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Yuan S, Han X, Zhang J, Xie Z, Fan C, Xiao Y, Gao YQ, Yang YI. Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms Using Molecular Configuration Transformer. J Phys Chem A 2024; 128:4378-4390. [PMID: 38759697 DOI: 10.1021/acs.jpca.4c01267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical calculations is the most commonly used method. However, this way is heavily dependent on individual experience and chemical intuition. In our previous study, we proposed a research paradigm that used enhanced sampling in molecular dynamics simulations to study chemical reactions. This approach can directly simulate the entire process of a chemical reaction. However, the computational speed limited the use of high-precision potential energy functions for simulations. To address this issue, we presented a scheme for training high-precision force fields for molecular modeling using a previously developed graph-neural-network-based molecular model, molecular configuration transformer. This potential energy function allowed for highly accurate simulations at a low computational cost, leading to more precise calculations of the mechanism of chemical reactions. We applied this approach to study a Claisen rearrangement reaction and a carbonyl insertion reaction catalyzed by manganese.
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Affiliation(s)
- Sihao Yuan
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xu Han
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jun Zhang
- Changping Laboratory, Beijing 102200, China
| | - Zhaoxin Xie
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Cheng Fan
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yunlong Xiao
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
- Changping Laboratory, Beijing 102200, China
| | - Yi Isaac Yang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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2
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Lei YK, Zhang Z, Han X, Yang YI, Zhang J, Gao YQ. Locating Transition Zone in Phase Space. J Chem Theory Comput 2022; 18:6124-6133. [PMID: 36135927 DOI: 10.1021/acs.jctc.2c00385] [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
Understanding the reaction mechanism is required for better control of chemical reactions and is usually achieved by locating transition states (TSs) along a proper one-dimensional coordinate called reaction coordinate (RC). The identification of RC can be very difficult for high-dimensional realistic systems. A number of methods have been proposed to tackle this problem. A machine learning method is developed here to incorporate the influence of velocity on the reaction process. The method is also free of the unbalanced label problem resulting from the rather low fraction of configurations near the TS and can be easily extended to large systems. It locates the transition zone in the phase space and defines the dividing surface with a high transmission coefficient. Moreover, considering that the reaction environment can not only change the reaction path but also activate the reactive mode through energy transfer, we devise two measures to quantify the influence of these two factors on the reaction process and find that solvents can assist the reaction by directly doing work along the reactive mode. Not surprisingly, there is a positive correlation between the efficiency of energy transfer into the reactive mode and the reaction rate.
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Affiliation(s)
- Yao-Kun Lei
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
| | - Zhen Zhang
- School of Physics and Technology, Tangshan Normal University, 063000 Tangshan, China
| | - Xu Han
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
| | - Yi Isaac Yang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China
| | - Jun Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, 100871 Beijing, China
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3
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Huang Y, Xia Y, Yang L, Wei J, Yang YI, Gao YQ. SPONGE
: A
GPU‐Accelerated
Molecular Dynamics Package with Enhanced Sampling and
AI‐Driven
Algorithms. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yu‐Peng Huang
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Biomedical Pioneering Innovation Center Peking University Beijing 100871 China
| | - Yijie Xia
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Biomedical Pioneering Innovation Center Peking University Beijing 100871 China
| | - Lijiang Yang
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Biomedical Pioneering Innovation Center Peking University Beijing 100871 China
- Beijing Advanced Innovation Center for Genomics Peking University Beijing 100871 China
| | - Jiachen Wei
- State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics Chinese Academy of Sciences Beijing 100190 China
- Shenzhen Bay Laboratory, Gaoke Innovation Center, Guangqiao Road, Guangming District Shenzhen Guangdong 518132 China
| | - Yi Isaac Yang
- Shenzhen Bay Laboratory, Gaoke Innovation Center, Guangqiao Road, Guangming District Shenzhen Guangdong 518132 China
| | - Yi Qin Gao
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Biomedical Pioneering Innovation Center Peking University Beijing 100871 China
- Beijing Advanced Innovation Center for Genomics Peking University Beijing 100871 China
- Shenzhen Bay Laboratory, Gaoke Innovation Center, Guangqiao Road, Guangming District Shenzhen Guangdong 518132 China
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4
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Besalú-Sala P, Solà M, Luis JM, Torrent-Sucarrat M. Fast and Simple Evaluation of the Catalysis and Selectivity Induced by External Electric Fields. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Pau Besalú-Sala
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | - Josep M. Luis
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Euskadi, Spain
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Euskadi, Spain
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5
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Gera R, Bakker HJ, Franklin-Mergarejo R, Morzan UN, Falciani G, Bergamasco L, Versluis J, Sen I, Dante S, Chiavazzo E, Hassanali AA. Emergence of Electric Fields at the Water-C12E6 Surfactant Interface. J Am Chem Soc 2021; 143:15103-15112. [PMID: 34498857 DOI: 10.1021/jacs.1c05112] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We study the properties of the interface of water and the surfactant hexaethylene glycol monododecyl ether (C12E6) with a combination of heterodyne-detected vibrational sum frequency generation (HD-VSFG), Kelvin-probe measurements, and molecular dynamics (MD) simulations. We observe that the addition of the hydrogen-bonding surfactant C12E6, close to the critical micelle concentration (CMC), induces a drastic enhancement in the hydrogen bond strength of the water molecules close to the interface, as well as a flip in their net orientation. The mutual orientation of the water and C12E6 molecules leads to the emergence of a broad (∼3 nm) interface with a large electric field of ∼1 V/nm, as evidenced by the Kelvin-probe measurements and MD simulations. Our findings may open the door for the design of novel electric-field-tuned catalytic and light-harvesting systems anchored at the water-surfactant-air interface.
