Ring puckering: a metric for evaluating the accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB carbohydrate QM/MM simulations.
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.
Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.
Christopher B
CB
Barnett
Kevin J
KJ
Naidoo
D002241:Carbohydrates / Q000737:chemistry*; D004798:Enzymes / Q000737:chemistry; D005947:Glucose / Q000737:chemistry; D011789:Quantum Theory; D012266:Ribose / Q000737:chemistry; D013816:Thermodynamics
D002241:Carbohydrates; D004798:Enzymes; D012266:Ribose; D005947:Glucose