The union of covalent and noncovalent chemistries manifested in the mechanical bond represents one of the great chemical triumphs of the last half century. However, until recently, the preparation of mechanically interlocked compounds has often been an inefficient and limiting process. This thesis provides a detailed account of the great strides taken to increase the synthetic accessibility of donor-acceptor mechanically interlocked molecules by the application of highly efficient and ultra mild chemical transformations during their template-directed synthesis. These new departures in synthesis have indeed played a transformative role in that more complex, higher-order, and functional architectures once only a dream are now comfortably within reach. Specifically, the formation of mechanical bonds in higher order rotaxanes and catenanes has become ever easier through the use of highly efficient click chemistries. The resulting mechanically interlocked compounds are functional molecular media for a host of applications including information storage, mechanical actuation, and drug release.