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A GROMOS Force Field for Furanose-Based Carbohydrates by Karina Nester; Karolina Gaweda; Wojciech Plazinski is a Physics and Astronomy article available to read on EtoBox.

What is A GROMOS Force Field for Furanose-Based Carbohydrates about?

The article describes a GROMOS force field parameter set for molecular dynamics simulations of furanose carbohydrates. The proposed united-atom force field is designed and validated with respect to the conformational properties of furanose mono-, di-, oligo-and polymers in aqueous solvent. The set accounts for the possibility of arbitrary glycosidic linkage connectivity between units, O-alkylation as well as of different anomery. The compatibility with the already existing, pyranose-dedicated GROMOS 56A6 CARBO/CARBO\_R set allows to use the presently proposed extension for studying more diverse and biologicallyrelevant carbohydrates that exploit both pyranose and furanose units. The validation performed against the quantum-mechanical and experimental data concerning the structural and conformational features shows that the newly-developed set is capable to reproduce conformational equilibrium within the furanose ring, relative free energies of anomers, hydroxymethyl rotamers, and glycosidic linkage conformers. Additionally, the results concerning the conformation of the furanose ring with relation to the two-state model as well as other conformational features of furanose-containin

Who reads A GROMOS Force Field for Furanose-Based Carbohydrates?

Author

Karina Nester; Karolina Gaweda; Wojciech Plazinski

Published

2019

Language

EN

Field

Physics and Astronomy (Physical Sciences)