The synthesis of amide rotaxanes, amide catenanes, and trefoil amide knots is based on template effects mediated by hydrogen bonds. While a large body of experimental data is available, in-depth theoretical studies of these template syntheses are virtually unavailable, although they would provide a more profound insight into the exact details of the hydrogen-bonding patterns involved in the formation of these mechanically interlocked species. In this article we present a density functional study of the conformational properties of tetralactam macrocycles and the threading mechanism that produces the immediate precursor for rotaxane and catenane formation. Predictions of the geometries and relative energies made on the basis of semi-empirical AM1 calculations are compared with these results in order to judge the reliability of the simpler approach. Since these calculations yield good agreement with the structural features, they have been used to extend the calculations in order to understand the mechanism of formation of a trefoil dodecaamide knot that has recently been synthesized. The inherent topological chirality of the knot is reflected in the intermediates generated during its formation; these involve helical loops. These loops parallel the rotaxane and catenane wheels with respect to the arrangement of the functional groups that mediate the template effect and may well serve as wheel analogues through which one of the precursor molecules can be threaded. This threading step finally results in the knotted structure. Good agreement between the results of the calculations presented here and experimental findings is achieved.