Multiscale electrostatic embedding simulations for modeling structure and dynamics of molecules in solution: A tutorial review

Dohn, Asmus Ougaard

doi:10.1002/qua.26343

Cited by 35 publications

(39 citation statements)

References 140 publications

(248 reference statements)

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“…The QM/MM scheme used in this work follows the recent [ 19 ] implementation resulting from interfacing SHARC and COBRAMM. Highlights in the QM/MM implementation include (i) a subtractive scheme for the calculation of the energy and the gradient of the electronic states [ 8 ], with the implementation of an electrostatic embedding scheme [ 27 ] to account for the polarization of the QM part due to the presence of the surrounding MM environment, included in the adopted Hamiltonian as point charges; (ii) the inclusion in the MM gradient of a state-specific term due to the force induced by the QM region on the point charges; (iii) the QM molecule surrounded by a droplet of homogeneous radius of water molecules and, in order to address the lack of periodical boundary conditions, the external shell of water molecules is kept frozen to furnish a constant potential and keep the droplet stable. Additional information and the full implementation can be found in the original publication [ 21 ].…”

Section: Methodsmentioning

confidence: 99%

Sampling effects in quantum mechanical/molecular mechanics trajectory surface hopping non-adiabatic dynamics

Avagliano

Lorini

González

2022

Phil. Trans. R. Soc. A.

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The impact of different initial conditions in non-adiabatic trajectory surface hopping dynamics within a hybrid quantum mechanical/molecular mechanics scheme is investigated. The influence of a quantum sampling, based on a Wigner distribution, a fully thermal sampling, based on classical molecular dynamics, and a quantum sampled system, but thermally equilibrated with the environment, is investigated on the relaxation dynamics of solvated fulvene after light irradiation. We find that the decay from the first singlet excited state to the ground state shows high dependency on the initial condition and simulation parameters. The three sampling methods lead to different distributions of initial geometries and momenta, which then affect the fate of the excited state dynamics. We evaluated both the effect of sampling geometries and momenta, analysing how the ultrafast decay of fulvene changes accordingly. The results are expected to be of interest to decide how to initialize non-adiabatic dynamics in the presence of the environment. This article is part of the theme issue ‘Chemistry without the Born–Oppenheimer approximation’.

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Section: Methodsmentioning

confidence: 99%

Sampling effects in quantum mechanical/molecular mechanics trajectory surface hopping non-adiabatic dynamics

Avagliano

Lorini

González

2022

Phil. Trans. R. Soc. A.

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“…This involves replacement of individual atoms in the MM region with their partial charges at their positions as optimized by MM using classical force‐field parameters (Figure 4(f)). 99 Thus, the cutoff used in selecting surrounding point charges for inclusion must be sufficiently large to fully account for the electrostatic force. Indeed, the polarization produced by the environment, as replicated by a spatial distribution of charge, can prove critical for accurate modeling and elucidation of spectral features.…”

Section: Methodsmentioning

confidence: 99%

Understanding flavin electronic structure and spectra

Kar

Miller

Mroginski

2021

WIREs Comput Mol Sci

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Flavins have emerged as central to electron bifurcation, signaling, and countless enzymatic reactions. In bifurcation, two electrons acquired as a pair are separated in coupled transfers wherein the energy of both is concentrated on one of the two. This enables organisms to drive demanding reactions based on abundant low‐grade chemical fuel. To enable incorporation of this and other flavin capabilities into designed materials and devices, it is essential to understand fundamental principles of flavin electronic structure that make flavins so reactive and tunable by interactions with protein. Emerging computational tools can now replicate spectra of flavins and are gaining capacity to explain reactivity at atomistic resolution, based on electronic structures. Such fundamental understanding can moreover be transferrable to other chemical systems. A variety of computational innovations have been critical in reproducing experimental properties of flavins including their electronic spectra, vibrational signatures, and nuclear magnetic resonance (NMR) chemical shifts. A computational toolbox for understanding flavin reactivity moreover must be able to treat all five oxidation and protonation states, in addition to excited states that participate in flavoprotein's light‐driven reactions. Therefore, we compare emerging hybrid strategies and their successes in replicating effects of hydrogen bonding, the surrounding dielectric, and local electrostatics. These contribute to the protein's ability to modulate flavin reactivity, so we conclude with a survey of methods for incorporating the effects of the protein residues explicitly, as well as local dynamics. Computation is poised to elucidate the factors that affect a bound flavin's ability to mediate stunningly diverse reactions, and make life possible. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Theoretical and Physical Chemistry > Spectroscopy

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“…Further technical details about the QM/MM approach in a beginner-friendly format can be found elsewhere. 51,56…”

Section: The Qm/mm Approachmentioning

confidence: 99%

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

Cruzeiro¹,

Manathunga²,

Merz³

et al. 2021

Preprint

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<div><div><div><p>The quantum mechanics/molecular mechanics (QM/MM) approach is an essential and well-established tool in computational chemistry that has been widely applied in a myriad of biomolecular problems in the literature. In this publication, we report the integration of the QUantum Interaction Computational Kernel (QUICK) program as an engine to perform electronic structure calculations in QM/MM simulations with AMBER. This integration is available through either a file-based interface (FBI) or an application programming interface (API). Since QUICK is an open-source GPU-accelerated code with multi-GPU parallelization, users can take advantage of “free of charge” GPU-acceleration in their QM/MM simulations. In this work, we discuss implementation details and give usage examples. We also investigate energy conservation in typical QM/MM simulations performed at the microcanonical ensemble. Finally, benchmark results for two representative systems, the N-methylacetamide (NMA) molecule and the photoactive yellow protein (PYP) in bulk water, show the performance of QM/MM simulations with QUICK and AMBER using a varying number of CPU cores and GPUs. Our results highlight the acceleration obtained from a single or multiple GPUs; we observed speedups of up to 38x between a single GPU vs. a single CPU core and of up to 2.6x when comparing four GPUs to a single GPU. Results also reveal speedups of up to 3.5x when the API is used instead of FBI.</p></div></div></div>

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Multiscale electrostatic embedding simulations for modeling structure and dynamics of molecules in solution: A tutorial review

Cited by 35 publications

References 140 publications

Sampling effects in quantum mechanical/molecular mechanics trajectory surface hopping non-adiabatic dynamics

Sampling effects in quantum mechanical/molecular mechanics trajectory surface hopping non-adiabatic dynamics

Understanding flavin electronic structure and spectra

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

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