Interlocked molecules complex catenanes

The most common classes of interlocked molecules are catenanes and rotaxanes derived from the Latin catena, rota, and axis (meaning chain, wheel, and axle, respectively). As depicted in Figure 10.1, a catenane is composed of interlocking rings (a). A rotaxane contains a macrocyclic component looped around an axle, held in place by two bulky stoppers (b). A related supramolecular structure is the pseudo-rotaxane (c)—an inclusion complex in which an axle without stoppers resides inside a macrocycle. This interpenetrated, but not interlocked, assembly is often a precursor to catenanes and rotaxanes. 

Fortunately, more efficient methods for the complexation of macrocyclic hosts with acyclic guest molecules have become available with the advent of supramo-lecular chemistry, resulting in higher yields in rotaxane and catenane synthesis. In the following sections, the preparation of different types of interlocked molecules, with the use of host-guest recognition, is discussed. It should be noted that these template-directed methods differ significantly from the above-mentioned stochastic approach [28]. 

A special issue devoted to molecular machines appeared in Accounts of Chemical Research in 2001. It reflects the current interest for this field in which ruthenium complexes act as important tools. Molecular machines are characterized by a mobile part and a stationary part. Photochemical and electrochemical inputs can make a machine work, offering the advantage of being switched on and off easily and rapidly. Mechanically interlocked molecules, such as rotaxanes and catenanes, are suitable candidates. Crown ethers, cyclophanes, and calixarenes are representative families of the cyclic... 

While rotaxanes are composed of wires and rings, catenanes consist of two or more interlocked rings. The word catenan comes from the Latin word catena , which means linked chains. Although the interlocked rings in catenanes are not bonded together by covalent bonds, they cannot be separated from each other. The molecule is stabilized simply by spatial interlocking. This characteristic is different to other supermolecules, where specific interactions play crucial roles when fixing the structures of complexes. 

Before going on to discuss molecular electronic machines, it will be useful to describe their structural foundation at a molecular level, namely those based on interlocked molecules. Interlocked molecules can take on a variety of forms, the most common being catenanes, rotaxanes, knots [16], and carceplexes [17]. For the purpose of this review, only catenanes, rotaxanes and their geometrically related complexes - pseudorotaxanes [18] - will be discussed. When conferred with the ability to undergo some mechanical motion as a result of an applied stimulus - be it chemical, electrochemical, or photochemical - these interlocked molecular and interpenetrated supramo-lecular systems often take on the characteristics of molecular machines [19]. 

The discovery that DNA forms catenanes and knots, some of them extremely complex, initiated a new field of research which has been called Biochemical Topology [21]. In 1967, Vinograd and co-workers detected in HeLa cell mitochondria isolable DNA molecules that consist of independent, double-stranded, closed circles that are topologically interlocked or catenated like the links in a chain [22, 23]. A few years later, catenanes had been observed everywhere that circular DNA molecules were known [24] and the first knot was found by Liu and coworkers in single-stranded circular phage fd DNA treated with Escherichia coli co-protein [25]. In 1980, knots could also be generated in double-stranded circular DNA [26]. 

While a DNA molecule may exist as a straight rod, the two ends are often covalently joined. Thus, the chromosomes of E. coli and of other bacteria are single closed circles. Circular DNA molecules are also found in mitochondria, chloroplasts, and many viruses. Further complexity arises from the fact that the circles of DNA are sometimes interlocked in chainlike fashion (catenated). An unusual example of this phenomenon is the presence of thousands of small catenated DNA circles in the single mitochondrion of a trypanosome (Fig. 5-16).183 Sometimes circular DNA is knotted as in Fig. 5-17.184-186 Knots and catenanes often appear as intermediate forms during replication and recombination, especially involving circular DNA.187 188... 

---