On the calculation of puckering free energy surfaces.
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 artifacts that are generated when a wrong parametrization is used.
Sega
M
M
Dipartimento di Fisica and INFN, Università degli Studi di Trento, via Sommarive 14, 38100 Trento, Italy. sega@science.unitn.it
Autieri
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E
Pederiva
F
F
D003198:Computer Simulation; D020723:Glucuronic Acid / Q000737:chemistry*; D008956:Models, Chemical; D013499:Surface Properties; D013816:Thermodynamics
D020723:Glucuronic Acid