Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association

Simple item page
dc.contributor.authorNaidoo, Kevin J
dc.date.accessioned2016-08-23T12:37:02Z
dc.date.available2016-08-23T12:37:02Z
dc.date.issued2012
dc.date.updated2016-08-23T12:35:19Z
dc.description.abstractFree energy is a central measure in statistical mechanics and the means by which other thermodynamic properties of a system may be accessed. Using an efficient numerical method referred to as the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) method it is shown that multidimensional free energy volumes (FEVs) are computable and that they are critical to the understanding of reactions, conformational analysis and molecular association. Specifically the FEV of the hydrolysis reaction catalysed by a cellobiohydrolase I is shown to reveal molecular details of the reaction mechanism. The reaction is understood from a combination of the two dimensional reaction free energy surface, W(x1, x2) and the three dimensional glucopyranose ring pucker FEV, W(x1, x2, x3). These studies provide for the first time details of the evolution of the oxocarbenium ion, which is a key to characterizing transition state structures seen in carbohydrate chemistry. A long-standing challenge has been the unambiguous assignment of the relative orientation of molecular pairs in solution. Here we describe how the molecular association of the benzene dimer in water and their relative orientational attraction are found from four dimensional, FEVs W(x1, x2, x3, x4).en_ZA
dc.identifierhttp://dx.doi.org/10.1039/c2cp23802k
dc.identifier.apacitationNaidoo, K. J. (2012). Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association. <i>Physical Chemistry Chemical Physics</i>, http://hdl.handle.net/11427/21465en_ZA
dc.identifier.chicagocitationNaidoo, Kevin J "Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association." <i>Physical Chemistry Chemical Physics</i> (2012) http://hdl.handle.net/11427/21465en_ZA
dc.identifier.citationNaidoo, K. J. (2012). Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association. Physical Chemistry Chemical Physics, 14(25), 9026-9036.en_ZA
dc.identifier.issn1463-9076en_ZA
dc.identifier.ris TY - Journal Article AU - Naidoo, Kevin J AB - Free energy is a central measure in statistical mechanics and the means by which other thermodynamic properties of a system may be accessed. Using an efficient numerical method referred to as the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) method it is shown that multidimensional free energy volumes (FEVs) are computable and that they are critical to the understanding of reactions, conformational analysis and molecular association. Specifically the FEV of the hydrolysis reaction catalysed by a cellobiohydrolase I is shown to reveal molecular details of the reaction mechanism. The reaction is understood from a combination of the two dimensional reaction free energy surface, W(x1, x2) and the three dimensional glucopyranose ring pucker FEV, W(x1, x2, x3). These studies provide for the first time details of the evolution of the oxocarbenium ion, which is a key to characterizing transition state structures seen in carbohydrate chemistry. A long-standing challenge has been the unambiguous assignment of the relative orientation of molecular pairs in solution. Here we describe how the molecular association of the benzene dimer in water and their relative orientational attraction are found from four dimensional, FEVs W(x1, x2, x3, x4). DA - 2012 DB - OpenUCT DP - University of Cape Town J1 - Physical Chemistry Chemical Physics LK - https://open.uct.ac.za PB - University of Cape Town PY - 2012 SM - 1463-9076 T1 - Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association TI - Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association UR - http://hdl.handle.net/11427/21465 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/21465
dc.identifier.urihttp://pubs.rsc.org/en/content/articlelanding/2012/cp/c2cp23802k#!divAbstract
dc.identifier.vancouvercitationNaidoo KJ. Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association. Physical Chemistry Chemical Physics. 2012; http://hdl.handle.net/11427/21465.en_ZA
dc.languageengen_ZA
dc.publisherRoyal Society of Chemistryen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.sourcePhysical Chemistry Chemical Physicsen_ZA
dc.source.urihttp://pubs.rsc.org/en/journals/journalissues/cp#!recentarticles&adv
dc.subject.otherMultidimensional free energy volumes
dc.subject.othermolecular conformation
dc.subject.othermolecular formation
dc.titleMultidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and associationen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Naidoo_Multidimensional_free_energy_2012.pdf
Size:
3.99 MB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
1.72 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Journal Articles