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Lin K, Peng J, Xu C, Gu FL, Lan Z. Trajectory Propagation of Symmetrical Quasi-classical Dynamics with Meyer-Miller Mapping Hamiltonian Using Machine Learning. J Phys Chem Lett 2022; 13:11678-11688. [PMID: 36511563 DOI: 10.1021/acs.jpclett.2c02159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The long short-term memory recurrent neural network (LSTM-RNN) approach is applied to realize the trajectory-based nonadiabatic dynamics within the framework of the symmetrical quasi-classical dynamics method based on the Meyer-Miller mapping Hamiltonian (MM-SQC). After construction, the LSTM-RNN model allows us to propagate the entire trajectory evolutions of all involved degrees of freedoms (DOFs) from initial conditions. The proposed idea is proven to be reliable and accurate in the simulations of the dynamics of several site-exciton electron-phonon coupling models and three Tully's scattering models. It indicates that the LSTM-RNN model perfectly captures the dynamical information on the trajectory evolution in the MM-SQC dynamics. Our work proposes a novel machine learning approach in the simulation of trajectory-based nonadiabatic dynamic of complex systems with a large number of DOFs.
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Affiliation(s)
- Kunni Lin
- School of Chemistry, South China Normal University, Guangzhou 510006, P. R. China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China
| | - Jiawei Peng
- School of Chemistry, South China Normal University, Guangzhou 510006, P. R. China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China
- 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
| | - Feng Long Gu
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China
- 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, South China Normal University, Guangzhou 510006, P. R. China
- 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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Du W, Yang X, Wu D, Ma F, Zhang B, Bao C, Huo Y, Jiang J, Chen X, Wang Y. Fusing 2D and 3D molecular graphs as unambiguous molecular descriptors for conformational and chiral stereoisomers. Brief Bioinform 2022; 24:6931719. [PMID: 36528804 PMCID: PMC9851338 DOI: 10.1093/bib/bbac560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/28/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022] Open
Abstract
The rapid progress of machine learning (ML) in predicting molecular properties enables high-precision predictions being routinely achieved. However, many ML models, such as conventional molecular graph, cannot differentiate stereoisomers of certain types, particularly conformational and chiral ones that share the same bonding connectivity but differ in spatial arrangement. Here, we designed a hybrid molecular graph network, Chemical Feature Fusion Network (CFFN), to address the issue by integrating planar and stereo information of molecules in an interweaved fashion. The three-dimensional (3D, i.e., stereo) modality guarantees precision and completeness by providing unabridged information, while the two-dimensional (2D, i.e., planar) modality brings in chemical intuitions as prior knowledge for guidance. The zipper-like arrangement of 2D and 3D information processing promotes cooperativity between them, and their synergy is the key to our model's success. Experiments on various molecules or conformational datasets including a special newly created chiral molecule dataset comprised of various configurations and conformations demonstrate the superior performance of CFFN. The advantage of CFFN is even more significant in datasets made of small samples. Ablation experiments confirm that fusing 2D and 3D molecular graphs as unambiguous molecular descriptors can not only effectively distinguish molecules and their conformations, but also achieve more accurate and robust prediction of quantum chemical properties.
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Affiliation(s)
- Wenjie Du
- School of Software Engineering, University of Science and Technology of China, Hefei 230026, China,Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Xiaoting Yang
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China,School of Computer Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Di Wu
- School of Software Engineering, University of Science and Technology of China, Hefei 230026, China,Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - FenFen Ma
- Suzhou Laboratory , Suzhou 215123, Jiangsu, China
| | - Baicheng Zhang
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Chaochao Bao
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Yaoyuan Huo
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Jun Jiang
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Xin Chen
- Corresponding authors: Yang Wang, School of Software Engineering, University of Science and Technology of China, Hefei 230026, China. E-mail: ; Xin Chen, Suzhou Laboratory, Suzhou 215123, Jiangsu, China. E-mail:
| | - Yang Wang
- Corresponding authors: Yang Wang, School of Software Engineering, University of Science and Technology of China, Hefei 230026, China. E-mail: ; Xin Chen, Suzhou Laboratory, Suzhou 215123, Jiangsu, China. E-mail:
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Tang D, Jia L, Shen L, Fang WH. Fewest-Switches Surface Hopping with Long Short-Term Memory Networks. J Phys Chem Lett 2022; 13:10377-10387. [PMID: 36317657 DOI: 10.1021/acs.jpclett.2c02299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The mixed quantum-classical dynamical simulation is essential for studying nonadiabatic phenomena in photophysics and photochemistry. In recent years, many machine learning models have been developed to accelerate the time evolution of the nuclear subsystem. Herein, we implement long short-term memory (LSTM) networks as a propagator to accelerate the time evolution of the electronic subsystem during the fewest-switches surface hopping (FSSH) simulations. A small number of reference trajectories are generated using the original FSSH method, and then the LSTM networks can be built, accompanied by careful examination of typical LSTM-FSSH trajectories that employ the same initial condition and random numbers as the corresponding reference. The constructed network is applied to FSSH to further produce a trajectory ensemble to reveal the mechanism of nonadiabatic processes. Taking Tully's three models as test systems, we qualitatively reproduced the collective results. This work demonstrates that LSTM can be applied to the most popular surface hopping simulations.