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Affiliation(s)
- Rahul Gera
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Huib J Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | | | - Uriel N Morzan
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Gabriele Falciani
- Energy Department, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Luca Bergamasco
- Energy Department, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Jan Versluis
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Indraneel Sen
- Uppsala University, Laegerhyddsvaegen 1, 751 20 Uppsala, Sweden
| | - Silvia Dante
- Materials Characterization Facility, Italian Institute of Technology, 16163 Genoa, Italy
| | - Eliodoro Chiavazzo
- Energy Department, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Ali A Hassanali
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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6
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Joy J, Stuyver T, Shaik S. Oriented External Electric Fields and Ionic Additives Elicit Catalysis and Mechanistic Crossover in Oxidative Addition Reactions. J Am Chem Soc 2020; 142:3836-3850. [DOI: 10.1021/jacs.9b11507] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Jyothish Joy
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Thijs Stuyver
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Algemene Chemie, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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7
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Li W, Wang N, Cao Y, Tang X, Dong C. A robust immobilization strategy in the nano-dispersed Ziegler–Natta catalyst: non-covalent O–Ti coordination. Chem Commun (Camb) 2020; 56:10843-10846. [DOI: 10.1039/d0cc04502k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A robust non-covalent O–Ti bond facilitates the synthesis of polyethylene with a narrow distribution.
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Affiliation(s)
- Wei Li
- Ningbo Key Laboratory of Specialty Polymers
- School of Material Science and Chemical Engineering
- Ningbo University
- Ningbo
- P. R. China
| | - Ning Wang
- Ningbo Key Laboratory of Specialty Polymers
- School of Material Science and Chemical Engineering
- Ningbo University
- Ningbo
- P. R. China
| | - Yu Cao
- Ningbo Key Laboratory of Specialty Polymers
- School of Material Science and Chemical Engineering
- Ningbo University
- Ningbo
- P. R. China
| | - Xin Tang
- Ningbo Key Laboratory of Specialty Polymers
- School of Material Science and Chemical Engineering
- Ningbo University
- Ningbo
- P. R. China
| | - Chuanding Dong
- Department of Physics
- Paderborn University, Warburger Strasse 100
- 33098 Paderborn
- Germany
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8
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Yang YI, Shao Q, Zhang J, Yang L, Gao YQ. Enhanced sampling in molecular dynamics. J Chem Phys 2019; 151:070902. [PMID: 31438687 DOI: 10.1063/1.5109531] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Although molecular dynamics simulations have become a useful tool in essentially all fields of chemistry, condensed matter physics, materials science, and biology, there is still a large gap between the time scale which can be reached in molecular dynamics simulations and that observed in experiments. To address the problem, many enhanced sampling methods were introduced, which effectively extend the time scale being approached in simulations. In this perspective, we review a variety of enhanced sampling methods. We first discuss collective-variables-based methods including metadynamics and variationally enhanced sampling. Then, collective variable free methods such as parallel tempering and integrated tempering methods are presented. At last, we conclude with a brief introduction of some newly developed combinatory methods. We summarize in this perspective not only the theoretical background and numerical implementation of these methods but also the new challenges and prospects in the field of the enhanced sampling.
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Affiliation(s)
- Yi Isaac Yang
- Institute of Systems Biology, Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong, China
| | - Qiang Shao
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jun Zhang
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, Berlin 14195, Germany
| | - Lijiang Yang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Institute of Systems Biology, Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong, China
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