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Article: A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes

TitleA pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes
Authors
Issue Date2008
PublisherAmerican Institute of Physics. The Journal's web site is located at http://jcp.aip.org/jcp/staff.jsp
Citation
Journal Of Chemical Physics, 2008, v. 129 n. 15, article no. 154106 How to Cite?
AbstractThe pseudobond method is used in quantum mechanical/molecular mechanical (QM/MM) simulations in which a covalent bond connects the quantum mechanical and classical subsystems. In this method, the molecular mechanical boundary atom is replaced by a special quantum mechanical atom with one free valence that forms a bond with the rest of the quantum mechanical subsystem. This boundary atom is modified through the use of a parametrized effective core potential and basis set. The pseudobond is designed to reproduce the properties of the covalent bond that it has replaced, while invoking as small a perturbation as possible on the system. Following the work of Zhang [J. Chem. Phys. 122, 024114 (2005)], we have developed new pseudobond parameters for use in the simulation of enzymatic systems. Our parameters yield improved electrostatics and deprotonation energies, while at the same time maintaining accurate geometries. We provide parameters for Cps (sp3) -C (sp3), C ps (sp3) -C (sp2,carbonyl), and Cps (sp 3) -N (sp3) pseudobonds, which allow the interface between the quantum mechanical and molecular mechanical subsystems to be constructed at either the Cα - CΒ bond of a given amino acid residue or along the peptide backbone. In addition, we demonstrate the efficiency of our parametrization method by generating residue-specific pseudobond parameters for a single amino acid. Such an approach may enable higher accuracy than general purpose parameters for specific QM/MM applications. © 2008 American Institute of Physics.
Persistent Identifierhttp://hdl.handle.net/10722/168339
ISSN
2015 Impact Factor: 2.894
2015 SCImago Journal Rankings: 0.959
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorParks, JMen_US
dc.contributor.authorHu, Hen_US
dc.contributor.authorCohen, AJen_US
dc.contributor.authorYang, Wen_US
dc.date.accessioned2012-10-08T03:17:47Z-
dc.date.available2012-10-08T03:17:47Z-
dc.date.issued2008en_US
dc.identifier.citationJournal Of Chemical Physics, 2008, v. 129 n. 15, article no. 154106en_US
dc.identifier.issn0021-9606en_US
dc.identifier.urihttp://hdl.handle.net/10722/168339-
dc.description.abstractThe pseudobond method is used in quantum mechanical/molecular mechanical (QM/MM) simulations in which a covalent bond connects the quantum mechanical and classical subsystems. In this method, the molecular mechanical boundary atom is replaced by a special quantum mechanical atom with one free valence that forms a bond with the rest of the quantum mechanical subsystem. This boundary atom is modified through the use of a parametrized effective core potential and basis set. The pseudobond is designed to reproduce the properties of the covalent bond that it has replaced, while invoking as small a perturbation as possible on the system. Following the work of Zhang [J. Chem. Phys. 122, 024114 (2005)], we have developed new pseudobond parameters for use in the simulation of enzymatic systems. Our parameters yield improved electrostatics and deprotonation energies, while at the same time maintaining accurate geometries. We provide parameters for Cps (sp3) -C (sp3), C ps (sp3) -C (sp2,carbonyl), and Cps (sp 3) -N (sp3) pseudobonds, which allow the interface between the quantum mechanical and molecular mechanical subsystems to be constructed at either the Cα - CΒ bond of a given amino acid residue or along the peptide backbone. In addition, we demonstrate the efficiency of our parametrization method by generating residue-specific pseudobond parameters for a single amino acid. Such an approach may enable higher accuracy than general purpose parameters for specific QM/MM applications. © 2008 American Institute of Physics.en_US
dc.languageengen_US
dc.publisherAmerican Institute of Physics. The Journal's web site is located at http://jcp.aip.org/jcp/staff.jspen_US
dc.relation.ispartofJournal of Chemical Physicsen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rightsCopyright (2008) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in (Journal Of Chemical Physics, 2008, v. 129 n. 15) and may be found at (http://jcp.aip.org/resource/1/jcpsa6/v129/i15/p154106_s1).-
dc.subject.meshDipeptides - Chemistryen_US
dc.subject.meshEnzymes - Chemistry - Metabolismen_US
dc.subject.meshModels, Chemicalen_US
dc.subject.meshQuantum Theoryen_US
dc.subject.meshStatic Electricityen_US
dc.titleA pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymesen_US
dc.typeArticleen_US
dc.identifier.emailHu, H:haohu@hku.hken_US
dc.identifier.authorityHu, H=rp00707en_US
dc.description.naturepublished_or_final_versionen_US
dc.identifier.doi10.1063/1.2994288en_US
dc.identifier.pmid19045175en_US
dc.identifier.scopuseid_2-s2.0-54849411916en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-54849411916&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume129, article no. 154106en_US
dc.identifier.issue15en_US
dc.identifier.isiWOS:000260280600006-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridParks, JM=10143634800en_US
dc.identifier.scopusauthoridHu, H=7404097564en_US
dc.identifier.scopusauthoridCohen, AJ=7404781388en_US
dc.identifier.scopusauthoridYang, W=7407757509en_US

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