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Shakiba M, Philips AB, Autschbach J, Akimov AV. Machine Learning Mapping Approach for Computing Spin Relaxation Dynamics. J Phys Chem Lett 2024:153-162. [PMID: 39707977 DOI: 10.1021/acs.jpclett.4c03293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2024]
Abstract
In this work, a machine learning mapping approach for predicting the properties of atomistic systems is reported. Within this approach, the atomic orbital overlap, density, or Kohn-Sham (KS) Fock matrix elements obtained at a low level of theory such as extended tight-binding have been used as input features to predict the electric field gradient (EFG) tensors at a higher level of theory such as those obtained with hybrid functionals. It is shown that the machine-learning-predicted EFG tensors can be used to compute spin relaxation rates of several ions in aqueous solutions. From only a fraction of data used in direct calculation, one can predict the quadrupolar isotropic spin relaxation rates with good accuracy, achieving relative errors between about 2-8% for different ions.
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Affiliation(s)
- Mohammad Shakiba
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Adam B Philips
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Alexey V Akimov
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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2
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Li Z, Zhang C, Shen Y, Wang L. Quasi-Diabatization Based on Minimizing Derivative Couplings in a Limited Configuration Space: Elimination of Boundary Condition Dependence. J Phys Chem Lett 2024; 15:10544-10553. [PMID: 39401127 DOI: 10.1021/acs.jpclett.4c02557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Due to the cuspidal ridges of adiabatic potential energy surfaces (PESs) and singularities of nonadiabatic couplings (NACs), obtaining an analytical expression for the adiabatic Hamiltonian is difficult. Thereby, nonadiabatic dynamics simulations are often carried out on-the-fly, which is time-consuming. This motivates us to construct quasi-diabatic representations, which have smooth PESs and diabatic couplings. In this study, we propose a new quasi-diabatization method based on minimizing derivative couplings (MDC) in a limited configuration space. The boundary conditions are first considered and finally released to obtain the adiabatic-to-diabatic rotation angles and transformation matrices. As demonstrated in representative one- and two-dimensional models and the widely studied linear H3 molecule, MDC performs significantly better than the direct integration quasi-diabatization approach. In particular, accurate diabatic potential energy matrices have been successfully obtained even when the NACs of all configurations in the considered space are nonnegligible.
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Affiliation(s)
- Zhaoyong Li
- Zhejiang Key Laboratory of Excited-State Energy Conversion and Energy Storage, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Chaoqun Zhang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Yifan Shen
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Linjun Wang
- Zhejiang Key Laboratory of Excited-State Energy Conversion and Energy Storage, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
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3
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Zhu Y, Peng J, Xu C, Lan Z. Unsupervised Machine Learning in the Analysis of Nonadiabatic Molecular Dynamics Simulation. J Phys Chem Lett 2024; 15:9601-9619. [PMID: 39270134 DOI: 10.1021/acs.jpclett.4c01751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
The all-atomic full-dimensional-level simulations of nonadiabatic molecular dynamics (NAMD) in large realistic systems has received high research interest in recent years. However, such NAMD simulations normally generate an enormous amount of time-dependent high-dimensional data, leading to a significant challenge in result analyses. Based on unsupervised machine learning (ML) methods, considerable efforts were devoted to developing novel and easy-to-use analysis tools for the identification of photoinduced reaction channels and the comprehensive understanding of complicated molecular motions in NAMD simulations. Here, we tried to survey recent advances in this field, particularly to focus on how to use unsupervised ML methods to analyze the trajectory-based NAMD simulation results. Our purpose is to offer a comprehensive discussion on several essential components of this analysis protocol, including the selection of ML methods, the construction of molecular descriptors, the establishment of analytical frameworks, their advantages and limitations, and persistent challenges.
