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Liu XY, Wang SR, Fang WH, Cui G. Nuclear Quantum Effects on Nonadiabatic Dynamics of a Green Fluorescent Protein Chromophore Analogue: Ring-Polymer Surface-Hopping Simulation. J Chem Theory Comput 2024; 20:3426-3439. [PMID: 38656202 DOI: 10.1021/acs.jctc.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Herein, we have used the "on-the-fly" ring-polymer surface-hopping simulation method with the centroid approximation (RPSH-CA), in combination with the multireference OM2/MRCI electronic structure calculations to study the photoinduced dynamics of a green fluorescent protein (GFP) chromophore analogue in the gas phase, i.e., o-HBI, at 50, 100, and 300 K with 1, 5, 10, and 15 beads (3600 1 ps trajectories). The electronic structure calculations identified five new minimum-energy conical intersection (MECI) structures, which, together with the previous one, play crucial roles in the excited-state decay dynamics of o-HBI. It is also found that the excited-state intramolecular proton transfer (ESIPT) occurs in an ultrafast manner and is completed within 20 fs in all the simulation conditions because there is no barrier associated with this ESIPT process in the S1 state. However, the other excited-state dynamical results are strongly related to the number of beads. At 50 and 100 K, the nuclear quantum effects (NQEs) are very important; therefore, the excited-state dynamical results change significantly with the bead number. For example, the S1 decay time deduced from time-dependent state populations becomes longer as the bead number increases. Nevertheless, an essentially convergent trend is observed when the bead number is close to 10. In contrast, at 300 K, the NQEs become weaker and the above dynamical results converge very quickly even with 1 bead. Most importantly, the NQEs seriously affect the excited-state decay mechanism of o-HBI. At 50 and 100 K, most trajectories decay to the S0 state via perpendicular keto MECIs, whereas, at 300 K, only twisted keto MECIs are responsible for the excited-state decay. The present work not only comprehensively explores the temperature-dependent photoinduced dynamics of o-HBI, but also demonstrates the importance and necessity of NQEs in nonadiabatic dynamics simulations, especially at relatively low temperatures.
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Affiliation(s)
- Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Sheng-Rui Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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2
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London N, Limbu DK, Momeni MR, Shakib FA. DL_POLY Quantum 2.0: A modular general-purpose software for advanced path integral simulations. J Chem Phys 2024; 160:132501. [PMID: 38557837 DOI: 10.1063/5.0197822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
DL_POLY Quantum 2.0, a vastly expanded software based on DL_POLY Classic 1.10, is a highly parallelized computational suite written in FORTRAN77 with a modular structure for incorporating nuclear quantum effects into large-scale/long-time molecular dynamics simulations. This is achieved by presenting users with a wide selection of state-of-the-art dynamics methods that utilize the isomorphism between a classical ring polymer and Feynman's path integral formalism of quantum mechanics. The flexible and user-friendly input/output handling system allows the control of methodology, integration schemes, and thermostatting. DL_POLY Quantum is equipped with a module specifically assigned for calculating correlation functions and printing out the values for sought-after quantities, such as dipole moments and center-of-mass velocities, with packaged tools for calculating infrared absorption spectra and diffusion coefficients.
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Affiliation(s)
- Nathan London
- Division of Energy, Matter and Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA
| | - Dil K Limbu
- Division of Energy, Matter and Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Mohammad R Momeni
- Division of Energy, Matter and Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA
| | - Farnaz A Shakib
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
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3
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Mutsuji A, Saita K, Maeda S. An energy decomposition and extrapolation scheme for evaluating electron transfer rate constants: a case study on electron self-exchange reactions of transition metal complexes. RSC Adv 2023; 13:32097-32103. [PMID: 37920761 PMCID: PMC10619204 DOI: 10.1039/d3ra05784d] [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: 08/24/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
A simple approach to the analysis of electron transfer (ET) reactions based on energy decomposition and extrapolation schemes is proposed. The present energy decomposition and extrapolation-based electron localization (EDEEL) method represents the diabatic energies for the initial and final states using the adiabatic energies of the donor and acceptor species and their complex. A scheme for the efficient estimation of ET rate constants is also proposed. EDEEL is semi-quantitative by directly evaluating the seam-of-crossing region of two diabatic potentials. In a numerical test, EDEEL successfully provided ET rate constants for electron self-exchange reactions of thirteen transition metal complexes with reasonable accuracy. In addition, its energy decomposition and extrapolation schemes provide all the energy values required for activation-strain model (ASM) analysis. The ASM analysis using EDEEL provided rational interpretations of the variation of the ET rate constants as a function of the transition metal complexes. These results suggest that EDEEL is useful for efficiently evaluating ET rate constants and obtaining a rational understanding of their magnitudes.
