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Interaction of Charged Amino-Acid Side Chains with Ions : An Optimization Strategy for Classical Force Fields

Interaction of Charged Amino-Acid Side Chains with Ions : An Optimization Strategy for Classical Force Fields

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KAHLEN, Jens, Leila SALIMI, Marialore SULPIZI, Christine PETER, Davide DONADIO, 2014. Interaction of Charged Amino-Acid Side Chains with Ions : An Optimization Strategy for Classical Force Fields. In: The Journal of Physical Chemistry B. 118(14), pp. 3960-3972. ISSN 1520-6106. eISSN 1520-5207

@article{Kahlen2014-04-10Inter-27832, title={Interaction of Charged Amino-Acid Side Chains with Ions : An Optimization Strategy for Classical Force Fields}, year={2014}, doi={10.1021/jp412490c}, number={14}, volume={118}, issn={1520-6106}, journal={The Journal of Physical Chemistry B}, pages={3960--3972}, author={Kahlen, Jens and Salimi, Leila and Sulpizi, Marialore and Peter, Christine and Donadio, Davide} }

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/27832"> <dcterms:rights rdf:resource="http://nbn-resolving.org/urn:nbn:de:bsz:352-20140905103605204-4002607-1"/> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2014-05-21T09:51:21Z</dc:date> <dc:contributor>Sulpizi, Marialore</dc:contributor> <dc:contributor>Peter, Christine</dc:contributor> <dc:contributor>Kahlen, Jens</dc:contributor> <dcterms:abstract xml:lang="eng">Many well-established classical biomolecular force fields, fitted on the solvation properties of single ions, do not necessarily describe all the details of ion pairing accurately, especially for complex polyatomic ions. Depending on the target application, it might not be sufficient to reproduce the thermodynamics of ion pairing, but it may also be necessary to correctly capture structural details, such as the coordination mode. In this work, we analyzed how classical force fields can be optimized to yield a realistic description of these different aspects of ion pairing. Given the prominent role of the interactions of negatively charged amino-acid side chains and divalent cations in many biomolecular systems, we chose calcium acetate as a benchmark system to devise a general optimization strategy that we applied to two popular force fields, namely, GROMOS and OPLS-AA. Using experimental association constants and first-principles molecular dynamics simulations as a reference, we found that small modifications of the van der Waals ion–ion interaction parameters allow a systematic improvement of the essential thermodynamic and structural properties of ion pairing.</dcterms:abstract> <dcterms:bibliographicCitation>The Journal of Physical Chemistry / B ; 118 (2014), 14. - S. 3960-3972</dcterms:bibliographicCitation> <dc:creator>Sulpizi, Marialore</dc:creator> <dc:language>eng</dc:language> <dc:creator>Peter, Christine</dc:creator> <dc:creator>Kahlen, Jens</dc:creator> <dc:creator>Donadio, Davide</dc:creator> <dc:contributor>Donadio, Davide</dc:contributor> <dcterms:issued>2014-04-10</dcterms:issued> <dc:rights>deposit-license</dc:rights> <dc:creator>Salimi, Leila</dc:creator> <bibo:uri rdf:resource="http://kops.uni-konstanz.de/handle/123456789/27832"/> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2014-05-21T09:51:21Z</dcterms:available> <dc:contributor>Salimi, Leila</dc:contributor> <dcterms:title>Interaction of Charged Amino-Acid Side Chains with Ions : An Optimization Strategy for Classical Force Fields</dcterms:title> </rdf:Description> </rdf:RDF>

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