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Affiliation(s)
- Yifei Zhu
- MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Jiawei Peng
- MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Zhenggang Lan
- MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
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Zhang Q, Shao X, Li W, Mi W, Pavanello M, Akimov AV. Nonadiabatic molecular dynamics with subsystem density functional theory: application to crystalline pentacene. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:385901. [PMID: 38866023 DOI: 10.1088/1361-648x/ad577d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/12/2024] [Indexed: 06/14/2024]
Abstract
In this work, we report the development and assessment of the nonadiabatic molecular dynamics approach with the electronic structure calculations based on the linearly scaling subsystem density functional method. The approach is implemented in an open-source embedded Quantum Espresso/Libra software specially designed for nonadiabatic dynamics simulations in extended systems. As proof of the applicability of this method to large condensed-matter systems, we examine the dynamics of nonradiative relaxation of excess excitation energy in pentacene crystals with the simulation supercells containing more than 600 atoms. We find that increased structural disorder observed in larger supercell models induces larger nonadiabatic couplings of electronic states and accelerates the relaxation dynamics of excited states. We conduct a comparative analysis of several quantum-classical trajectory surface hopping schemes, including two new methods proposed in this work (revised decoherence-induced surface hopping and instantaneous decoherence at frustrated hops). Most of the tested schemes suggest fast energy relaxation occurring with the timescales in the 0.7-2.0 ps range, but they significantly overestimate the ground state recovery rates. Only the modified simplified decay of mixing approach yields a notably slower relaxation timescales of 8-14 ps, with a significantly inhibited ground state recovery.
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Affiliation(s)
- Qingxin Zhang
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, United States of America
| | - Xuecheng Shao
- Department of Physics, Rutgers University, The State University of New Jersey, Newark, NJ 07102, United States of America
| | - Wei Li
- School of Chemistry and Materials Science, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Wenhui Mi
- Key Laboratory of Material Simulation Methods & Software of Ministry of Education, College of Physics, Jilin University, Changchun 130012, People's Republic of China
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Michele Pavanello
- Department of Physics, Rutgers University, The State University of New Jersey, Newark, NJ 07102, United States of America
| | - Alexey V Akimov
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, United States of America
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5
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Shakiba M, Akimov AV. Machine-Learned Kohn-Sham Hamiltonian Mapping for Nonadiabatic Molecular Dynamics. J Chem Theory Comput 2024; 20:2992-3007. [PMID: 38581699 DOI: 10.1021/acs.jctc.4c00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2024]
Abstract
In this work, we report a simple, efficient, and scalable machine-learning (ML) approach for mapping non-self-consistent Kohn-Sham Hamiltonians constructed with one kind of density functional to the nearly self-consistent Hamiltonians constructed with another kind of density functional. This approach is designed as a fast surrogate Hamiltonian calculator for use in long nonadiabatic dynamics simulations of large atomistic systems. In this approach, the input and output features are Hamiltonian matrices computed from different levels of theory. We demonstrate that the developed ML-based Hamiltonian mapping method (1) speeds up the calculations by several orders of magnitude, (2) is conceptually simpler than alternative ML approaches, (3) is applicable to different systems and sizes and can be used for mapping Hamiltonians constructed with arbitrary density functionals, (4) requires a modest training data, learns fast, and generates molecular orbitals and their energies with the accuracy nearly matching that of conventional calculations, and (5) when applied to nonadiabatic dynamics simulation of excitation energy relaxation in large systems yields the corresponding time scales within the margin of error of the conventional calculations. Using this approach, we explore the excitation energy relaxation in C60 fullerene and Si75H64 quantum dot structures and derive qualitative and quantitative insights into dynamics in these systems.
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Affiliation(s)
- Mohammad Shakiba
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Alexey V Akimov
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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Akimov AV. Energy-Conserving and Thermally Corrected Neglect of Back-Reaction Approximation Method for Nonadiabatic Molecular Dynamics. J Phys Chem Lett 2023; 14:11673-11683. [PMID: 38109379 DOI: 10.1021/acs.jpclett.3c03029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
In this work, the energy-conserving and thermally corrected neglect of the back-reaction approximation approach for nonadiabatic molecular dynamics in extended atomistic systems is developed. The new approach introduces three key corrections to the original method: (1) it enforces the total energy conservation, (2) it introduces an explicit coupling of the system to its environment, and (3) it introduces a renormalization of nonadiabatic couplings to account for a difference between the instantaneous nuclear kinetic energy and the kinetic energy of guiding trajectories. In the new approach, an auxiliary kinetic energy variable is introduced as an independent dynamical variable. The new approach produces nonzero equilibrium populations, whereas the original neglect of the back-reaction approximation method does not. It yields population relaxation time scales that are favorably comparable to the reference values, and it introduces an explicit and controllable way of dissipating energy into a bath without an assumption of the bath being at equilibrium.
