Photochemistry of Biological Systems: Excited-State Electronic Structure Calculations and Nonadiabatic Dynamics Simulations with QM/MM Methods

Liu, Xiang­-Yang; Fang, Wei‐Hai; Cui, Ganglong

doi:10.1016/b978-0-12-821978-2.00047-7

Comprehensive Computational Chemistry 2024

DOI: 10.1016/b978-0-12-821978-2.00047-7

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Photochemistry of Biological Systems: Excited-State Electronic Structure Calculations and Nonadiabatic Dynamics Simulations with QM/MM Methods

Xiang-Yang Liu¹,

Wei‐Hai Fang²,

Ganglong Cui³

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2024

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Nonadiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation

Tracy,

Fernandez-Alberti,

Galindo

et al. 2024

J. Phys. Chem. B

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In this article, the nonadiabatic excited-state Molecular dynamics (NEXMD) package is linked with the SANDER package, provided by AMBERTOOLS. The combination of these software packages enables the simulation of photoinduced dynamics of large multichromophoric conjugated molecules involving several coupled electronic excited states embedded in an explicit solvent by using the quantum/mechanics/molecular mechanics (QM/MM) methodology. The fewest switches surface hopping algorithm, as implemented in NEXMD, is used to account for quantum transitions among the adiabatic excited-state simulations of the photoexcitation and subsequent nonadiabatic electronic transitions, and vibrational energy relaxation of a substituted polyphenylenevinylene oligomer (PPV3-NO2) in vacuum and methanol as an explicit solvent has been used as a test case. The impact of including specific solvent molecules in the QM region is also analyzed. Our NEXMD-SANDER QM/MM implementation provides a useful computational tool to simulate qualitatively solvent-dependent effects, like electron transfer, stabilization of charge-separated excited states, and the role of solvent reorganization in the molecular optical properties, observed in solution-based spectroscopic experiments.

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Nonadiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation

Tracy,

Fernandez-Alberti,

Galindo

et al. 2024

J. Phys. Chem. B

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show abstract

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Photochemistry of Biological Systems: Excited-State Electronic Structure Calculations and Nonadiabatic Dynamics Simulations with QM/MM Methods

Cited by 1 publication

References 435 publications

Nonadiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation

Nonadiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation

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