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dc.contributor.authorReinholdt, Peter
dc.contributor.authorKjellgren, Erik Rosendahl
dc.contributor.authorSteinmann, Casper
dc.contributor.authorOlsen, Jógvan Magnus Haugaard
dc.date.accessioned2020-03-31T06:44:18Z
dc.date.available2020-03-31T06:44:18Z
dc.date.issued2019-12-19
dc.description.abstractThe fragment-based polarizable embedding (PE) 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 PE-based 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 that of 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.en_US
dc.descriptionThis document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review. To access the final edited and published work see <a href=https://doi.org/10.1021/acs.jctc.9b00616>https://doi.org/10.1021/acs.jctc.9b00616</a>en_US
dc.identifier.citationReinholdt P, Kjellgren ER, Steinmann C, Olsen JMH. Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments. Journal of Chemical Theory and Computation. 2020en_US
dc.identifier.cristinIDFRIDAID 1768860
dc.identifier.doihttps://doi.org/10.1021/acs.jctc.9b00616
dc.identifier.issn1549-9618
dc.identifier.issn1549-9626
dc.identifier.urihttps://hdl.handle.net/10037/17929
dc.language.isoengen_US
dc.publisherAmerican Chemical Societyen_US
dc.relation.journalJournal of Chemical Theory and Computation
dc.relation.projectIDNorges forskningsråd: 262695en_US
dc.relation.projectIDinfo:eu-repo/grantAgreement/RCN/SFF/262695/Norway/Hylleraas Centre for Quantum Molecular Sciences//en_US
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright © 2019 American Chemical Societyen_US
dc.subjectVDP::Matematikk og naturvitenskap: 400::Kjemi: 440::Teoretisk kjemi, kvantekjemi: 444en_US
dc.subjectVDP::Mathematics and natural scienses: 400::Chemistry: 440::Theoretical chemistry, quantum chemistry: 444en_US
dc.subjectMultiskalasimulering / Multiscale modellingen_US
dc.titleCost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environmentsen_US
dc.type.versionacceptedVersionen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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