We use methodologies (e.g. threading-followed-by-stoppering, slipping or clipping) to transform interpenetrated molecules into permanently interlocked molecules such as rotaxanes and catenanes.
For example:
[2]Rotaxanes based on the 1,2-bis(pyridinium)ethane − 24-crown-8 templating motif, Eur. J. Org. Chem. 2011, 1763-1770.
Host-guest interactions template: the synthesis of a [3]catenane, ChemCommun. 2004, 138-139