Studies of Disaccharide Solvation—Molecular Dynamics versus HPLC Retention

Norman W. H. Cheetham; Paramita Dasgupta

doi:10.1071/CH04158

RESEARCH ARTICLE

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Studies of Disaccharide Solvation—Molecular Dynamics versus HPLC Retention

Norman W. H. Cheetham ^A ^B ^D and Paramita Dasgupta ^A ^C

+ Author Affiliations

- Author Affiliations

^A School of Chemistry, University of New South Wales, Sydney NSW 2052, Australia.

^B Present address: Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore QLD 4558, Australia.

^C Present address: Computer-Aided Molecular Design Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic of Medicine, Rochester, MN 55905, USA.

^D Corresponding author. Email: ncheetham@usc.edu.au

Australian Journal of Chemistry 58(11) 803-809 https://doi.org/10.1071/CH04158
Submitted: 30 June 2004 Accepted: 24 October 2005 Published: 9 December 2005

Abstract

Molecular dynamics simulations have been used to assess the conformational behaviour of seven disaccharides in aqueous solution. Solvation decreased the overall conformational fluctuations of the sugars, compared to in vacuo simulations using a high dielectric constant. The most significant finding was a linear correlation between the experimental chromatographic retention parameter K´ and a molecular modelling parameter based on the next-nearest oxygen–oxygen distances in the disaccharides. The results support previous proposals for a stereospecific hydration model for carbohydrates and demonstrate the utility of a combined experimental/molecular modelling approach to its study.

Acknowledgment

This research was carried during the tenure of an Australian Postgraduate Award to P.D.

References

^* Torsion angles for a 1→x linkage connecting two pyranose rings are defined as follows:
φ = O-5–C-1–O-1–C′-x
Note: Convention dictates formal and cursive φ; is used; in the online version φ is equivalent to the formal (full vertical line) character
φ = C-1–O-1–C′-x–C′-(x + 1) x ≠ 6
φ = C-1–O-1–C′-x–C′-(x − 1) x = 6
ω = O-5–C-5–C-6–O-6
ω₁ = O-1–C-6′–C-5′–O-5′ reducing residue of 1 → 6 linked sugars
ω₁ = O-6′–C-6′–C-5′–O-5′ reducing residue (x ≠ 6) or non-reducing residue (x = 6)

^† Compatibility definitions
∂_O-O = (next-nearest O–O distance [Å] for the carbohydrate) minus (nearest [2.85 Å] or next-nearest [5.1 Å] O–O distance in SPC water)
Σ∂_O-O = Sum ∂_O-O values for a disaccharide
Σ∂_{gly O-O} = Σ∂_O-O + (absolute value [2.85 or 5.10 Å] minus [smallest distance between O-2 of non-reducing ring and an oxygen of the other]) + (absolute value [2.85 or 5.10 Å] minus [smallest O-5–O′-x of other ring])
(O-2 and O-5 are the next-neighbours of the glycosidic oxygen)

Studies of Disaccharide Solvation—Molecular Dynamics versus HPLC Retention

Abstract

Acknowledgment

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