Octa-O-propanoyl-β-maltose: crystal structure, acyl stacking, related structures, and conformational analysis

The hypothesis of tautomeric equilibrium between epimers in ciquitins A and B

Recently, ciquitins A and B isolated from the powdered and defatted airdried aerial parts of Leucophyllum ambiguum were reported as a mixture of conformers in a solution at room temperature. Considering the existence of a hemiacetal hydroxyl fragment in the ciquitins A and B, they are more likely to exist in the form of epimer rather than the mixture of conformers. To confirm this hypothesis, the NMR calculations of two epimers at C-9 (1-a and 1-b) were performed and the results matched well with experimental NMR data of mixtures (1). Moreover, a brief discussion on the reason for this hypothesis was also presented.

Energy maps for glycosidic linkage conformations

Glycosidic linkage conformations are the main factors in determining the shapes of disaccharide, oligosaccharide, and polysaccharide molecules. The conformations are expressed in terms of the torsion angles about the bonds from each ring of the disaccharide moiety to its glycosidic oxygen atom, and the probability of a given conformation is often expressed in terms of its free or potential energy. The energy surface or map for a disaccharide is a display of the energy plotted against the two torsion angles. Successful mapping allows a particular kind of energy calculation to provide the energy values for each conformation and avoids possible pitfalls. Although different methods are discussed, the main emphasis of this chapter is on the technical production of the maps and their exploitation in further understanding the shape of the molecule in question.

Peracetylated alpha-D-glucopyranosyl fluoride and peracetylated alpha-maltosyl fluoride

The X-ray analyses of 2,3,4,6-tetra-O-acetyl-alpha-D-glucopyranosyl fluoride, C(14)H(19)FO(9), (I), and the corresponding maltose derivative 2,3,4,6-tetra-O-acetyl-alpha-D-glucopyranosyl-(1-->4)-2,3,6-tri-O-acetyl-alpha-D-glucopyranosyl fluoride, C(26)H(35)FO(17), (II), are reported. These add to the series of published alpha-glycosyl halide structures; those of the peracetylated alpha-glucosyl chloride [James & Hall (1969). Acta Cryst. A25, S196] and bromide [Takai, Watanabe, Hayashi & Watanabe (1976). Bull. Fac. Eng. Hokkaido Univ. 79, 101-109] have been reported already. In our structures, which have been determined at 140 K, the glycopyranosyl ring appears in a regular (4)C(1) chair conformation with all the substituents, except for the anomeric fluoride (which adopts an axial orientation), in equatorial positions. The observed bond lengths are consistent with a strong anomeric effect, viz. the C1-O5 (carbohydrate numbering) bond lengths are 1.381 (2) and 1.381 (3) A in (I) and (II), respectively, both significantly shorter than the C5-O5 bond lengths, viz. 1.448 (2) A in (I) and 1.444 (3) A in (II).

Comparison of different force fields for the study of disaccharides

Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying beta-cellobiose, alpha-maltose, and alpha-galabiose [alpha-D-Galp-(1-->4)-alpha-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.

Twisting of glycosidic bonds by hydrolases

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 alpha-maltose and three for different forms of methyl alpha-acarviosinide to provide energies for twisting of alpha-(1,4) glycosidic bonds. Maps were also made for beta-thiocellobiose and for three beta-cellobiose conformers having different glycon ring shapes to model distortions of beta-(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.

Linkage and pyranosyl ring twisting in cyclodextrins

Acylated beta-cyclodextrins (beta-CDs) were studied to gain perspective on maltose octapropanoate, the crystal structure of which was reported in the preceding paper in this issue. Acylated beta-CDs are distorted so we looked at other CDs and gained increased understanding of distortion in CDs and possibly, shapes in starch. Classic CDs have six to eight glucose residues in a doughnut shape that is stabilized by a ring of inter-residue O3,,,O2' hydrogen bonds. On a phi,psi energy map for a maltose analog that does not form hydrogen bonds, classic CD linkages have higher energies than structures that are stabilized by the exo-anomeric effect. In distorted beta-CDs, which lack hydrogen bonding, some linkages attain low-energies from the exo-anomeric effect and acyl stacking. Those linkages result in left-handed helical geometry so other linkages are forced by the CD macrocycle to have counter-balancing right-handed character. Permethylated gamma-CDs have two 'flipping' linkages as do some larger native CDs. Flipping linkages allow two left-handed segments to join into a macrocycle, thus avoiding the higher-energy, right-handed forms. Some glucose rings in derivatized beta-CDs have substantial positive twists of the pseudo torsion angle O1-C1...C4-O4, adding right-handed character to balance the left-handed linkages. In substituted gamma-CD, all residues have negative twists, giving extra left-handed character to the short, pseudo-helical segments. In non-macrocyclic molecules the twists ranged from -14 degrees to +2 degrees , averaging -6.1 degrees. In these beta- and gamma-CDs, the twists ranged from -22 degrees to +16 degrees for (4)C(1) rings, and the (O)S(2) ring in acetylated beta-CD has a twist of +34 degrees . Glucose residues in other CDs were less twisted.