A QM/MM analysis of the conformations of crystalline sucrose moieties

French, Alfred D.; Kelterer, Anne‐Marie; Cramer, Christopher J.; Johnson, Glenn P.; Dowd, Michael K.

doi:10.1016/s0008-6215(00)00051-3

Cited by 48 publications

(34 citation statements)

References 65 publications

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“…3a) is fairly different from our previously published 17 HF/6-31G * surface for the analog that lacks the methyl group. There is a considerably better fit of the crystal structures on the surface of this more complete methylated model.…”

Section: The Individual Analog Surfacescontrasting

confidence: 87%

“…The methyl group on the furanose ring is over the interresidue linkage on the present sucrose analog, and the map for the α,β-trehalose analog is more similar to the map for the sucrose analog without the methyl group. 17 Secondly, the β-fructose ring in sucrose (α-D-glucopyranosyl-1,2 -β-D-fructofuranoside) has five atoms. That flatter, more flexible ring would be expected to have different steric interactions with the α-glucose analog ring than would the six-membered β-ring in the α,β-trehalose analog.…”

Section: The Individual Analog Surfacesmentioning

confidence: 99%

“…We have recently developed a simple hybrid method for making Ramachandran plots. 17 It involves the separate calculation of the MM energy surface for the complete disaccharide, with the requisite extensive variation of the exo-cyclic orientations. Also required are separate MM and QM energy surfaces for the critical part of the disaccharide.…”

Section: Introductionmentioning

confidence: 99%

“…The fit of the crystal structures to the energy surfaces for each molecule will be discussed in greater detail elsewhere (e.g., see ref. 17.) The crystal structures include molecules whose hydroxyl groups have substantial substitution or are missing, and molecules that form complexes with ions are included.…”

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confidence: 99%

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HF/6-31G* energy surfaces for disaccharide analogs

et al. 2000

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ABSTRACT:The HF/6-31G * level of theory was used to calculate relaxed potential energy surfaces for 12 analogs of disaccharides. The analogs were made by replacing glucose with tetrahydropyran and fructose with 2-methyltetrahydrofuran. Molecules had zero, one or two anomeric carbon atoms, and di-axial, axial-equatorial, and di-equatorial linkages. Despite the absence of hydroxyl groups, the surfaces account well for conformations that are observed in crystals of the parent disaccharides. Thus, torsional energy and the simple bulk of ring structures are major factors in determining disaccharide conformation. The contour shapes around the global minima depend on the number of anomeric carbons involved in the linkage, while the presence of alternative minima that have relative energies less than 4 kcal/mol mostly requires equatorial bonds. However, molecules with two adjacent anomeric centers gave exceptions to these rules. Flexibility values related to a partition function show that the di-axial trehalose analog is the most rigid. The di-equatorial pseudodisaccharide analog with no anomeric centers is most flexible. Reproduction of these surfaces is proposed as a simple test of force fields for modeling carbohydrates. Also, these surfaces can be used in a simple hybrid method for calculating disaccharide energy surfaces.

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Section: The Individual Analog Surfacescontrasting

confidence: 87%

Section: The Individual Analog Surfacesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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confidence: 99%

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HF/6-31G* energy surfaces for disaccharide analogs

et al. 2000

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“…15 Furthermore, the distribution of energies follows a Boltzmann-like exponential decay curve, indicating that the method is predictive for condensed-phase systems. 18 The elevated dielectric constant diminishes by 80% the otherwise dominating influence of intramolecular hydrogen bonds without the need to explicitly consider neighboring molecules.…”

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Twisting of glycosidic bonds by hydrolases

Johnson¹,

Petersen²,

French³

et al. 2009

Carbohydrate Research

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Patterns of scissile bond twisting have been found in crystal structures of glycoside hydrolases (GHs) that are complexed with substrates and inhibitors. To estimate the increased potential energy in the substrates that results from this twisting, we have plotted torsion angles for the scissile bonds on hybrid Quantum Mechanics::Molecular Mechanics energy surfaces. Eight such maps were constructed, including one for α-maltose and three for different forms of methyl α-acarviosinide to provide energies for twisting of α-(1,4) glycosidic bonds. Maps were also made for β-thiocellobiose and for three β-cellobiose conformers having different glycon ring shapes to model distortions of β-(1,4) glycosidic bonds. Different GH families twist scissile glycosidic bonds differently, increasing their potential energies from 0.5 to 9.5 kcal/mol. In general, the direction of twisting of the glycosidic bond away from the conformation of lowest intramolecular energy correlates with the position (syn or anti) of the proton donor with respect to the glycon's ring oxygen atom. This correlation suggests that glycosidic bond distortion is important for the optimal orientation of one of the glycosidic oxygen lone pairs toward the enzyme's proton donor. ring oxygen atom. That correlation suggests that glycosidic bond distortion is important for the optimal orientation of one of the glycosidic oxygen lone pairs toward the enzyme's proton donor.

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Sucrose in aqueous solution revisited, Part 2: Adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation

Xia¹,

Case²

2011

Biopolymers

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We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4 M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic φ and ψ torsion angles. NMR relaxation parameters, including longitudinal (R1) and transverse (R2) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S2) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80–90% of the conformations having φ – ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures.

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A QM/MM analysis of the conformations of crystalline sucrose moieties

Cited by 48 publications

References 65 publications

HF/6-31G* energy surfaces for disaccharide analogs

HF/6-31G* energy surfaces for disaccharide analogs

Twisting of glycosidic bonds by hydrolases

Sucrose in aqueous solution revisited, Part 2: Adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation

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