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Pure and Applied Chemistry

The Scientific Journal of IUPAC

Ed. by Burrows, Hugh / Stohner, Jürgen


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ISSN
1365-3075
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Volume 83, Issue 8

Issues

Does glycosyl transfer involve an oxacarbenium intermediate? Computational simulation of the lifetime of the methoxymethyl cation in water

Ian H. Williams / J. Javier Ruiz Pernía / Iñaki Tuñón
Published Online: 2011-04-04 | DOI: https://doi.org/10.1351/PAC-CON-10-10-12

2D free-energy surfaces for transfer of the methoxymethyl cation between two water molecules are constructed from molecular dynamics (MD) simulations in which these atoms are treated quantum-mechanically within a box of 1030 classical solvent water molecules at 300 K. This provides a simple model for glycosyl transfer in water. The AM1/TIP3P surfaces with 2D-spline corrections at either MPWB1K/6-31+G(d,p) or MP2/6-31+G(d,p) contain a shallow free-energy well corresponding to an oxacarbenium ion intermediate in a DN*AN mechanism. MD 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 about 1 ps, in agreement with the best experimental estimate. This suggests that computational simulation, with appropriate high-level correction, is a reliable tool to obtain detailed and reliable mechanistic descriptions for glycosidases. In view of the importance of developing improved anti-influenza drugs, simulations of sialidases that considered both sialyl oxacarbenium ion and covalent sialyl-enzyme as possible intermediates could provide particular insight.

Keywords: computational simulation; glycosyl transfer; lifetime; oxacarbenium ion; quantum mechanics/molecular mechanics (QM/MM); solvent dynamics

Conference

International Conference on Physical Organic Chemistry (ICPOC-20), International Conference on Physical Organic Chemistry, ICPOC, Physical Organic Chemistry, 20th, Busan, Korea, 2010-08-22–2010-08-27

References

About the article

Published Online: 2011-04-04

Published in Print: 2011-04-04


Citation Information: Pure and Applied Chemistry, Volume 83, Issue 8, Pages 1507–1514, ISSN (Online) 1365-3075, ISSN (Print) 0033-4545, DOI: https://doi.org/10.1351/PAC-CON-10-10-12.

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