Comparison of different force fields for the study of disaccharides

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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, C.A
Otros Autores: Johnson, G.P, French, A.D, Csonka, G.I
Formato: Capítulo de libro
Lenguaje:Inglés
Publicado: 2009
Acceso en línea:Registro en Scopus
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024 7 |2 scopus  |a 2-s2.0-70349769322 
024 7 |2 cas  |a cellobiose, 16462-44-5, 528-50-7; Disaccharides; Hydroxides; Solvents; hydroxide ion, 14280-30-9 
040 |a Scopus  |b spa  |c AR-BaUEN  |d AR-BaUEN 
030 |a CRBRA 
100 1 |a Stortz, C.A. 
245 1 0 |a Comparison of different force fields for the study of disaccharides 
260 |c 2009 
270 1 0 |m Stortz, C.A.; Departamento de Química Orgánica-CIHIDECAR, FCEyN-Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina; email: stortz@qo.fcen.uba.ar 
506 |2 openaire  |e Política editorial 
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520 3 |a 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.  |l eng 
536 |a Detalles de la financiación: Umweltbundesamt 
536 |a Detalles de la financiación: National Council for Scientific Research 
536 |a Detalles de la financiación: U.S. Department of Agriculture 
536 |a Detalles de la financiación: Agricultural Research Service 
536 |a Detalles de la financiación: Consejo Nacional de Investigaciones Científicas y Técnicas 
536 |a Detalles de la financiación: This work was supported by grants from UBA and CONICET (C.A.S.), and normal research funds from the Agricultural Research Service of the U.S. Department of Agriculture (A.D.F. and G.P.J.). C.A.S. is a Research Member of the National Research Council of Argentina (CONICET). 
593 |a Departamento de Química Orgánica-CIHIDECAR, FCEyN-Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina 
593 |a Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, United States 
593 |a Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Szent Gellért tér 4, Budapest, H-1521, Hungary 
690 1 0 |a CELLOBIOSE 
690 1 0 |a DISACCHARIDES 
690 1 0 |a FORCE FIELD 
690 1 0 |a GALABIOSE 
690 1 0 |a MALTOSE 
690 1 0 |a MOLECULAR MECHANICS 
690 1 0 |a BEST CHOICE 
690 1 0 |a CELLOBIOSE 
690 1 0 |a CRYSTAL STRUCTURE DATA 
690 1 0 |a DIELECTRIC CONSTANT VALUES 
690 1 0 |a DIELECTRIC CONSTANTS 
690 1 0 |a DISACCHARIDES 
690 1 0 |a EMPIRICAL FORCE 
690 1 0 |a FORCE FIELD 
690 1 0 |a FORCE FIELDS 
690 1 0 |a GALABIOSE 
690 1 0 |a GLYCOSIDIC LINKAGES 
690 1 0 |a LEVEL DENSITY 
690 1 0 |a PARAMETERIZATIONS 
690 1 0 |a QUANTUM METHODS 
690 1 0 |a SEMI-EMPIRICAL 
690 1 0 |a TORSION ANGLE 
690 1 0 |a CERAMIC CAPACITORS 
690 1 0 |a DENSITY FUNCTIONAL THEORY 
690 1 0 |a DIELECTRIC WAVEGUIDES 
690 1 0 |a MALTOSE 
690 1 0 |a METHANOL 
690 1 0 |a MOLECULAR MECHANICS 
690 1 0 |a PARAMETERIZATION 
690 1 0 |a PERMITTIVITY 
690 1 0 |a POLYSACCHARIDES 
690 1 0 |a CRYSTAL STRUCTURE 
690 1 0 |a ALPHA GALABIOSE 
690 1 0 |a ALPHA MALTOSE 
690 1 0 |a CELLOBIOSE 
690 1 0 |a DISACCHARIDE 
690 1 0 |a HYDROXYL GROUP 
690 1 0 |a UNCLASSIFIED DRUG 
690 1 0 |a ARTICLE 
690 1 0 |a CONTROLLED STUDY 
690 1 0 |a CRYSTAL STRUCTURE 
690 1 0 |a DENSITY FUNCTIONAL THEORY 
690 1 0 |a DIELECTRIC CONSTANT 
690 1 0 |a MOLECULAR MECHANICS 
690 1 0 |a PRIORITY JOURNAL 
690 1 0 |a QUANTUM MECHANICS 
690 1 0 |a SENSITIVITY ANALYSIS 
690 1 0 |a CARBOHYDRATE CONFORMATION 
690 1 0 |a COMPUTER SIMULATION 
690 1 0 |a DISACCHARIDES 
690 1 0 |a HYDROXIDES 
690 1 0 |a MODELS, MOLECULAR 
690 1 0 |a QUANTUM THEORY 
690 1 0 |a SOLVENTS 
700 1 |a Johnson, G.P. 
700 1 |a French, A.D. 
700 1 |a Csonka, G.I. 
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