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Affiliation(s)
- Diandong Tang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Luyang Jia
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lin Shen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
- Yantai-Jingshi Institute of Material Genome Engineering, Yantai 265505, Shandong, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
- Yantai-Jingshi Institute of Material Genome Engineering, Yantai 265505, Shandong, China
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Lin K, Peng J, Xu C, Gu FL, Lan Z. Automatic Evolution of Machine-Learning-Based Quantum Dynamics with Uncertainty Analysis. J Chem Theory Comput 2022; 18:5837-5855. [DOI: 10.1021/acs.jctc.2c00702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kunni Lin
- School of Chemistry, South China Normal University, Guangzhou510006, P. R. China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou510006, P. R. China
| | - Jiawei Peng
- School of Chemistry, South China Normal University, Guangzhou510006, P. R. China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou510006, P. R. China
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou510006, P. R. China
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou510006, P. R. China
| | - Feng Long Gu
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou510006, P. R. China
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou510006, P. R. China
| | - Zhenggang Lan
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou510006, P. R. China
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou510006, P. R. China
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Hu Z, Sun X. All-Atom Nonadiabatic Semiclassical Mapping Dynamics for Photoinduced Charge Transfer of Organic Photovoltaic Molecules in Explicit Solvents. J Chem Theory Comput 2022; 18:5819-5836. [PMID: 36073792 DOI: 10.1021/acs.jctc.2c00631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Direct all-atom simulation of nonadiabatic dynamics in disordered condensed phases like liquid solutions and amorphous solids has been challenging. The first all-atom simulation of the photoinduced charge-transfer dynamics of a prototypical organic photovoltaic carotenoid-porphyrin-C60 molecular triad in explicit tetrahydrofuran is presented. Based on the Meyer-Miller mapping Hamiltonian, various semiclassical and mixed quantum-classical dynamics are employed, including the linearized semiclassical, symmetrical quasiclassical, mean-field Ehrenfest, classical mapping model, and spin-mapping model approaches. The all-atom nonadiabatic dynamics were compared to multi-state harmonic models with a globally shared bath, and the models built using the ensemble averages on the initial electronic state could reproduce the all-atom results. The solvent effect was found to be critical for the photoinduced charge transfer, and the time-dependent solute-solvent radial distribution functions revealed that only the nonadiabatic dynamics started with the effective forces on the initial electronic state could capture the correct nuclear dynamics. The proposed strategy for modeling condensed-phase nonadiabatic dynamics with atomistic details is readily applied to complex condensed-phase systems.
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Affiliation(s)
- Zhubin Hu
- Division of Arts and Sciences, New York University Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry, New York University Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Xiang Sun
- Division of Arts and Sciences, New York University Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry, New York University Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
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Abstract
Nonadiabatic quantum dynamics is important for understanding light-harvesting processes, but its propagation with traditional methods can be rather expensive. Here we present a one-shot trajectory learning approach that allows us to directly make an ultrafast prediction of the entire trajectory of the reduced density matrix for a new set of such simulation parameters as temperature and reorganization energy. The whole 10-ps-long propagation takes 70 ms as we demonstrate on the comparatively large quantum system, the Fenna-Matthews-Olsen (FMO) complex. Our approach also significantly reduces time and memory requirements for training.
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Affiliation(s)
- Arif Ullah
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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