Comparison of different force fields for the study of disaccharides

Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying β-cellobiose, α-maltose, and α-galabiose [α-d-Galp-(1→4)-α-d-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl, and glycosidic linkage orientati...

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Autor principal:	Stortz, Carlos Arturo
Publicado:	2009
Materias:	Cellobiose Disaccharides Force field Galabiose Maltose Molecular mechanics Best choice Crystal structure data Dielectric constant values Dielectric constants Empirical force Force fields Glycosidic linkages Level density Parameterizations Quantum methods Semi-empirical Torsion angle Ceramic capacitors Density functional theory Dielectric waveguides Methanol Parameterization Permittivity Polysaccharides Crystal structure alpha galabiose alpha maltose cellobiose disaccharide hydroxyl group unclassified drug article controlled study crystal structure density functional theory dielectric constant molecular mechanics priority journal quantum mechanics sensitivity analysis Carbohydrate Conformation Computer Simulation Hydroxides Models, Molecular Quantum Theory Solvents
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00086215_v344_n16_p2217_Stortz http://hdl.handle.net/20.500.12110/paper_00086215_v344_n16_p2217_Stortz
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	paper:paper_00086215_v344_n16_p2217_Stortz
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spelling	paper:paper_00086215_v344_n16_p2217_Stortz2023-06-08T14:32:57Z Comparison of different force fields for the study of disaccharides Stortz, Carlos Arturo Cellobiose Disaccharides Force field Galabiose Maltose Molecular mechanics Best choice Cellobiose Crystal structure data Dielectric constant values Dielectric constants Disaccharides Empirical force Force field Force fields Galabiose Glycosidic linkages Level density Parameterizations Quantum methods Semi-empirical Torsion angle Ceramic capacitors Density functional theory Dielectric waveguides Maltose Methanol Molecular mechanics Parameterization Permittivity Polysaccharides Crystal structure alpha galabiose alpha maltose cellobiose disaccharide hydroxyl group unclassified drug article controlled study crystal structure density functional theory dielectric constant molecular mechanics priority journal quantum mechanics sensitivity analysis Carbohydrate Conformation Computer Simulation Disaccharides Hydroxides Models, Molecular Quantum Theory Solvents Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying β-cellobiose, α-maltose, and α-galabiose [α-d-Galp-(1→4)-α-d-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl, and glycosidic linkage orientations were minimized by the different methods, some at two dielectric constants. By comparing these results and the available crystal structure data and/or higher level density functional theory results, it was concluded that the newer parameterizations for force fields (GROMOS, GLYCAM06, OPLS-2005 and CSFF) give results that are reasonably similar to each other, whereas the older parameterizations for Amber, charmm or OPLS were more divergent. However, MM3, an older force field, gave energy and geometry values comparable to those of the newer parameterizations, but with less sensitivity to dielectric constant values. These systems worked better than MM2 variants, which were still acceptable. PM3CARB-1 also gave adequate results in terms of linkage and exocyclic torsion angles. GROMOS, GLYCAM06, and MM3 appear to be the best choices, closely followed by MM4, CSFF, and OPLS-2005. With GLYCAM06 and to a lesser extent, CSFF, and OPLS-2005, a number of the conformers that were stable with MM3 changed to other forms. © 2009 Elsevier Ltd. Fil:Stortz, C.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2009 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00086215_v344_n16_p2217_Stortz http://hdl.handle.net/20.500.12110/paper_00086215_v344_n16_p2217_Stortz
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Cellobiose Disaccharides Force field Galabiose Maltose Molecular mechanics Best choice Cellobiose Crystal structure data Dielectric constant values Dielectric constants Disaccharides Empirical force Force field Force fields Galabiose Glycosidic linkages Level density Parameterizations Quantum methods Semi-empirical Torsion angle Ceramic capacitors Density functional theory Dielectric waveguides Maltose Methanol Molecular mechanics Parameterization Permittivity Polysaccharides Crystal structure alpha galabiose alpha maltose cellobiose disaccharide hydroxyl group unclassified drug article controlled study crystal structure density functional theory dielectric constant molecular mechanics priority journal quantum mechanics sensitivity analysis Carbohydrate Conformation Computer Simulation Disaccharides Hydroxides Models, Molecular Quantum Theory Solvents
