| Abstract
| - Combined quantum mechanical (QM) and molecular mechanical (MM) calculations are reported for thetriosephosphate isomerase-catalyzed conversion of dihydroxyacetone phosphate into glyceraldehyde 3-phosphate. The minima and transition states for the relevant proton-transfer reactions have been located on QM/MM potential surfaces. The primary objective of this work is to study the sensitivity of optimized structuresand relative energies toward variations in the QM/MM model, including the choice of the QM method, thesize of the QM region, the size of the optimized MM region, and the treatment of the QM/MM boundary.The QM methods that have been applied in combination with the CHARMm force field range fromsemiempirical (AM1) to density functional (BP86, B3LYP) and ab initio (MP2) methods, the most extensiveQM calculations involving 275 atoms and 2162 basis functions at the density functional level. Implicationsof the different choices of QM/MM options on the energy profile are discussed. From a mechanistic point ofview, the present QM/MM results support a four-step proton-transfer pathway via an enediol, with involvementof neutral His95 acting as a proton donor, since the alternative direct intramolecular proton transfer in theenediolate is disfavored by the protein environment.
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