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

Tracy, Dustin A.; Fernández-Alberti, Sebastián; Tretiak, Sergei; Roitberg, Adrián E.

doi:10.1021/acs.jctc.2c00561

Cited by 4 publications

(1 citation statement)

References 48 publications

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“…Furthermore, several software interfaces have been developed for on-the-fly QM/MM TSH calculations. 40,53,[101][102][103][104] Cui and Thiel proposed the generalized trajectory-based surface-hopping method and combined it with Chemshell to stimulate internal conversion and intersystem crossing nonadiabatic dynamics. 40 The SHARC/COBRAMM interface were presented to simulate the excited-state dynamics using onthe-fly QM/MM TSH dynamics, in which COBRAMM allows for ground-and excited-state QM/MM calculations using a subtractive scheme.…”

Section: Introductionmentioning

confidence: 99%

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

Huang,

Peng,

et al. 2024

Preprint

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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 the 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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Section: Introductionmentioning

confidence: 99%

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

Huang,

Peng,

et al. 2024

Preprint

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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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An efficient protocol for excited states of large biochromophores

Feighan

Manby

Worster

2023

The Journal of Chemical Physics

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Efficient energy transport in photosynthetic antenna is a long-standing source of inspiration for artificial light harvesting materials. However, characterizing the excited states of the constituent chromophores poses a considerable challenge to mainstream quantum chemical and semiempirical excited state methods due to their size and complexity and the accuracy required to describe small but functionally important changes in their properties. In this paper, we explore an alternative approach to calculating the excited states of large biochromophores, exemplified by a specific method for calculating the Q y transition of bacteriochlorophyll a, which we name Chl-xTB. Using a diagonally dominant approximation to the Casida equation and a bespoke parameterization scheme, Chl-xTB can match time-dependent density functional theory’s accuracy and semiempirical speed for calculating the potential energy surfaces and absorption spectra of chlorophylls. We demonstrate that Chl-xTB (and other prospective realizations of our protocol) can be integrated into multiscale models, including concurrent excitonic and point-charge embedding frameworks, enabling the analysis of biochromophore networks in a native environment. We exploit this capability to probe the low-frequency spectral densities of excitonic energies and interchromophore interactions in the light harvesting antenna protein LH2 (light harvesting complex 2). The impact of low-frequency protein motion on interchromophore coupling and exciton transport has routinely been ignored due to the prohibitive costs of including it in simulations. Our results provide a more rigorous basis for continued use of this approximation by demonstrating that exciton transition energies are unaffected by low-frequency vibrational coupling to exciton interaction energies.

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

Cited by 4 publications

References 48 publications

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

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

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

An efficient protocol for excited states of large biochromophores

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