Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations
| dc.contributor.author | Barnett, C B | |
| dc.contributor.author | Naidoo, Kevin J | |
| dc.date.accessioned | 2016-08-15T14:10:56Z | |
| dc.date.available | 2016-08-15T14:10:56Z | |
| dc.date.issued | 2010 | |
| dc.date.updated | 2016-08-15T11:19:02Z | |
| dc.description.abstract | The puckered conformations of furanose and pyranose carbohydrate rings are central to analyzing the action of enzymes on carbohydrates. Enzyme reaction mechanisms are generally inaccessible to experiments and so have become the focus of QM(semiempirical)/MM simulations. We show that the complete free energy of puckering is required to evaluate the accuracy of semiempirical methods used to study reactions involving carbohydrates. Interestingly, we find that reducing the free energy space to lower dimensions results in near meaningless minimum energy pathways. We analyze the furanose and pyranose free energy pucker surfaces and volumes using AM1, PM3, PM3CARB-1, and SCC-DFTB. A comparison with DFT optimized structures and a HF free energy surface reveals that SCC-DFTB provides the best semiempirical description of five- and six-membered carbohydrate ring deformation. | en_ZA |
| dc.identifier | http://dx.doi.org/http://pubs.acs.org/doi/abs/10.1021/jp107620h | |
| dc.identifier.apacitation | Barnett, C. B., & Naidoo, K. J. (2010). Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations. <i>J. Phys. Chem. B.</i>, http://hdl.handle.net/11427/21257 | en_ZA |
| dc.identifier.chicagocitation | Barnett, C B, and Kevin J Naidoo "Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations." <i>J. Phys. Chem. B.</i> (2010) http://hdl.handle.net/11427/21257 | en_ZA |
| dc.identifier.citation | Barnett, C. B., & Naidoo, K. J. (2010). Ring puckering: a metric for evaluating the accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB carbohydrate QM/MM simulations. The Journal of Physical Chemistry B, 114(51), 17142-17154. | en_ZA |
| dc.identifier.issn | 1520-6106 | en_ZA |
| dc.identifier.ris | TY - Journal Article AU - Barnett, C B AU - Naidoo, Kevin J AB - The puckered conformations of furanose and pyranose carbohydrate rings are central to analyzing the action of enzymes on carbohydrates. Enzyme reaction mechanisms are generally inaccessible to experiments and so have become the focus of QM(semiempirical)/MM simulations. We show that the complete free energy of puckering is required to evaluate the accuracy of semiempirical methods used to study reactions involving carbohydrates. Interestingly, we find that reducing the free energy space to lower dimensions results in near meaningless minimum energy pathways. We analyze the furanose and pyranose free energy pucker surfaces and volumes using AM1, PM3, PM3CARB-1, and SCC-DFTB. A comparison with DFT optimized structures and a HF free energy surface reveals that SCC-DFTB provides the best semiempirical description of five- and six-membered carbohydrate ring deformation. DA - 2010 DB - OpenUCT DP - University of Cape Town J1 - J. Phys. Chem. B. LK - https://open.uct.ac.za PB - University of Cape Town PY - 2010 SM - 1520-6106 T1 - Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations TI - Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations UR - http://hdl.handle.net/11427/21257 ER - | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/11427/21257 | |
| dc.identifier.vancouvercitation | Barnett CB, Naidoo KJ. Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations. J. Phys. Chem. B.. 2010; http://hdl.handle.net/11427/21257. | en_ZA |
| dc.language | eng | en_ZA |
| dc.publisher | American Chemical Society | en_ZA |
| dc.publisher.institution | University of Cape Town | |
| dc.rights | Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) | * |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc/4.0/ | en_ZA |
| dc.source | J. Phys. Chem. B. | en_ZA |
| dc.source.uri | http://pubs.acs.org/journal/jpcbfk | |
| dc.title | Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations | en_ZA |
| dc.type | Journal Article | en_ZA |
| uct.type.filetype | Text | |
| uct.type.filetype | Image | |
| uct.type.publication | Research | en_ZA |
| uct.type.resource | Article | en_ZA |