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Informing Saccharide Structural NMR Studies with Density Functional Theory Calculations

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Glycoinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1273))

Abstract

Density functional theory (DFT) is a powerful computational tool to enable structural interpretations of NMR spin–spin coupling constants ( J-couplings) in saccharides, including the abundant 1H–1H ( J HH), 13C–1H ( J CH), and 13C–13C ( J CC) values that exist for coupling pathways comprised of 1–4 bonds. The multiple hydroxyl groups in saccharides, with their attendant lone-pair orbitals, exert significant effects on J-couplings that can be difficult to decipher and quantify without input from theory. Oxygen substituent effects are configurational and conformational in origin (e.g., axial/equatorial orientation of an OH group in an aldopyranosyl ring; C–O bond conformation involving an exocyclic OH group). DFT studies shed light on these effects, and if conducted properly, yield quantitative relationships between a specific J-coupling and one or more conformational elements in the target molecule. These relationships assist studies of saccharide structure and conformation in solution, which are often challenged by the presence of conformational averaging. Redundant J-couplings, defined as an ensemble of J-couplings sensitive to the same conformational element, are particularly helpful when the element is flexible in solution (i.e., samples multiple conformational states on the NMR time scale), provided that algorithms are available to convert redundant J-values into meaningful conformational models. If the latter conversion is achievable, the data can serve as a means of testing, validating, and refining theoretical methods like molecular dynamics (MD) simulations, which are currently relied upon heavily to assign conformational models of saccharides in solution despite a paucity of experimental data needed to independently validate the method.

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Notes

  1. 1.

    “Redundancy” is defined herein as access to multiple NMR J-couplings that report on the same molecular torsion angle, θ. Furthermore, plots of J-coupling magnitude as a function of θ should not be superimposable, but rather should be phase-shifted so as to maximize the ability of these multiple couplings to discrimiate between different conformational models. If the plots overlap, the use of redundant J-couplings will not improve conformational analyses appreciably.

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Author notes

  1. Thomas Klepach, Hongqiu Zhao, Xiaosong Hu & Roland Stenutz

    Present address: Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556-5670, USA

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556-5670, USA

    Wenhui Zhang, Matthew J. Hadad & Anthony S. Serianni

  2. Department of Chemistry, Colby College, Waterville, ME, 04901-5750, USA

    Thomas Klepach

  3. Department of Biology, Colby College, Waterville, ME, 04901-5750, USA

    Thomas Klepach

  4. Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis (IUPUI), LD326, 402 N. Blackfort Street, Indianapolis, IN, 46202, USA

    Hongqiu Zhao

  5. Department of Chemistry, School of Science, Wuhan University of Technology, Wuhan, 430070, P.R. China

    Xiaosong Hu

  6. IsoSep AB, Dalkärrsvägen 11, 146 36, Tullinge, Sweden

    Roland Stenutz

  7. Radiation Laboratory, University of Notre Dame, Notre Dame, IN, 46556-5670, USA

    Ian Carmichael

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  1. Justus-Liebig-University, Giessen, Germany

    Thomas Lütteke

  2. Biognos AB, Göteborg, Sweden

    Martin Frank

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Klepach, T. et al. (2015). Informing Saccharide Structural NMR Studies with Density Functional Theory Calculations. In: Lütteke, T., Frank, M. (eds) Glycoinformatics. Methods in Molecular Biology, vol 1273. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2343-4_20

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  • DOI: https://doi.org/10.1007/978-1-4939-2343-4_20

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