Conformational dynamics of carbohydrates: Raman optical activity of D-glucuronic acid and N-acetyl-D-glucosamine using a combined molecular dynamics and quantum chemical approach

As two biologically and medically relevant monosaccharides, the constituents of hyaluronic acid, d-glucuronic acid and N-acetyl-d-glucosamine, constitute perfect test cases for the development of carbohydrate-specific structural methods. These two molecules have been analysed by Raman optical activi...

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Bibliographic Details
Published in:Physical chemistry chemical physics : PCCP 2015-01, Vol.17 (8), p.6016-6027
Main Authors: Mutter, Shaun T, Zielinski, François, Cheeseman, James R, Johannessen, Christian, Popelier, Paul L A, Blanch, Ewan W
Format: Article
Language:English
Subjects:
Acetylglucosamine - chemistry
Biomolecules
Carbohydrates
Dynamics
Glucuronic Acid - chemistry
Mathematical models
Molecular dynamics
Molecular Dynamics Simulation
Monosaccharides
Optical activity
Quantum chemistry
Quantum Theory
Spectra
Spectrum Analysis, Raman
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Summary:As two biologically and medically relevant monosaccharides, the constituents of hyaluronic acid, d-glucuronic acid and N-acetyl-d-glucosamine, constitute perfect test cases for the development of carbohydrate-specific structural methods. These two molecules have been analysed by Raman optical activity (ROA), a spectroscopic technique exhibiting exquisite sensitivity to stereochemistry. We show that it is possible to support the experiment with a simulation approach combining density functional theory (DFT) and molecular dynamics (MD), both using explicit solvation. Thus, we have gained new insight into the crucial hydration effects that contribute to the conformational dynamics of carbohydrates and managed to characterize in detail the poorly understood vibrational nature of this class of biomolecules. Experimental and calculated ROA spectra of these two molecules are reported and excellent agreement has been found. More specifically, comparison has been made with the more commonly used gas phase and implicitly solvated calculation approaches, which offer poor or zero modelling of solvent interactions. The calculated spectra have been used to resolve the structural origins of the observed bands, a current challenge in the study of carbohydrates due to a lack of definitive vibrational assignments. We report and analyse major features in the fingerprint region of the ROA spectra, with recurrent structural and spectral features between the two monosaccharides observed.
ISSN:1463-9076
1463-9084
DOI:10.1039/c4cp05517a