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Huang H, Peng J, Zhang Y, Gu FL, Lan Z, Xu C. The development of the QM/MM interface and its application for the on-the-fly QM/MM nonadiabatic dynamics in JADE package: Theory, implementation, and applications. J Chem Phys 2024; 160:234101. [PMID: 38884395 DOI: 10.1063/5.0215036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024] Open
Abstract
Understanding the nonadiabatic dynamics of complex systems is a challenging task in computational photochemistry. Herein, we present an efficient and user-friendly quantum mechanics/molecular mechanics (QM/MM) interface to run on-the-fly nonadiabatic dynamics. Currently, this interface consists of an independent set of codes designed for general-purpose use. Herein, we demonstrate the ability and feasibility of the QM/MM interface by integrating it with our long-term developed JADE package. Tailored to handle nonadiabatic processes in various complex systems, especially condensed phases and protein environments, we delve into the theories, implementations, and applications of on-the-fly QM/MM nonadiabatic dynamics. The QM/MM approach is established within the framework of the additive QM/MM scheme, employing electrostatic embedding, link-atom inclusion, and charge-redistribution schemes to treat the QM/MM boundary. Trajectory surface-hopping dynamics are facilitated using the fewest switches algorithm, encompassing classical and quantum treatments for nuclear and electronic motions, respectively. Finally, we report simulations of nonadiabatic dynamics for two typical systems: azomethane in water and the retinal chromophore PSB3 in a protein environment. Our results not only illustrate the power of the QM/MM program but also reveal the important roles of environmental factors in nonadiabatic processes.
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Affiliation(s)
- Haiyi Huang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
- MOE Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiawei Peng
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Yulin Zhang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Feng Long Gu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhenggang Lan
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
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Catalán J, Martin-Somer A, Hopf H. Evidence of the torsion of a polyene chain in a strongly hindered molecular environment: The ttbP4 crystal. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2023.114679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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Cavaletto SM, Keefer D, Rouxel JR, Aleotti F, Segatta F, Garavelli M, Mukamel S. Unveiling the spatial distribution of molecular coherences at conical intersections by covariance X-ray diffraction signals. Proc Natl Acad Sci U S A 2021; 118:e2105046118. [PMID: 34050030 PMCID: PMC8179141 DOI: 10.1073/pnas.2105046118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The outcomes and timescales of molecular nonadiabatic dynamics are decisively impacted by the quantum coherences generated at localized molecular regions. In time-resolved X-ray diffraction imaging, these coherences create distinct signatures via inelastic photon scattering, but they are buried under much stronger background elastic features. Here, we exploit the rich dynamical information encoded in the inelastic patterns, which we reveal by frequency-dispersed covariance ultrafast powder X-ray diffraction of stochastic X-ray free-electron laser pulses. This is demonstrated for the photoisomerization of azobenzene involving the passage through a conical intersection, where the nuclear wave packet branches and explores different quantum pathways. Snapshots of the coherence dynamics are obtained at high frequency shifts, not accessible with conventional diffraction measurements. These provide access to the timing and to the confined spatial distribution of the valence electrons directly involved in the conical intersection passage. This study can be extended to full three-dimensional imaging of conical intersections with ultrafast X-ray and electron diffraction.
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Affiliation(s)
- Stefano M Cavaletto
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Physics & Astronomy, University of California, Irvine, CA 92697
| | - Daniel Keefer
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Physics & Astronomy, University of California, Irvine, CA 92697
| | - Jérémy R Rouxel
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Physics & Astronomy, University of California, Irvine, CA 92697
- University Lyon, UJM-Saint-Étienne, CNRS, Graduate School Optics Institute, Laboratoire Hubert Curien UMR 5516, Saint-Étienne 42023, France
| | - Flavia Aleotti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, 40136 Bologna, Italy
| | - Francesco Segatta
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, 40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, 40136 Bologna, Italy
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, CA 92697;
- Department of Physics & Astronomy, University of California, Irvine, CA 92697
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