3D superposition of chemical fragments for N-membered rings: application to conformational analysis



In this paper a procedure is suggested for the 3D superposition of chemical fragments, which is specifically designed for rings molecules and can be combined with statistical multivariate procedures to extract useful conformational information. The procedure relies on the plane introduced by Cremer and Pople ‘A general definition of ring puckering coordinates. J. Am. Chem. Soc. 1975; 97(6): 1354–1358’ to define the celebrated puckering coordinates, and provides a measure of distance between two geometrical conformations. Real datasets are analyzed to illustrate how it can be used as input to agglomerative clustering methods, multidimensional scaling analysis and allows to compute the centroid of a group of fragments. Copyright © 2010 John Wiley & Sons, Ltd.