FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms

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dc.contributor.authorNaidoo, Kevin J
dc.date.accessioned2016-08-22T12:23:40Z
dc.date.available2016-08-22T12:23:40Z
dc.date.issued2011
dc.date.updated2016-08-22T12:19:08Z
dc.description.abstractThe development and implementation of a computational method able to produce free energies in multiple dimensions, descriptively named the free energies from adaptive reaction coordinate forces (FEARCF) method is described in this paper. While the method can be used to calculate free energies of association, conformation and reactivity here it is shown in the context of chemical reaction landscapes. A reaction free energy surface for the Claisen rearrangement of chorismate to prephenate is used as an illustration of the method’s efficient convergence. FEARCF simulations are shown to achieve flat histograms for complex multidimensional free energy volumes. The sampling efficiency by which it produces multidimensional free energies is demonstrated on the complex puckering of a pyranose ring, that is described by a three dimensional W(1, 2, 3) potential of mean force.en_ZA
dc.identifierhttp://dx.doi.org/http://link.springer.com/content/pdf/10.1007%2Fs11426-011-4423-7.pdf#page-1
dc.identifier.apacitationNaidoo, K. J. (2011). FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms. <i>Science China</i>, http://hdl.handle.net/11427/21418en_ZA
dc.identifier.chicagocitationNaidoo, Kevin J "FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms." <i>Science China</i> (2011) http://hdl.handle.net/11427/21418en_ZA
dc.identifier.citationNaidoo, K. J. (2011). FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms. Science China Chemistry, 54(12), 1962-1973.en_ZA
dc.identifier.issn1674-7291en_ZA
dc.identifier.ris TY - Journal Article AU - Naidoo, Kevin J AB - The development and implementation of a computational method able to produce free energies in multiple dimensions, descriptively named the free energies from adaptive reaction coordinate forces (FEARCF) method is described in this paper. While the method can be used to calculate free energies of association, conformation and reactivity here it is shown in the context of chemical reaction landscapes. A reaction free energy surface for the Claisen rearrangement of chorismate to prephenate is used as an illustration of the method’s efficient convergence. FEARCF simulations are shown to achieve flat histograms for complex multidimensional free energy volumes. The sampling efficiency by which it produces multidimensional free energies is demonstrated on the complex puckering of a pyranose ring, that is described by a three dimensional W(1, 2, 3) potential of mean force. DA - 2011 DB - OpenUCT DP - University of Cape Town J1 - Science China LK - https://open.uct.ac.za PB - University of Cape Town PY - 2011 SM - 1674-7291 T1 - FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms TI - FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms UR - http://hdl.handle.net/11427/21418 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/21418
dc.identifier.urihttp://link.springer.com/article/10.1007/s11426-011-4423-7
dc.identifier.vancouvercitationNaidoo KJ. FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms. Science China. 2011; http://hdl.handle.net/11427/21418.en_ZA
dc.languageengen_ZA
dc.publisherSpringer Verlagen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.sourceScience Chinaen_ZA
dc.source.urihttp://link.springer.com/journal/11426
dc.subject.otherfree energy calculations
dc.subject.otherreaction dynamics
dc.subject.otherreaction surfaces
dc.subject.othermultidimensional free energy surface
dc.titleFEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanismsen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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