuclear vibrational frequency is observed, and the internuclear distance is lowered. The gap between the zero point energy of different molecular isotopes increases with confinement. The confinement of the electron pair might play a role in chemical reactivity, providing an alternative explanation for the tunnel effect, when large values of primary kinetic isotopic effect are observed. The Swain-Schaad relation is still verified when confinement changes the zero point energy. A semiquantitative illustration is proposed using the data relative to an hydrogen transfer involving a C-H cleavage catalyzed by the bovine serum amine oxidase. Changes on the confining conditions, corresponding to a confinement/deconfinement process, result in a significant decrease in the activation energy of the chemical transformation. It is proposed that confinement/deconfinement of the electron-pair bonding by external electrostatic forces inside the active pocket of an enzyme could be one of the basic mechanisms of the enzyme catalysis.
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Affiliation(s)
- Antonio Sarsa
- Departamento de Física, Facultad de Ciencias, Universidad de Córdoba , Campus de Rabanales, Edif. C2, E-14071 Córdoba, Spain
| | - José M Alcaraz-Pelegrina
- Departamento de Física, Facultad de Ciencias, Universidad de Córdoba , Campus de Rabanales, Edif. C2, E-14071 Córdoba, Spain
| | - Claude Le Sech
- Université Paris Sud 11, CNRS, Institut des Sciences Moleculaires d'Orsay-ISMO (UMR 8214), 91405 Orsay Cedex, France
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Nava M, Quhe R, Palazzesi F, Tiwary P, Parrinello M. de Broglie Swapping Metadynamics for Quantum and Classical Sampling. J Chem Theory Comput 2015; 11:5114-9. [DOI: 10.1021/acs.jctc.5b00818] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Nava
- Department
of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà
di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Ticino, Switzerland
| | - Ruge Quhe
- Department
of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà
di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Ticino, Switzerland
- State Key Laboratory of Information Photonics and Optical Communications & School of Science, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Ferruccio Palazzesi
- Department
of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà
di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Ticino, Switzerland
| | - Pratyush Tiwary
- Department
of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà
di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Ticino, Switzerland
- Department
of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Michele Parrinello
- Department
of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà
di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Ticino, Switzerland
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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: 3.8] [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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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: 34] [Impact Index Per Article: 3.8] [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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Sinitskiy AV, Voth GA. A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals. J Chem Phys 2015; 143:094104. [DOI: 10.1063/1.4929790] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anton V. Sinitskiy
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago, 5735 S. Ellis Ave., Chicago, Illinois 60637, USA
| | - Gregory A. Voth
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago, 5735 S. Ellis Ave., Chicago, Illinois 60637, USA
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50
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Hele TJH, Suleimanov YV. Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates? J Chem Phys 2015; 143:074107. [DOI: 10.1063/1.4928599] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Timothy J. H. Hele
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Yury V. Suleimanov
- Computation-based Science and Technology Research Center, Cyprus Institute, 20 Kavafi St., Nicosia 2121, Cyprus
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
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