An averaged polarizable potential for multiscale modeling in phospholipid membranes

Witzke, Sarah; List, Nanna Holmgaard; Olsen, Jógvan Magnus Haugaard; Steinmann, Casper; Petersen, Michael; Beerepoot, Maarten T. P.; Kongsted, Jacob

doi:10.1002/jcc.24718

Cited by 13 publications

(23 citation statements)

References 93 publications

(121 reference statements)

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“…We have shown in several studies that an embedding potential built from fragment‐based calculations of atom‐centered multipoles truncated at second order (quadrupoles) and atom‐centered dipole‐dipole polarizabilities derived using the LoProp procedure provides a highly accurate representation both for solvents, proteins, DNA, and lipids . An example of the accuracy that can be obtained with this type of embedding potential (often denoted M2P2) is shown in Figure .…”

Section: Practical Aspectsmentioning

confidence: 99%

“…Fragments that are close to the quantum region are treated as before, that is, the embedding parameters are determined based on fragment calculations, whereas averaged parameters can be used for fragments that are farther away from the quantum region. Such averaged parameters exist for a series of solvents, lipids, and nucleotides, or, alternatively, the parameters can also be extracted from standard molecular‐mechanics force fields. To determine a suitable distance threshold, it is necessary to perform benchmark calculations (see, eg, Reference ).…”

Section: Practical Aspectsmentioning

confidence: 99%

“…The user is thus able to choose among different electronic‐structure methods and select the one that is known to perform best from a cost‐efficiency point of view for a given property. The PE model is per definition not restricted to any specific kind of environment but may be used on the same footing for different environments such as solvents, proteins, DNA, or lipids . However, the complexity of setting up calculations may vary depending essentially on the fragmentation procedure used for the environment.…”

Section: Introductionmentioning

confidence: 99%

“…proteins [32], DNA [33], or lipids [34]. However, the complexity of setting up calculations may vary depending essentially on the fragmentation procedure used for the environment.…”

Section: Introductionmentioning

confidence: 99%

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Response properties of embedded molecules through the polarizable embedding model

Steinmann

Reinholdt

Nørby

et al. 2018

Int J of Quantum Chemistry

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The polarizable embedding (PE) model is a fragment-based quantum-classical approach aimed at accurate inclusion of environment effects in quantum-mechanical response property calculations. The aim of this tutorial review is to give insight into the practical use of the PE model.Starting from a set of molecular structures and until you arrive at the final property, there are many crucial details to consider in order to obtain trustworthy results in an efficient manner. To lower the threshold for new users wanting to explore the use of the PE model, we describe and discuss important aspects related to its practical use. This includes directions on how to generate input files and how to run a calculation. K E Y W O R D S computational spectroscopy, molecular properties, polarizable embedding, QM/MM, response properties 1 | INTRODUCTION Hybrid quantum-classical approaches for modeling of chemical or biological systems have in recent years gained considerable interest. The reasonfor such popularity of these models relies, to a large degree, on their efficiency and the fact that such models enable calculations on systems of sizes that are otherwise impossible using pure quantum-mechanical methods. The dielectric continuum models belong to the simplest of the quantum-classical approaches, [1,2] and models like the polarizable continuum model [3,4] are today implemented in many of the available electronic-structure programs. In addition, such models are very easy to use: based on a predefined set of atomic radii and the dielectric constant of the solvent, the user can include solvation effects based only on a single calculation. Only one calculation is needed because the dielectric continuum models implicitly include sampling of solvent configurations. On the other hand, it is well-known that the dielectric continuum models possess several drawbacks, such as the inability to model the directionality of specific intermolecular interactions like hydrogen bonding or π-π stacking. Because of this, modeling of environment anisotropies, as found in, for example, protein matrices is lost.Another class of quantum-classical approaches consists of discrete models where the atomistic detail of the environment is kept, that is, models based on the concept of combined quantum mechanics and molecular mechanics (QM/MM). [5][6][7][8] Discrete models, compared to the dielectric continuum models, realistically describe the environment, but at an increased level of both complexity and computational requirements.Regarding the latter point, the increase in computational time is not linked to the discrete nature of the environment as such but rather that

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Section: Practical Aspectsmentioning

confidence: 99%

Section: Practical Aspectsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…proteins [32], DNA [33], or lipids [34]. However, the complexity of setting up calculations may vary depending essentially on the fragmentation procedure used for the environment.…”

Section: Introductionmentioning

confidence: 99%

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Response properties of embedded molecules through the polarizable embedding model

Steinmann

Reinholdt

Nørby

et al. 2018

Int J of Quantum Chemistry

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“…Alternatively, the multipoles and polarizabilities can be taken from existing preparametrized potentials that have been derived for proteins, 57 a series of solvents, 55 and a few lipids. 76 …”

Section: Theorymentioning

confidence: 99%

Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model

Dundas

Beerepoot

Ringholm

et al. 2021

J. Chem. Theory Comput.

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We present a fully analytic approach to calculate infrared (IR) and Raman spectra of molecules embedded in complex molecular environments modeled using the fragment-based polarizable embedding (PE) model. We provide the theory for the calculation of analytic second-order geometric derivatives of molecular energies and first-order geometric derivatives of electric dipole moments and dipole–dipole polarizabilities within the PE model. The derivatives are implemented using a general open-ended response theory framework, thus allowing for an extension to higher-order derivatives. The embedding-potential parameters used to describe the environment in the PE model are derived through first-principles calculations, thus allowing a wide variety of systems to be modeled, including solvents, proteins, and other large and complex molecular environments. Here, we present proof-of-principle calculations of IR and Raman spectra of acetone in different solvents. This work is an important step toward calculating accurate vibrational spectra of molecules embedded in realistic environments.

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Fast Approximate but Accurate QM/MM Interactions for Polarizable Embedding

Reinholdt

Kongsted

Lipparini

2021

J. Chem. Theory Comput.

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The coupling between the quantum (QM) and classical (MM) regions is often one of the computational bottlenecks when applying polarizable QM/MM to computational spectroscopy. In this Article, we explore three strategies to approximate the QM/MM coupling based on multipole expansion techniques. The implementations of these approximations are benchmarked in terms of both accuracy and computational efficiency and are furthermore applied to the calculation of spectroscopic properties including both one-and two-photon absorption strengths. We show that the proposed strategies provide significant computational savings without compromising the accuracy of the calculated spectroscopic properties.

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An averaged polarizable potential for multiscale modeling in phospholipid membranes

Cited by 13 publications

References 93 publications

Response properties of embedded molecules through the polarizable embedding model

Response properties of embedded molecules through the polarizable embedding model

Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model

Fast Approximate but Accurate QM/MM Interactions for Polarizable Embedding

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