Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

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

A reoptimized GROMOS force field for hexopyranose‐based carbohydrates accounting for the relative... 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 56ACARBO (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 56ACARBO 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 56ACARBO 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 56ACARBO 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 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Computational Chemistry Wiley

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

Download PDF
35 pages

Loading next page...
 
/lp/wiley/a-reoptimized-gromos-force-field-for-hexopyranose-based-carbohydrates-ZD0AFfoGnh

References (338)

Publisher
Wiley
Copyright
Copyright © 2010 Wiley Periodicals, Inc.
ISSN
0192-8651
eISSN
1096-987X
DOI
10.1002/jcc.21675
pmid
21387332
Publisher site
See Article on Publisher Site

Abstract

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 56ACARBO (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 56ACARBO 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 56ACARBO 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 56ACARBO 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

Journal

Journal of Computational Chemistry – Wiley

Published: Apr 30, 2011

There are no references for this article.