Structural investigations and modeling of cavities in clathrates

A molecular-graphics study has been performed in order to build and visualize the shape of cavities within different clathrates from X-ray diffraction data [e.g. Dianin's compound, Werner complexes Ni(SCN)2(3-methylpyridine)4, Fe(acetylacetonate)3 and Ni(ethylxanthate)2(4,4'-dimethyl-2,2'-bipyridyl) complexes]. The algorithm of the solvent-accessible surfaces representation has been applied to a part of the whole crystal structure rather than to isolated host molecules, by using the MOLCAD molecular modeling package. This type of modelization has been found very efficient both to study the shape properties of the host cavities (cage or channel types) and to approach the structural features of the host/guest interactions.