Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments

Reinholdt, Peter; Kjellgren, Erik; Steinmann, Casper; Olsen, Jógvan Magnus Haugaard

doi:10.1021/acs.jctc.9b00616

Cited by 16 publications

(17 citation statements)

References 78 publications

(170 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For the protein, we used the parameters described in Ref. 44, while parameters for the water molecules and ions were taken from Ref. 45.…”

Section: Setup For Nile Redmentioning

confidence: 99%

Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees

Scheurer

Reinholdt²,

Olsen³

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

<div>We present open-source implementations of the linear-scaling Fast Multipole Method (FMM) within the Polarizable Embedding (PE) model for efficient treatment of large polarizable environments in computational spectroscopy simulations. The implementations are tested for accuracy, efficiency, and usability on model systems as well as more realistic biomolecular systems. We explain how FMM parameters affect the calculation of molecular properties and show that PE calculations employing FMM can be carried out in a black-box manner. The efficiency of the linear-scaling approach is demonstrated by simulating the UV/Vis spectrum of a chromophore in an environment of more than one million polarizable sites. Our implementations are interfaced to several open-source quantum chemistry programs, making computational spectroscopy</div><div>simulations within the PE model and FMM available to a large variety of methods and a broad user base.</div>

show abstract

“…For the protein, we used the parameters described in Ref. 44, while parameters for the water molecules and ions were taken from Ref. 45.…”

Section: Setup For Nile Redmentioning

confidence: 99%

Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees

Scheurer

Reinholdt²,

Olsen³

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…The final set of fitted parameters as well as the structures and electric potentials used in the fitting procedure are available at https://doi.org/10.5281/zenodo.3250016. 32…”

Section: Computational Details 31 Fittingmentioning

confidence: 99%

Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments

Reinholdt¹,

Kjellgren²,

Steinmann³

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

<div>The fragment-based polarizable embedding model combined with an appropriate electronic-structure method constitutes a highly efficient and accurate multiscale approach for computing spectroscopic properties of a central moiety including effects from its molecular environment through an embedding potential. There is, however, a comparatively high computational overhead associated with the computation of the embedding potential which is derived from first principles calculations on individual fragments of the environment. To reduce the computational cost associated with the calculation of embedding-potential parameters, we developed a set of amino-acid-specific transferable parameters tailored for large-scale polarizable embedding calculations that include proteins. The amino-acid-based parameters are obtained by simultaneously fitting to a set of reference electric potentials based on structures derived from a backbone-dependent rotamer library. The developed cost-effective polarizable protein potential (CP<sup>3</sup>) consists of atom-centered charges and isotropic dipole-dipole polarizabilities of the standard amino acids. In terms of reproduction of electric potentials, the CP<sup>3</sup> is shown to perform consistently and with acceptable accuracy across both small tripeptide test systems and larger proteins. We show, through applications on realistic protein systems, that acceptable accuracy can be obtained by using a pure CP<sup>3</sup> representation of the protein environment, thus altogether omitting the cost associated with the calculation of embedding-potential parameters. High accuracy comparable to the full fragment-based approach can be achieved through a mixed description where the CP<sup>3</sup> is used only to describe amino acids beyond a threshold distance from the central quantum part.</div>

show abstract

“…The environment is treated classically, however, the parameters (multipoles and polarizabilities) can be derived from first-principles calculations on each individual fragment in the environment. This approach has been shown to yield highly accurate embedding potentials. − …”

Section: Introductionmentioning

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.

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments

Cited by 16 publications

References 78 publications

Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees

Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees

Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments

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

Contact Info

Product

Resources

About