mm3 Potential energy surfaces of α-3-linked l-fucobiose and fucotriose and their sulfated counterparts

Stortz, Carlos A.

doi:10.1016/j.carres.2004.06.024

Cited by 5 publications

(17 citation statements)

References 31 publications

(65 reference statements)

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“…12 The partition function for β-mannobiose at ε=3 is 890 deg 2 (Table 3). This value is slightly lower than that encountered by the all-equatorial cellobiose, 12 and other disaccharides like maltose, 12 sophorose, kojibiose 14 and a fucobiose, 15 but similar to other disaccharides. 10 The flexibility increases by raising the dielectric constant (Table 3).…”

Section: Introductionmentioning

confidence: 61%

“…This fact can also be deduced by observing Figure 2: the low energy surface is more extended when working at ε=80. The absolute flexibility measurements also give a value (0.0078) lower than those of other 4-linked disaccharides like maltose or cellobiose, 12 but higher than those of other disaccharides 14,15 which exhibit a larger distance between minima A and B, and thus a higher potential barrier. As expected from its reduced potential barrier (Table 1), the absolute flexibility also increases at ε=80 (Table 3).…”

Section: Introductionmentioning

confidence: 79%

“…The minima are named by a two-letter code according to the minimum energy region (A or B) of the Man"→Man' linkage (first letter) and the Man'→Man linkage (second letter). [12][13][14][15] Table 3 shows the flexibility measurements carried out using the data obtained for the di-and trisaccharides under study. Table 1.…”

Section: Introductionmentioning

confidence: 99%

“…Those studies were recently extended to different trisaccharides, [12][13][14][15] in an attempt to achieve a better knowledge of the conformational features of polysaccharides. For β-mannobiose at ε=3, present calculations show the typical pattern (Figs.…”

Section: Introductionmentioning

confidence: 99%

“…Modeling at ε=80 was found to give better coincidence with experimental data in water than that at lower dielectric constants in a couple of examples. 3,15 However, the absence of hydrogen bonding and electrostatic forces at such high dielectric constant may be inducing deformations in the calculations not predicted by its parameterization, expected to work at lower dielectric constants.…”

Section: Introductionmentioning

confidence: 99%

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MM3 Potential energy surfaces of β-4-linked mannobiose and mannotriose at different dielectric constants

Stortz¹

2005

Arkivoc

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The adiabatic potential energy surface (PES) of β-4-linked mannobiose was obtained using the MM3 force field at ε=3 and ε=80, and plotted as contour maps and as 2D graphs representing the energy vs. the ψ angle. The surfaces of the corresponding trisaccharide were also obtained and represented by a single 3D contour map for which the energy is plotted against the two ψ glycosidic angles. The PES of the disaccharide contains a low-energy well comprising two different minima, and three more minima in different locations. No major change was observed by changing the dielectric constant. For the trisaccharide, four main minima were observed, located within one minimum-energy region. The minima have a geometry close to that experimentally obtained for mannobiose, mannotriose and mannan I in solid state, but differ from that expected in aqueous solutions. The flexibility of the glycosidic linkage increases at higher dielectric constant, whereas it decreases for the linkage closer to the reducing end when passing from the di-to the trisaccharide.

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Section: Introductionmentioning

confidence: 61%

Section: Introductionmentioning

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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MM3 Potential energy surfaces of β-4-linked mannobiose and mannotriose at different dielectric constants

Stortz¹

2005

Arkivoc

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Comparative performance of MM3(92) and two TINKER™ MM3 versions for the modeling of carbohydrates

Stortz

2005

J Comput Chem

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The 1992 version of MM3 was largely used for modeling mono-, di-, and trisaccharides. In later versions of MM3 improvements were made in some parameters that may be important for carbohydrates. This corrected MM3 force field is part of the Tinker package, freely available (as its 4.1 version), and included in the Chem 3D Ultra 8.0 package (as the 3.7 version). The latter version lacks the corrections to the standard bond lengths produced by electronegativity and anomeric effects, whereas the Tinker 4.1 version only lacks the latter correction. The present work compares the performance of the three MM3 versions (and in some cases, DFT and/or HF/ab initio procedures) on several carbohydrate model problems as the chair and rotamer equilibria in 2-hydroxy- and 2-methoxytetrahydropyran, hydrogen bonding in cis-2,3-dihydroxytetrahydropyran, and the potential energy surfaces around the glycosidic bonds of two sulfated disaccharides and two trisaccharides. Tinker MM3 can be used accurately to estimate carbohydrate energies and geometries, and-with the help of some programming-to pursue studies on the potential energy surfaces of di- and trisaccharides. In most cases results obtained using the three MM3 versions are similar, although large energy differences are obtained when comparing a rotameric distribution around a O-C-O-H dihedral, which is almost forced to the exo-anomeric position by the Tinker versions. In other systems smaller energy differences are found, but they can nevertheless lead to a different global minimum when comparing conformers of similar energy. MM3(92) establishes better the differences between the bond lengths in both anomers, as an expected expression of the anomeric correction.

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Differentiation of the fucoidan sulfated l-fucose isomers constituents by CE-ESIMS and molecular modeling

Tissot¹,

Salpin²,

Martínez³

et al. 2006

Carbohydrate Research

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Alpha-L-fucose, the monosaccharide component of fucoidan, is found in the polysaccharide mainly as its sulfated form where sulfate groups are in position 2 and/or 4 and/or 3. The correlation between biological activities and structure of fucoidan requires the determination of the sulfation pattern of the fucose residues. Therefore, it is of importance to discriminate between the isobaric sulfated fucose isomers. For this purpose, the three isomers 2-O-, 3-O-, and 4-O-sulfated fucose have been analyzed using electrospray ion trap mass spectrometry and capillary electrophoresis. The results reported herein show that it is possible to differentiate between these three positional isomers of sulfated fucose based on their fragmentation pattern upon MS/MS experiments. 3-O-Sulfated fucose was characterized by the loss of the hydrogenosulfate anion HSO4- as the main fragmentation product, while the two other isomers 2-O-, and 4-O-sulfated fucose exhibited cross-ring fragmentation yielding to distinctive (0,2)X and (0,2)A daughter ion, respectively. A computational study of the conformation of the sulfated fucose isomers was carried out providing an understanding of the fragmentation pattern with respect to the position of the sulfate group.

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mm3 Potential energy surfaces of α-3-linked l-fucobiose and fucotriose and their sulfated counterparts

Cited by 5 publications

References 31 publications

MM3 Potential energy surfaces of β-4-linked mannobiose and mannotriose at different dielectric constants

MM3 Potential energy surfaces of β-4-linked mannobiose and mannotriose at different dielectric constants

Comparative performance of MM3(92) and two TINKER™ MM3 versions for the modeling of carbohydrates

Differentiation of the fucoidan sulfated l-fucose isomers constituents by CE-ESIMS and molecular modeling

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