We have tested and discussed the accuracy of hybrid quantum mechanics/molecular mechanics molecular dynamics free energy calculations for the investigation of the mechanism of dehydration of biomass-derived carbohydrates in solution. In this respect and taking into account earlier calculations of this type, we have developed a microkinetic model for the dehydration of fructose to 5-hydroxymethylfurfural (HMF) in acidic water and embedded it in a reaction network that includes fructose and HMF degradation reactions. Sensitivity analysis of the kinetic model has shown the rate-limiting step of the reaction network under consideration to be an intramolecular hydride transfer that takes place right after the first water removal from fructose. We predict the formation of two stable intermediates, one of which is structurally similar to the (4R,5R)-4-hydroxy-5-hydroxymethyl-4,5-dihydrofuran-2-carbaldehyde intermediate identified by NMR studies in pure DMSO solution. We find remarkable agreement between calculated and experimental concentration profiles over a wide range of temperatures and over the entire range of timescales considered in the kinetic study of Asghari and Yoshida. We demonstrate that the microkinetic model cannot capture the correct temperature dependence of the rates unless one uses Marcus theory rate constants for those elementary steps of the mechanism that involve hydride transfer. The computed apparent activation energy and Arrhenius frequency factor for fructose conversion to HMF are also found to be in excellent agreement with those obtained from experiments.