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Affiliation(s)
- Alexey V Akimov
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260 United States
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Lei Y, Xie X, Ma H, Ma J. Vitality of Intralayer Vibration in hBN for Effective Long-Range Interlayer Hole Transfer across High Barriers in MoSe 2/hBN/WSe 2 Heterostructures. J Phys Chem Lett 2023:11190-11199. [PMID: 38055859 DOI: 10.1021/acs.jpclett.3c03040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Introducing the two-dimensional (2D) hexagonal boron nitride (hBN) between 2D transition metal dichalcogenide (TMD) layers promises convenient manipulation of the interlayer exciton (IX) and interlayer charge transfer in TMD/hBN/TMD heterostructures, while the role of inserted hBN layers during IX formation is controversial. Employing ab initio nonadiabatic molecular dynamics (NAMD) simulations and the electron-phonon coupling model, we systematically investigate interlayer hole transfer in MoSe2/WSe2 bilayers intercalated by hBN layers with various thicknesses. The conventional direct hole transfer from MoSe2 to WSe2 is decelerated by 2-3 orders of magnitude after the hBN insertion. Meanwhile, a novel channel intermediated by a deeper hole of WSe2 becomes dominant, where the intralayer shear mode of hBN plays a crucial role by reducing the energy barriers for this new channel. The unique role of hBN layers is revealed for the first time, enriching the knowledge of the underlying microscopic mechanisms and providing instructive guidance to practical van der Waals optoelectronic devices.
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Affiliation(s)
- Yuli Lei
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiaoyu Xie
- Qingdao Institute for Theoretical and Computational Sciences, Qingdao Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
| | - Haibo Ma
- Qingdao Institute for Theoretical and Computational Sciences, Qingdao Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Wang B, Wu Y, Liu D, Vasenko AS, Casanova D, Prezhdo OV. Efficient Modeling of Quantum Dynamics of Charge Carriers in Materials Using Short Nonequilibrium Molecular Dynamics. J Phys Chem Lett 2023; 14:8289-8295. [PMID: 37681642 PMCID: PMC10518862 DOI: 10.1021/acs.jpclett.3c02187] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 09/05/2023] [Indexed: 09/09/2023]
Abstract
Nonadiabatic molecular dynamics provides essential insights into excited-state processes, but it is computationally intense and simplifications are needed. The classical path approximation provides critical savings. Still, long heating and equilibration steps are required. We demonstrate that practical results can be obtained with short, partially equilibrated ab initio trajectories. Once the system's structure is adequate and essential fluctuations are sampled, the nonadiabatic Hamiltonian can be constructed. Local structures require only 1-2 ps trajectories, as demonstrated with point defects in metal halide perovskites. Short trajectories represent anharmonic motions common in defective structures, an essential improvement over the harmonic approximation around the optimized geometry. Glassy systems, such as grain boundaries, require different simulation protocols, e.g., involving machine learning force fields. 10-fold shorter trajectories generate 10-20% time scale errors, which are acceptable, given experimental uncertainties and other approximations. The practical NAMD protocol enables fast screening of excited-state dynamics for rapid exploration of new materials.
