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A reoptimized GROMOS force field for hexopyranose‐based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers
Author(s) -
Hansen Halvor S.,
Hünenberger Philippe H.
Publication year - 2010
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21675
Subject(s) - conformational isomerism , force field (fiction) , chemistry , ring (chemistry) , hydroxymethyl , glycosidic bond , anomeric effect , computational chemistry , lone pair , stereochemistry , anomer , crystallography , molecule , organic chemistry , physics , quantum mechanics , enzyme
This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose‐based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56A CARBO (nearly equivalent to 53A6 for non‐carbohydrate systems). This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the force field to properties that had not been included previously into the parameterization procedure. The new 56A CARBO force field is characterized by: (i) the formulation of systematic build‐up rules for the automatic generation of force‐field topologies over a large class of compounds including (but not restricted to) unfunctionalized polyhexopyranoses with arbritrary connectivities; (ii) the systematic use of enhanced sampling methods for inclusion of experimental thermodynamic data concerning slow or unphysical processes into the parameterization procedure; and (iii) an extensive validation against available experimental data in solution and, to a limited extent, theoretical (quantum‐mechanical) data in the gas phase. At present, the 56A CARBO force field is restricted to compounds of the elements C, O, and H presenting single bonds only, no oxygen functions other than alcohol, ether, hemiacetal, or acetal, and no cyclic segments other than six‐membered rings (separated by at least one intermediate atom). After calibration, this force field is shown to reproduce well the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. As a result, the 56A CARBO force field should be suitable for: (i) the characterization of the dynamics of pyranose ring conformational transitions (in simulations on the microsecond timescale); (ii) the investigation of systems where alternative ring conformations become significantly populated; (iii) the investigation of anomerization or epimerization in terms of free‐energy differences; and (iv) the design of simulation approaches accelerating the anomerization process along an unphysical pathway. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011