Rotaxane natural

The dynamic nature of the system offers the crown ether access to the ammonium centre allowing self-assembly of the corresponding dynamic [2]ro-taxanes 31 to occur. Fixing of the interlocked assembly can be achieved by reducing the imine groups in 31 to the corresponding amine so that a kinetically inert [2]rotaxane forms. 

Stoddart and co-workers have made use of Frechet-type dendrons as dendritic stoppers for self-assembled [n]rotaxanes [65]. The solubility enhancement that results from incorporating dendritic wedges at the termini facilitated the purification of these materials by column chromatography despite the polycationic nature of their bipyridinium backbone. Again, the dendritic wedges did not alter the electrochemical characteristics of the viologen subunits. Flowever, the enhanced solubility resulting from the presence of the dendritic components en-... 

Interestingly, the dumbbell component of a molecular shuttle exerts on the ring motion the same type of directional restriction as imposed by the protein track for linear biomolecular motors (an actin filament for myosin and a microtubule for kinesin and dynein).4 It should also be noted that interlocked molecular architectures are largely present in natural systems—for instance, DNA catenanes and rotaxanes... 

Dumbbell 34+ exhibits two bielectronic and reversible processes that can be attributed to the simultaneous first and second reduction of the two bipyridinium units contained in its axle-like section. The bielectronic nature of the processes indicates, as expected, that the bipyridinium units are equivalent and behave independently. Also, model rotaxane 44+ shows two bielectronic and reversible processes that are straightforwardly assigned to the bipyridinium units contained in its dumbbell component they are, however, shifted to more negative potentials compared to dumbbell 34+. These shifts can be attributed to the CT interactions with the electron donor ring that make the electron acceptor bipyridinium units more difficult to reduce, whereas the bielectronic nature of the processes indicates the such units are noninteracting and equivalent—both of them are surrounded by a ring—in full agreement with the supramolecular structure of 44+. 

The cyclic voltammetry behavior of the Cu(II) rotaxane, 4(5)2+ (Fig. 14.8b), is very different from that of 4, t l +. The potential sweep for the measurement was started at - 0.9 V, a potential at which no electron transfer should occur, regardless of the nature of the surrounding of the central Cu(II) center (penta- or tetracoordinate). Curve i shows two cathodic peaks a very small one, located at + 0.53 V, followed by an intense one at —0.13V. Only one anodic peak at 0.59 V appears during the reverse sweep. If a second scan ii follows immediately the first one i, the intensity of the cathodic peak at 0.53 V increases noticeably. The main cathodic peak at —0.15 V is characteristic of pentacoordinate Cu(II). Thus, in 4(5)2+ prepared from the free rotaxane by metalation with Cu(II) ions, the central metal is coordinated to the terdentate terpyridine of the wheel and to the bidentate dpp of the axle. On the other hand, the irreversibility of this peak means that the pentacoordinate Cu(I) species formed in the diffusion layer when sweeping cathodically is transformed very rapidly and in any case before the electrode potential becomes again more anodic than the potential of the pentacoordinate Cu2 + /Cu+ redox system. The irreversible character of the wave at —0.15 V and the appearance of an anodic peak at the value of + 0.53 V indicate that the transient species, formed by reduction of 4(5)2 +, has undergone a complete reorganization, which leads to a tetracoordinate copper rotaxane. The second scan ii, which follows immediately the first one i, confirms this assertion. 

The nonionic template strategy based on hydrogen bonds and to a certain extent on n-n interactions has made catenanes and rotaxanes readily available. The molecular recognition and self-organization process which is responsible for the formation of intertwined and interlocked structures is founded upon the same weak interactions that govern many biological processes. Amide-based catenanes and rotaxanes can thus serve as valuable models for complex molecular recognition patterns in nature. 

To overcome the low yields encountered in statistical methods, Schill and coworkers imaginatively introduced the chemical conversion method [4, 5, 16]. As illustrated in Figure 2, this method requires very careful design (i) the cavity of a cyclic species covalendy linked to a difunctional linear species should be penetrated by the linear species, structure 14 and (ii) both the cyclic and the linear moieties must be inert to the cleavage reaction of the covalent linkage Z between them. By this means, the yield for rotaxane synthesis was increased to about 40% in last step. The disadvantages of this method are its multiple steps and time-consuming nature. 

Our vision is to use the knotanophanes and the linear oligomeric knotanes as chiral wheel and axle components, respectively, in future giant rotaxanes which would mimic naturally occurring enzyme complexes [60],... 

The choice of one of these four routes for the preparation of a rotaxane depends mainly on the chemical nature of the different components and the chemistry required to establish the interlocked molecule. An interaction between the two individual components is very often the driving force in the synthesis of rotaxanes. 

Two-terminal devices might seem more natural for the molecular-scale systems than three-terminal ones because of the technological difficulties in manipulating small structures. Furthermore, chemical assembly of molecular devices usually results in a periodic structure. This observation resulted in the idea to have a two-terminal switch, electronically reconfigurable, where a relatively high voltage (e.g. —2V or +2V in [62], which uses a 2-catenane-based molecule) (Fig. (7a)) is applied to close or open the switch, but a relatively low voltage to read (M). 1 V) [60]. These molecular switches [62], a mono-layer of rotaxane molecules, are not field-activated but can be described as small electro-chemical cells, which are characterized by... 

Any artificial rotaxane-based mimic of the natural ATP synthase motor must bear a chiral element that helps to define the direction of rotation. Chirality can, of course, be implemented in such molecules by adding chiral groups as the stoppers or the wheel. Rotaxanes with cyclodextrins as the wheels have been described [11], and rotaxanes with glucose-containing stoppers are known [14]. Rotaxanes with elements of planar chirality have also been realized [15]. 

Interlocked molecules are those assemblies of two or more molecules which are linked by a so-called mechanical bond [2]. The individual molecules are not connected covalently in any way but are linked via their spatial relationship to one another. The nature of this phenomenon is such that it necessarily involves a macrocyclic component as one or more of the molecules which compose the assembly. The simplest forms of these assemblies are represented by a [2]rotaxane and a [2]catenane (Figure 10.1), where the bracketed numeral preceding the name indicates the number of individual molecules comprising the interlocked product. The synthesis of a rotaxane may be executed by a number of different routes, only one of which involves the formation of a macrocyclic component in the final... 

The ribosome structure is perhaps the most impressive natural rotaxane. Messenger RNA, as the rotaxane thread, is clamped by the ribosomal protein subunits which read each codon and transcribe it into a sequence of amino acids that are introduced by transfer RNAs to build up the desired protein. The importance of the ribosomes has been reflected in the number of Nobel Prize recipients associated with their discovery (Palade in 1974) and elucidation of their structures and functions (Ramakrishnan, Steitz and Yonath in 2009). 

The purpose of the rotaxane is to protect the squaraine from nucleophilic attack, likely to occur under physiological conditions, and so enhance the lifetime of the probe in vivo. Indeed, the half-life of the probe is 100 times longer than a non-rotaxane analogue that incorporates a commercial sulfonated carbocyanine dye in place of the squaraine moiety. Furthermore the near infrared spectral nature of the dye means that it gives a strong signal even through centimetres of soft tissue. 

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