spellingShingle	Cellobiose Disaccharides Force field Galabiose Maltose Molecular mechanics Best choice Cellobiose Crystal structure data Dielectric constant values Dielectric constants Disaccharides Empirical force Force field Force fields Galabiose Glycosidic linkages Level density Parameterizations Quantum methods Semi-empirical Torsion angle Ceramic capacitors Density functional theory Dielectric waveguides Maltose Methanol Molecular mechanics Parameterization Permittivity Polysaccharides Crystal structure alpha galabiose alpha maltose cellobiose disaccharide hydroxyl group unclassified drug article controlled study crystal structure density functional theory dielectric constant molecular mechanics priority journal quantum mechanics sensitivity analysis Carbohydrate Conformation Computer Simulation Disaccharides Hydroxides Models, Molecular Quantum Theory Solvents Stortz, Carlos Arturo Comparison of different force fields for the study of disaccharides
topic_facet	Cellobiose Disaccharides Force field Galabiose Maltose Molecular mechanics Best choice Cellobiose Crystal structure data Dielectric constant values Dielectric constants Disaccharides Empirical force Force field Force fields Galabiose Glycosidic linkages Level density Parameterizations Quantum methods Semi-empirical Torsion angle Ceramic capacitors Density functional theory Dielectric waveguides Maltose Methanol Molecular mechanics Parameterization Permittivity Polysaccharides Crystal structure alpha galabiose alpha maltose cellobiose disaccharide hydroxyl group unclassified drug article controlled study crystal structure density functional theory dielectric constant molecular mechanics priority journal quantum mechanics sensitivity analysis Carbohydrate Conformation Computer Simulation Disaccharides Hydroxides Models, Molecular Quantum Theory Solvents
description	Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying β-cellobiose, α-maltose, and α-galabiose [α-d-Galp-(1→4)-α-d-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl, and glycosidic linkage orientations were minimized by the different methods, some at two dielectric constants. By comparing these results and the available crystal structure data and/or higher level density functional theory results, it was concluded that the newer parameterizations for force fields (GROMOS, GLYCAM06, OPLS-2005 and CSFF) give results that are reasonably similar to each other, whereas the older parameterizations for Amber, charmm or OPLS were more divergent. However, MM3, an older force field, gave energy and geometry values comparable to those of the newer parameterizations, but with less sensitivity to dielectric constant values. These systems worked better than MM2 variants, which were still acceptable. PM3CARB-1 also gave adequate results in terms of linkage and exocyclic torsion angles. GROMOS, GLYCAM06, and MM3 appear to be the best choices, closely followed by MM4, CSFF, and OPLS-2005. With GLYCAM06 and to a lesser extent, CSFF, and OPLS-2005, a number of the conformers that were stable with MM3 changed to other forms. © 2009 Elsevier Ltd.
author	Stortz, Carlos Arturo
author_facet	Stortz, Carlos Arturo
author_sort	Stortz, Carlos Arturo
title	Comparison of different force fields for the study of disaccharides
title_short	Comparison of different force fields for the study of disaccharides
title_full	Comparison of different force fields for the study of disaccharides
title_fullStr	Comparison of different force fields for the study of disaccharides
title_full_unstemmed	Comparison of different force fields for the study of disaccharides
title_sort	comparison of different force fields for the study of disaccharides
publishDate	2009
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00086215_v344_n16_p2217_Stortz http://hdl.handle.net/20.500.12110/paper_00086215_v344_n16_p2217_Stortz
work_keys_str_mv	AT stortzcarlosarturo comparisonofdifferentforcefieldsforthestudyofdisaccharides
_version_	1768545169915772928

Comparison of different force fields for the study of disaccharides

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