Chapter 18: Ring dihedral Principal Component Analysis of furanose conformation
Published:20 Mar 2014
C. Coiffier, C. Barberot, J. Nuzillard, P. Goekjian, E. Hénon, and A. Haudrechy, in Carbohydrate Chemistry: Chemical and Biological Approaches, Volume 40, ed. A. Pilar Rauter, T. Lindhorst, and Y. Queneau, The Royal Society of Chemistry, 2014, vol. 40, ch. 18, pp. 378-400.
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The complete description of the conformational behaviour of sugars involves assessing exocyclic dihedral angles and ring conformations, both in terms of static conformations and dynamic behaviour within these limiting conformers. We have focused here on the conformation of the tetrahydrofuran ring and its deviation from planarity. Beyond the well-knownpseudo-rotational analysis based on two parameters, puckering angle and amplitude, we present a complementary and new approach to describe ring conformational dynamics which is better able to describe unsymmetrical conformations that are lost bypseudo-rotational analysis. Principal Component Analysis (PCA) of the endocyclic dihedral angles proved to be an efficient method to describe collective, global motions of the carbohydrate ring, with two or three principal components containing the largest mean-square fluctuation. Our ring dihedral principal component analysis model (RdPCA) describes ring conformational dynamics based on inherent ring motions rather than arbitrarily restrictive descriptors. RdPCA analysis of both classical and full quantum mechanical molecular dynamics indicates that furanosides have dominant minimum energy conformations but are rather flexible within these conformers, showing broad wells from a thermodynamic point of view. This RdPCA model also gave indications on the kinetic behaviour of such systems suggesting possible energy pathways for ring motions on the energy landscape. We believe that this useful tool can give a better understanding of the behaviour of the tetrahydrofuran ring, and hence of carbohydrate conformation.