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Zhu Y, Peng J, Kang X, Xu C, Lan Z. The principal component analysis of the ring deformation in the nonadiabatic surface hopping dynamics. Phys Chem Chem Phys 2022; 24:24362-24382. [PMID: 36178471 DOI: 10.1039/d2cp03323b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The analysis of the leading active molecular motions in the on-the-fly trajectory surface hopping simulation provides the essential information to understand the geometric evolution in nonadiabatic dynamics. When the ring deformation is involved, the identification of the key active coordinates becomes challenging. A "hierarchical" protocol based on the dimensionality reduction and clustering approaches is proposed for the automatic analysis of the ring deformation in the nonadiabatic molecular dynamics. The representative system keto isocytosine is taken as the prototype to illustrate this protocol. The results indicate that the current hierarchical analysis protocol is a powerful way to clearly clarify both the major and minor active molecular motions of the ring distortion in nonadiabatic dynamics.
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Affiliation(s)
- Yifei Zhu
- 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. .,MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China
| | - Jiawei Peng
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.,School of Chemistry, South China Normal University, Guangzhou 510006, P. R. China
| | - Xu Kang
- 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. .,MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China
| | - Chao Xu
- 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. .,MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China
| | - Zhenggang Lan
- 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. .,MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China
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Li J, Lopez SA. Excited-State Distortions Promote the Photochemical 4π-Electrocyclizations of Fluorobenzenes via Machine Learning Accelerated Photodynamics Simulations. Chemistry 2022; 28:e202200651. [PMID: 35474348 DOI: 10.1002/chem.202200651] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Indexed: 02/02/2023]
Abstract
Benzene fluorination increases chemoselectivities for Dewar-benzenes via 4π-disrotatory electrocyclization. However, the origin of the chemo- and regioselectivities of fluorobenzenes remains unexplained because of the experimental limitations in resolving the excited-state structures on ultrafast timescales. The computational cost of multiconfigurational nonadiabatic molecular dynamics simulations is also currently cost-prohibitive. We now provide high-fidelity structural information and reaction outcome predictions with machine-learning-accelerated photodynamics simulations of a series of fluorobenzenes, C6 F6-n Hn , n=0-3, to study their S1 →S0 decay in 4 ns. We trained neural networks with XMS-CASPT2(6,7)/aug-cc-pVDZ calculations, which reproduced the S1 absorption features with mean absolute errors of 0.04 eV (<2 nm). The predicted nonradiative decay constants for C6 F4 H2 , C6 F6 , C6 F3 H3 , and C6 F5 H are 116, 60, 28, and 12 ps, respectively, in broad qualitative agreement with the experiments. Our calculations show that a pseudo Jahn-Teller distortion of fluorinated benzenes leads to an S1 local-minimum region that extends the excited-state lifetimes of fluorobenzenes. The pseudo Jahn-Teller distortions reduce when fluorination decreases. Our analysis of the S1 dynamics shows that the pseudo-Jahn-Teller distortions promote an excited-state cis-trans isomerization of a πC-C bond. We characterized the surface hopping points from our NAMD simulations and identified instantaneous nuclear momentum as a factor that promotes the electrocyclizations.
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Affiliation(s)
- Jingbai Li
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
| | - Steven A Lopez
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
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Peng J, Xie Y, Hu D, Lan Z. Analysis of bath motion in MM-SQC dynamics via dimensionality reduction approach: Principal component analysis. J Chem Phys 2021; 154:094122. [PMID: 33685149 DOI: 10.1063/5.0039743] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The system-plus-bath model is an important tool to understand the nonadiabatic dynamics of large molecular systems. Understanding the collective motion of a large number of bath modes is essential for revealing their key roles in the overall dynamics. Here, we applied principal component analysis (PCA) to investigate the bath motion in the basis of a large dataset generated from the symmetrical quasi-classical dynamics method based on the Meyer-Miller mapping Hamiltonian nonadiabatic dynamics for the excited-state energy transfer in the Frenkel-exciton model. The PCA method clearly elucidated that two types of bath modes, which either display strong vibronic coupling or have frequencies close to that of the electronic transition, are important to the nonadiabatic dynamics. These observations were fully consistent with the physical insights. The conclusions were based on the PCA of the trajectory data and did not involve significant pre-defined physical knowledge. The results show that the PCA approach, which is one of the simplest unsupervised machine learning dimensionality reduction methods, is a powerful one for analyzing complicated nonadiabatic dynamics in the condensed phase with many degrees of freedom.
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Affiliation(s)
- Jiawei Peng
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Yu Xie
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Deping Hu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhenggang Lan
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
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Li X, Hu D, Xie Y, Lan Z. Analysis of trajectory similarity and configuration similarity in on-the-fly surface-hopping simulation on multi-channel nonadiabatic photoisomerization dynamics. J Chem Phys 2018; 149:244104. [DOI: 10.1063/1.5048049] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Xusong Li
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Sino-Danish Center for Education and Research/Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deping Hu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Xie
- The Environmental Research Institute, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhenggang Lan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Sino-Danish Center for Education and Research/Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- The Environmental Research Institute, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
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Abstract
In 1998, the first successful quantum control experiment with application to a molecular framework was conducted with a shaped laser pulse, optimizing the branching ratio between different organometallic reaction channels. This work induced a vast activity in quantum control during the next 10 years, and different optimization aims were achieved in the gas phase, liquid phase, and even in biologically relevant molecules like light-harvesting complexes. Accompanying and preceding this development were important advances in theoretical quantum control simulations. They predicted several control scenarios and explained how and why quantum control experiments work. After many successful proofs of concept in molecular science, the big challenge is to expand its huge conceptual potential of directly being able to steer nuclear and/or electronic motion to more applied implementations. In this Account, based on several recent advances, we give a personal evaluation of where the field of molecular quantum control is at the moment and especially where we think promising applications can be in the near future. One of these paths leads to synthetic chemistry. The synthesis of novel pharmaceutical compounds or natural products often involves many synthetic steps, each one devouring resources and lowering the product yield. Shaped laser pulses can possibly act as photonic reagents and shorten the synthetic route toward the desired product. Chemical synthesis usually takes place in solution, and by including explicit solvent molecules in our quantum control simulations, we were able to identify their highly inhomogeneous influence on chemical reactions and how this affects potential quantum control. More important, we demonstrated for a synthetically relevant example that these complications can be overcome in theory, and laser pulses can be optimized to initiate the desired carbon-carbon bond formation. Putting this into context with the recently emerging concept of flow chemistry, which brings several practical advantages to the application of laser pulses, we want to encourage experimental groups to exploit this concept. Another path was opened by several additions to the commonly used laser pulse optimization algorithm (optimal control theory, OCT), several of which were developed in our group. The OCT algorithm as such is a purely mathematical optimization procedure, with no direct relation to experimental requirements. This means that usually the electric fields obtained out of OCT optimizations do not resemble laser pulses that can be achieved experimentally. However, the previously mentioned additions are aimed at closing the gap toward the experiment. In a recent quantum control study of our group, these algorithmic developments came to fruition. We were able to suggest a shaped laser pulse which can induce a long-living wave packet in the excited state of uracil. This might pave the way for novel experiments dedicated to investigating the formation of biological photodamage in DNA and RNA. The pulse we suggest is surprisingly simple because of the extended OCT algorithm and fulfills all criteria to be experimentally accessible.
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Affiliation(s)
- Daniel Keefer
- Department Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
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