Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions : A continuum electrostatics study

Lade...
Vorschaubild
Dateien
Bergdorf_2-jq90ai8ow3gu2.pdf
Bergdorf_2-jq90ai8ow3gu2.pdfGröße: 257.9 KBDownloads: 94
Datum
2003
Autor:innen
Bergdorf, Michael
Hünenberger, Philippe H.
Herausgeber:innen
Kontakt
ISSN der Zeitschrift
Electronic ISSN
ISBN
Bibliografische Daten
Verlag
Schriftenreihe
Auflagebezeichnung
DOI (zitierfähiger Link)
ArXiv-ID
Internationale Patentnummer
Angaben zur Forschungsförderung
Projekt
Open Access-Veröffentlichung
Open Access Green
Sammlungen
Core Facility der Universität Konstanz
Gesperrt bis
Titel in einer weiteren Sprache
Forschungsvorhaben
Organisationseinheiten
Zeitschriftenheft
Publikationstyp
Zeitschriftenartikel
Publikationsstatus
Published
Erschienen in
The Journal of Chemical Physics. 2003, 119(17), pp. 9129-9144. ISSN 0021-9606. eISSN 1089-7690. Available under: doi: 10.1063/1.1614202
Zusammenfassung

A new algorithm relying on finite integration is presented that solves the equations of continuum electrostatics for truncated (and possibly reaction-field corrected) solute–solvent and solvent–solvent interactions under either nonperiodic or periodic boundary conditions. After testing and validation by comparison with existing methods, the algorithm is applied to investigate the effect of cut-off truncation and artificial periodicity in explicit-solvent simulations of ionic solvation and ion–ion interactions. Both cut-off truncation and artificial periodicity significantly alter the polarization around a spherical ion and thus, its solvation free energy. The nature and magnitude of the two perturbations are analyzed in details, and correction terms are proposed for both effects. Cut-off truncation is also shown to induce strong alterations in the potential of mean force for ion–ion interaction. These observations help to rationalize artifacts previously observed in explicit–solvent simulations, namely spurious features in the radial distribution functions close to the cut-off distance and alterations in the relative stabilities of contact, solvent-separated and free ion pairs.

Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
540 Chemie
Schlagwörter
Konferenz
Rezension
undefined / . - undefined, undefined
Zitieren
ISO 690BERGDORF, Michael, Christine PETER, Philippe H. HÜNENBERGER, 2003. Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions : A continuum electrostatics study. In: The Journal of Chemical Physics. 2003, 119(17), pp. 9129-9144. ISSN 0021-9606. eISSN 1089-7690. Available under: doi: 10.1063/1.1614202
BibTex
@article{Bergdorf2003-11Influ-40243,
  year={2003},
  doi={10.1063/1.1614202},
  title={Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions : A continuum electrostatics study},
  number={17},
  volume={119},
  issn={0021-9606},
  journal={The Journal of Chemical Physics},
  pages={9129--9144},
  author={Bergdorf, Michael and Peter, Christine and Hünenberger, Philippe H.}
}
RDF
<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/40243">
    <dc:rights>terms-of-use</dc:rights>
    <dcterms:abstract xml:lang="eng">A new algorithm relying on finite integration is presented that solves the equations of continuum electrostatics for truncated (and possibly reaction-field corrected) solute–solvent and solvent–solvent interactions under either nonperiodic or periodic boundary conditions. After testing and validation by comparison with existing methods, the algorithm is applied to investigate the effect of cut-off truncation and artificial periodicity in explicit-solvent simulations of ionic solvation and ion–ion interactions. Both cut-off truncation and artificial periodicity significantly alter the polarization around a spherical ion and thus, its solvation free energy. The nature and magnitude of the two perturbations are analyzed in details, and correction terms are proposed for both effects. Cut-off truncation is also shown to induce strong alterations in the potential of mean force for ion–ion interaction. These observations help to rationalize artifacts previously observed in explicit–solvent simulations, namely spurious features in the radial distribution functions close to the cut-off distance and alterations in the relative stabilities of contact, solvent-separated and free ion pairs.</dcterms:abstract>
    <dc:contributor>Hünenberger, Philippe H.</dc:contributor>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/29"/>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-10-05T07:59:11Z</dc:date>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dc:creator>Bergdorf, Michael</dc:creator>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-10-05T07:59:11Z</dcterms:available>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/40243/1/Bergdorf_2-jq90ai8ow3gu2.pdf"/>
    <dc:creator>Peter, Christine</dc:creator>
    <dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/29"/>
    <dc:language>eng</dc:language>
    <dc:contributor>Peter, Christine</dc:contributor>
    <dc:creator>Hünenberger, Philippe H.</dc:creator>
    <dc:contributor>Bergdorf, Michael</dc:contributor>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/40243"/>
    <dcterms:title>Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions : A continuum electrostatics study</dcterms:title>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/40243/1/Bergdorf_2-jq90ai8ow3gu2.pdf"/>
    <dcterms:issued>2003-11</dcterms:issued>
  </rdf:Description>
</rdf:RDF>
Interner Vermerk
xmlui.Submission.submit.DescribeStep.inputForms.label.kops_note_fromSubmitter
Kontakt
URL der Originalveröffentl.
Prüfdatum der URL
Prüfungsdatum der Dissertation
Finanzierungsart
Kommentar zur Publikation
Allianzlizenz
Corresponding Authors der Uni Konstanz vorhanden
Internationale Co-Autor:innen
Universitätsbibliographie
Nein
Begutachtet
Diese Publikation teilen