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Affiliation(s)
- Akihiro Mutsuji
- Graduate School of Chemical Sciences and Engineering, Hokkaido University Sapporo Hokkaido 060-8628 Japan
| | - Kenichiro Saita
- Department of Chemistry, Graduate School of Science, Hokkaido University Sapporo Hokkaido 060-0810 Japan
| | - Satoshi Maeda
- Department of Chemistry, Graduate School of Science, Hokkaido University Sapporo Hokkaido 060-0810 Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Sapporo Hokkaido 001-0021 Japan
- ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Hokkaido University Sapporo Hokkaido 060-0810 Japan
- Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS) Tsukuba Ibaraki 305-0044 Japan
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4
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Bañuelos JL, Borguet E, Brown GE, Cygan RT, DeYoreo JJ, Dove PM, Gaigeot MP, Geiger FM, Gibbs JM, Grassian VH, Ilgen AG, Jun YS, Kabengi N, Katz L, Kubicki JD, Lützenkirchen J, Putnis CV, Remsing RC, Rosso KM, Rother G, Sulpizi M, Villalobos M, Zhang H. Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment. Chem Rev 2023; 123:6413-6544. [PMID: 37186959 DOI: 10.1021/acs.chemrev.2c00130] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.
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Affiliation(s)
- José Leobardo Bañuelos
- Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Eric Borguet
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Gordon E Brown
- Department of Earth and Planetary Sciences, The Stanford Doerr School of Sustainability, Stanford University, Stanford, California 94305, United States
| | - Randall T Cygan
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843, United States
| | - James J DeYoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Patricia M Dove
- Department of Geosciences, Department of Chemistry, Department of Materials Science and Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France
| | - Franz M Geiger
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2Canada
| | - Vicki H Grassian
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, United States
| | - Anastasia G Ilgen
- Geochemistry Department, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Young-Shin Jun
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Nadine Kabengi
- Department of Geosciences, Georgia State University, Atlanta, Georgia 30303, United States
| | - Lynn Katz
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Kubicki
- Department of Earth, Environmental & Resource Sciences, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Johannes Lützenkirchen
- Karlsruher Institut für Technologie (KIT), Institut für Nukleare Entsorgung─INE, Eggenstein-Leopoldshafen 76344, Germany
| | - Christine V Putnis
- Institute for Mineralogy, University of Münster, Münster D-48149, Germany
| | - Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Kevin M Rosso
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Gernot Rother
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Marialore Sulpizi
- Department of Physics, Ruhr Universität Bochum, NB6, 65, 44780, Bochum, Germany
| | - Mario Villalobos
- Departamento de Ciencias Ambientales y del Suelo, LANGEM, Instituto De Geología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Huichun Zhang
- Department of Civil and Environmental Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
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Reese DL, Steele RP. Molecular Motion in the Interconverting σ-H 2, Di-, and Tri-hydride Regimes: Mo(PH3)5H2. J Phys Chem A 2022; 126:6834-6848. [PMID: 36154020 DOI: 10.1021/acs.jpca.2c03397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The transition-metal complex Mo(PH3)5H2 is known to exist in three possible isomeric forms, including a nonclassical, σ-bound dihydrogen complex and two classical dihydride isomers. As such, it has served as a model complex for the energies of conversion between these limiting structural regimes. In the present study, ab initio molecular dynamics computer simulations, combined with enhanced sampling techniques, were utilized to directly assess the degree of motion and isomerization of the dihydrogen/dihydride moieties in this complex. Ligand rotations (for both the H2 unit and the phosphine units) were found to be dominant in the low-temperature (298 K) regime, and the classical thermodynamic distribution showed no probability of thermally accessing dihydride forms, although unrestrained molecular dynamics trajectories showed fleeting configurations outside of the σ-H2 configuration. Simulations at higher temperatures surprisingly revealed new tri-hydride isomers that are energetically competitive with the σ-H2 and cis-/trans-dihydride isomers. Low-energy pathways to hydrogen/hydride transfer and phosphine dissociation were readily accessible, which considerably expands the known isomeric flexibility of this complex.
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Affiliation(s)
- Diana L Reese
- Department of Chemistry and Biochemistry, Utah Tech University, 225 South University Avenue, St. George, Utah 84770, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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6
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Ananth N. Path Integrals for Nonadiabatic Dynamics: Multistate Ring Polymer Molecular Dynamics. Annu Rev Phys Chem 2022; 73:299-322. [PMID: 35081325 DOI: 10.1146/annurev-physchem-082620-021809] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review focuses on a recent class of path-integral-based methods that simulate nonadiabatic dynamics in the condensed phase using only classical molecular dynamics trajectories in an extended phase space. Specifically, a semiclassical mapping protocol is used to derive an exact, continuous, Cartesian variable path-integral representation for the canonical partition function of a system in which multiple electronic states are coupled to nuclear degrees of freedom. Building on this exact statistical foundation, multistate ring polymer molecular dynamics methods are developed for the approximate calculation of real-time thermal correlation functions. The remarkable promise of these multistate ring polymer methods, their successful applications, and their limitations are discussed in detail.Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Nandini Ananth
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA;
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7
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Thakurta S, Maiti M, Rosair GM, Kuznetsov A. A Rare Angular Trinuclear Mixed Valence Cobalt(III-II-III) Complex With Azido Bridges And Salpn-Type Schiff-Base Ligand: Synthesis, Crystal Structure And DFT Study. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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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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9
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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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10
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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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11
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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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