Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates

Lii, Jenn‐Huei; Ma, Buyong; Allinger, Norman L.

doi:10.1002/(sici)1096-987x(19991130)20:15<1593::aid-jcc1>3.0.co;2-a

Cited by 134 publications

(134 citation statements)

References 30 publications

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“…The Becke3LYP DFT theory was chosen instead of the MP2 because of computing-time consideration and concerns about the intramolecular basis set superposition errors (BSSE). According to Lii and Allinger's [30] carbohydrate study, Becke3LYP theory usually results in a smaller BSSE than MP2. Each conformer was minimized.…”

Section: Methodsmentioning

confidence: 99%

Conformational analysis of thioglycoside derivatives of histo-blood group ABH antigens using an ab initio-derived reparameterization of MM4: implications for design of non-hydrolysable mimetics

Strino

Lii

Gabius

et al. 2009

J Comput Aided Mol Des

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Histo-blood group ABH antigens serve as recognition sites for infectious microorganisms and tissue lectins in intercellular communication, e.g. in tumor progression. Thus, they are of interest as a starting point for drug design. In this respect, potent non-hydrolysable derivatives such as thioglycosides are of special interest. As prerequisite to enable estimations of ligand properties relative to their natural counterparts, conformational properties of the thioglycosidic derivatives of ABH trisaccharides and their disaccharide units were calculated using systematic and filtered systematic searches with the MM4 force field. Parameters for the glycosidic torsions of thioglycosides were independently derived from ab initio calculations. The resulting energy deviations required a reparameterization of MM4 to a new parameter set called MM4R. The data sets obtained using MM4R reveal that the thioglycosides have somewhat increased levels of flexibility about the major low-energy conformations shared with the corresponding O-glycosides. In the trisaccharides, the thiosubstitution of the Gal[NAc]alpha1-3Gal linkage leads to a preference for a conformation which is the secondary minimum of the natural counterparts. This conformation also generates contacts between the N-acetyl group and the fucose moiety in the blood group A derivative. Calculations further indicate that thiosubstitution of only the Fucalpha1-2Gal linkage does not affect the conformational preferences compared to the natural trisaccharide. Thiosubstitution of both linkages in the trisaccharide results in increased flexibility but the favored conformation of the natural trisaccharides is preferred. The study suggests that thioglycoside derivatives of ABH antigens could have pharmaceutical interest as ligands of lectins and other carbohydrate-binding proteins.

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Section: Methodsmentioning

confidence: 99%

Conformational analysis of thioglycoside derivatives of histo-blood group ABH antigens using an ab initio-derived reparameterization of MM4: implications for design of non-hydrolysable mimetics

Strino

Lii

Gabius

et al. 2009

J Comput Aided Mol Des

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“…[47][48][49] Similar conclusions were also drawn from the studies of supermolecular interaction energies in both hydrogen-bonded 50,51 and π-π interacting 52 systems, molecular electric moments and polarizabilities, 53 and so-called correlated cumulative atomic multipole moments. 54 Our results confirm that augmenting a given basis set is more important for the calculation of E es , and also E int , 52 than adding a shell of valence functions (i.e., aug-cc-pVDZ vs cc-pVTZ).…”

Section: Effect Of Inclusion Of Diffuse Functions In the Basis Setsmentioning

confidence: 99%

Dependence of the Intermolecular Electrostatic Interaction Energy on the Level of Theory and the Basis Set

Volkov

King

Coppens

2005

J. Chem. Theory Comput.

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Abstract:As electrostatic forces play a prominent role in the process of folding and binding of biological macromolecules, an examination of the method dependence of the electrostatic interaction energy is of great importance. An extensive analysis of the basis set and method dependence of electrostatic interaction energies (E es ) in molecular systems using six test dimers of R-glycine is presented. A number of Hartree-Fock, Kohn-Sham, Møller-Plesset, configuration interaction (CI), quadratic CI, and coupled cluster calculations were performed using several double-, triple-, and quadruple--quality Gaussian-and Slater-type (Kohn-Sham calculations only) basis sets. The main factor affecting E es was found to be the inclusion of diffuse functions in the basis set expansions. Møller-Plesset (even at second order), quadratic CI, and coupled cluster calculations produce the most consistent results. Hartree-Fock and CI methods usually overestimate the E es , while the Kohn-Sham approach tends to underestimate the magnitude of the electrostatic interaction. The combination of the transferable-pseudoatom databank and the exact potential and multipole moment method reproduces Kohn-Sham B3LYP/6-31G** results on which it is based, confirming the excellent transferability of the pseudoatom densities within the systems studied. However, because Kohn-Sham calculations with double--quality basis sets show considerable deviations from advanced correlated methods, further development of the databank using electron densities from such methods is highly desirable.

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“…There is considerable ab initio and density functional literature on a-and b-D D -glucopyranose [4][5][6][7][8][9][10][11][12][13][14][15][16][17] . Many of these studies are calculations in which small basis sets were applied to carbohydrates (i.e., semi-empirical, HF/ 4-31G, HF/6-31G Ã ), 4-10;12;16;17 or the geometry results of smaller basis sets have been used to get energies at larger basis sets without further geometry optimization using the larger basis sets 12;14;15 .…”

Section: Introductionmentioning

confidence: 95%

B3LYP/6-311++G** study of α- and β-d-glucopyranose and 1,5-anhydro-d-glucitol: 4C1 and 1C4 chairs, 3,OB and B3,O boats, and skew-boat conformations

Appell

Strati

Willett

et al. 2004

Carbohydrate Research

121

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Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates

Cited by 134 publications

References 30 publications

Conformational analysis of thioglycoside derivatives of histo-blood group ABH antigens using an ab initio-derived reparameterization of MM4: implications for design of non-hydrolysable mimetics

Conformational analysis of thioglycoside derivatives of histo-blood group ABH antigens using an ab initio-derived reparameterization of MM4: implications for design of non-hydrolysable mimetics

Dependence of the Intermolecular Electrostatic Interaction Energy on the Level of Theory and the Basis Set

B3LYP/6-311++G** study of α- and β-d-glucopyranose and 1,5-anhydro-d-glucitol: 4C1 and 1C4 chairs, 3,OB and B3,O boats, and skew-boat conformations

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