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Mapping of the cyclodextrin cavity using the cylindrical coordinate system.

This paper describes the mapping of the inner cavity of cyclodextrin and the guest molecule using the cylindrical coordinate system. Each cavity structure of alpha-, beta-, and gamma-cyclodextrin was examined using the coordinate system, in which, the Z-axis passes through the molecular axis; a normal of the plane that consists of 6, 7, or 8 C(1) atoms of glucose units was obtained using the least-squares methods and that passes through the center of C(1) atoms. The radius rho is the distance from the Z-axis to the solvent-accessible surface of a cavity. The psi-axis is defined such that the nearest C(1) atom of the glucose unit to the Z-axis is its origin. The atomic character of the inner surface of the cavity was also obtained and plotted in the same coordinates. The guest molecule was plotted with the same coordinate system as cyclodextrin to see atoms with large rho distance of the guest molecule on the solvent-accessible surface map of cyclodextrin. It was confirmed from the map that cyclodextrin molecules have an ellipsoidal shape, have pseudo-n-hold symmetry (n=6 to alpha, 7 to beta, and 8 to gamma) in relation to their molecular axis, and guest molecules are located in relatively hydrophobic regions. It was also confirmed that the maps of this system give insights into the complementary characters of structures between the host and the guest by plotting the guest molecule in the same coordinate system.