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Abstract:

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.

Registro:

Documento: Artículo
Título:Comparison of different force fields for the study of disaccharides
Autor:Stortz, C.A.; Johnson, G.P.; French, A.D.; Csonka, G.I.
Filiación:Departamento de Química Orgánica-CIHIDECAR, FCEyN-Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, United States
Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Szent Gellért tér 4, Budapest, H-1521, Hungary
Palabras clave: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
Año:2009
Volumen:344
Número:16
Página de inicio:2217
Página de fin:2228
DOI: http://dx.doi.org/10.1016/j.carres.2009.08.019
Título revista:Carbohydrate Research
Título revista abreviado:Carbohydr. Res.
ISSN:00086215
CODEN:CRBRA
CAS:cellobiose, 16462-44-5, 528-50-7; Disaccharides; Hydroxides; Solvents; hydroxide ion, 14280-30-9
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00086215_v344_n16_p2217_Stortz

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Citas:

---------- APA ----------
Stortz, C.A., Johnson, G.P., French, A.D. & Csonka, G.I. (2009) . Comparison of different force fields for the study of disaccharides. Carbohydrate Research, 344(16), 2217-2228.
http://dx.doi.org/10.1016/j.carres.2009.08.019
---------- CHICAGO ----------
Stortz, C.A., Johnson, G.P., French, A.D., Csonka, G.I. "Comparison of different force fields for the study of disaccharides" . Carbohydrate Research 344, no. 16 (2009) : 2217-2228.
http://dx.doi.org/10.1016/j.carres.2009.08.019
---------- MLA ----------
Stortz, C.A., Johnson, G.P., French, A.D., Csonka, G.I. "Comparison of different force fields for the study of disaccharides" . Carbohydrate Research, vol. 344, no. 16, 2009, pp. 2217-2228.
http://dx.doi.org/10.1016/j.carres.2009.08.019
---------- VANCOUVER ----------
Stortz, C.A., Johnson, G.P., French, A.D., Csonka, G.I. Comparison of different force fields for the study of disaccharides. Carbohydr. Res. 2009;344(16):2217-2228.
http://dx.doi.org/10.1016/j.carres.2009.08.019