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Affiliation(s)
- Bipeng Wang
- Department
of Chemical Engineering, University of Southern
California, Los Angeles, California 90089, United States
| | - Yifan Wu
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | | | - Andrey S. Vasenko
- HSE
University, 101000 Moscow, Russia
- Donostia
International Physics Center (DIPC), 20018 San Sebastián-Donostia, Euskadi, Spain
| | - David Casanova
- Donostia
International Physics Center (DIPC), 20018 San Sebastián-Donostia, Euskadi, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Euskadi, Spain
| | - Oleg V. Prezhdo
- Department
of Chemical Engineering, University of Southern
California, Los Angeles, California 90089, United States
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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Li W, Akimov AV. How Good Is the Vibronic Hamiltonian Repetition Approach for Long-Time Nonadiabatic Molecular Dynamics? J Phys Chem Lett 2022; 13:9688-9694. [PMID: 36218389 DOI: 10.1021/acs.jpclett.2c02765] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Multiple applied studies of slow nonadiabatic processes in nanoscale and condensed matter systems have adopted the "repetition" approximation in which long trajectories for such simulations are obtained by concatenating shorter trajectories, directly available from ab initio calculations, many times. Here, we comprehensively assess this approximation using model Hamiltonians with parameters covering a wide range of regimes. We find that state transition time scales may strongly depend on the length of the repeated data, although the convergence is not monotonic and may be slow. The repetition approach may under- or overestimate the time scales by a factor of ≤7-8, does not directly depend on the dispersion of energy gap and nonadiabatic coupling (NAC) frequencies, but may depend on the magnitude of the NACs. We suggest that the repetition-based nonadiabatic dynamics may be inaccurate in simulations with very small NACs, where intrinsic transition times are on the order of ≥100 ps.
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Affiliation(s)
- Wei Li
- School of Chemistry and Materials Science, Hunan Agricultural University, Changsha410128, China
| | - Alexey V Akimov
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York14260, United States
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Xie H, Xu X, Wang L, Zhuang W. Surface hopping dynamics in periodic solid-state materials with a linear vibronic coupling model. J Chem Phys 2022; 156:154116. [PMID: 35459287 DOI: 10.1063/5.0085759] [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 report a surface hopping approach in which the implemented linear vibronic coupling Hamiltonian is constructed and the electronic wavefunction is propagated in the reciprocal space. The parameters of the linear vibronic coupling model, including onsite energies, phonon frequencies, and electron-phonon couplings, are calculated with density-functional theory and density-functional perturbation theory and interpolated in fine sampling points of the Brillouin zone with maximally localized Wannier functions. Using this approach, we studied the relaxation dynamics of the photo-excited hot carrier in a one-dimensional periodic carbon chain. The results show that the completeness of the number of Hilbert space k points and the number of phonon q points plays an important role in the hot carrier relaxation processes. By calculating the relaxation times of hot carriers under different reciprocal space sampling and extrapolating with the stretched-compressed exponential function, the relaxation times of hot electrons and holes in the quasi-continuous energy band are obtained. By considering the feedback effect in the hopping processes and analyzing the time-dependent phonon energy in different normal modes, we found that the long-wave longitudinal optical phonons play a major role in the relaxation dynamics of hot electrons and holes. We, therefore, provided herein an efficient and accurate approach for modeling the photophysical processes in periodic solid-state material systems.
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Affiliation(s)
- Hua Xie
- Key Laboratory of Strongly-Coupled Quantum Matter Physics, Chinese Academy of Sciences, School of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaoliang Xu
- Key Laboratory of Strongly-Coupled Quantum Matter Physics, Chinese Academy of Sciences, School of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Linjun Wang
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
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Qiu J, Lu Y, Wang L. Multilayer Subsystem Surface Hopping Method for Large-Scale Nonadiabatic Dynamics Simulation with Hundreds of Thousands of States. J Chem Theory Comput 2022; 18:2803-2815. [PMID: 35380833 DOI: 10.1021/acs.jctc.2c00130] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a multilayer subsystem surface hopping (MSSH) method to deal with nonadiabatic dynamics in large-scale systems. A small subsystem instead of the full system is adopted for surface hopping and is updated on-the-fly to achieve a reliable description of important adiabatic states and the wave function evolution. Additional subsystems for molecular dynamics and statistical description are introduced to further improve the simulation reliability. The global flux hopping probabilities with optimal state assignments are utilized to treat the complex surface crossings. As demonstrated in a series of one- and two-dimensional Holstein models with up to hundreds of thousands of states, MSSH shows weak parameter dependence in all investigated systems. Especially, the computational costs are reduced by 2-6 orders of magnitude compared to traditional surface hopping simulations in full systems, and size-independent results are achieved with a large time-step size of 2-5 fs. The new method is compatible with different decoherence correction strategies and achieves a much better balance between efficiency and reliability, thus promising for applications in general charge and exciton dynamics simulations.
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Affiliation(s)
- Jing Qiu
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Yao Lu
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Linjun Wang
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
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