Ruiz-Pernia, J. J., Tunon, I. and Williams, I., 2010. Computational simulation of the lifetime of the methoxymethyl cation in water. A simple model for a glycosyl cation: when is an intermediate an intermediate? Journal of Physical Chemistry B, 114 (17), pp. 5769-5774.
A two-dimensional free-energy surface is constructed for transfer of the methoxymethyl cation between two water molecules. These atoms are treated quantum mechanically within a box of >1000 classical solvent water molecules, and the molecular dynamics of the whole system is considered at 300 K. This provides a simple model for glycosyl transfer in water. The best surface obtained (MPWB1K/6-31+G(d,p) corrected AMI/TIP3P) contains a shallow free-energy well corresponding to an oxacarbenium ion intermediate in a stepwise mechanism. Molecular dynamics analysis at three temperatures leads to a classical estimate of the lifetime of the methoxymethyl cation in water; when quantum corrections for vibrational zero-point energy are included, the lifetime is estimated to be 1 ps. This result is in complete agreement with the best experimental estimate and suggests that computational simulation is a reliable tool for elucidation of glycosyl-transfer mechanisms in enzymes and whether these involve glycosyl cations as intermediates.
|Item Type ||Articles|
|Creators||Ruiz-Pernia, J. J., Tunon, I. and Williams, I.|
|Departments||Faculty of Science > Chemistry|
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