On the Calculation of Puckering Free Energy Surfaces

Details On the Calculation of Puckering Free Energy Surfaces On the Calculation of Puckering Free Energy Surfaces

2009-04-09

arxiv.org/abs/0904.1473v1

Physics

Chemical Physics

14 pages, 4 figures, REVTeX4, submitted to J. Chem. Phys

Scientific paper

Cremer-Pople puckering coordinates appear to be the natural candidate variables to explore the conformational space of cyclic compounds, and in literature different parametrizations have been used to this end. However, while every parametrization is equivalent in identifying conformations, it is not obvious that they can also act as proper collective variables for the exploration of the puckered conformations free energy surface. It is shown that only the polar parametrization is fit to produce an unbiased estimate of the free energy landscape. As an example, the case of a six-membered ring, glucuronic acid, is presented, showing the artefacts that are generated when a wrong parametrization is used.

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