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| Main Authors: | , , , , , , , |
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| Format: | Preprint |
| Published: |
2023
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2401.00499 |
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| _version_ | 1866917636704567296 |
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| author | Yuan, Sihao Han, Xu Zhang, Jun Xie, Zhaoxin Fan, Cheng Xiao, Yunlong Gao, Yi Qin Yang, Yi Isaac |
| author_facet | Yuan, Sihao Han, Xu Zhang, Jun Xie, Zhaoxin Fan, Cheng Xiao, Yunlong Gao, Yi Qin Yang, Yi Isaac |
| contents | 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 uses 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 limits the use of high-precision potential energy functions for simulations. To address this issue, we present 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 allows 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2401_00499 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms using Molecular Configuration Transformer Yuan, Sihao Han, Xu Zhang, Jun Xie, Zhaoxin Fan, Cheng Xiao, Yunlong Gao, Yi Qin Yang, Yi Isaac Chemical Physics Soft Condensed Matter Artificial Intelligence 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 uses 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 limits the use of high-precision potential energy functions for simulations. To address this issue, we present 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 allows 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. |
| title | Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms using Molecular Configuration Transformer |
| topic | Chemical Physics Soft Condensed Matter Artificial Intelligence |
| url | https://arxiv.org/abs/2401.00499 |