Knots hydrogen bonded

Hydrogen bonding is thought to be responsible for the formation of such molecules as the catenane 37 [17], rotaxane 396 [18] and even knot 397 [19]. 

These domains are connected by hydrogen bonds, which act as knots or crosslinking centers to create flexible blocks.13 Microphase separation and the appearance of domain structure are considered to be the main factors, which determine the unique properties of this class of polymers. 

Figure 10.88 X-ray crystal structure of a hydrogen-bonded trefoil knot produced in a one-pot synthesis.104...

Reuter, C., Schmeider, R. and Vogtle, F. (2000) From rotaxanes to knots. Templating, hydrogen bond patterns, and cyclochirality, PureAppl. Chem. 72, 2233-2241. 

The functionalisation also allows extending the complexity of intertwined molecular assemblies involving molecular catenanes, rotaxanes and knots. Elaborate interlocked assemblies constructed by means of metal-templation techniques and ji-ji-stacking preorganisation were reviewed [3, 11], Our last survey was devoted to the hydrogen bond templated synthesis of amide-based catenanes and rotaxanes [32], Since then a considerable advancement in elucidation of mechanisms of templation and derivatisation of the amide-based interlocked structures has been reached. Moreover, in 2000 we reported a one pot synthesis of amide-based knots such as 8 [21], which is so far the easiest preparation of molecular knots. In the following, specific possibilities of functionalisation of amide-based catenanes, rotaxanes and knots will be discussed. 

Figure 6. The formation of knot from a helical intermediate preorganized through hydrogen bonds.

However, preorganization by reversible interactions via hydrogen bonds does not necessarily need a further template such as an anion. Direct intermolecular hydrogen bonds between derivatives of isophthalic acid and 2,6-pyridine diacid were used to synthesize a series of new catenanes [17,18], rotaxanes [18c,19], and trefoil knots [20]. The interaction of dibenzylammonium cations and dibenzo[24]crown[8] [21] led to the preparation of rotaxanes by the attachment of stoppers to the thread ends (Scheme 5.5) [22], or similarly by clipping of the crown ether chain wrapped around the ammonium dumbbell [23]. Recently, several novel catenanes were synthesized via the macrocydic connection of three ammonium cations threaded through three crown ether rings attached to a triptycene core [24]. 

Fig. 11 Left. Synthesis of a trefoil knot thanks to hydrogen bonding. Right. Crystal structure of the compound, with the non-covalent interactions indicated by dashed lines...

We have seen how elegantly transition metals can template the formation of knots, but what about Nature s favourite templating interaction, the hydrogen bond A remarkably efficient molecular trefoil knot synthesis based on this interaction was reported by Vogtle and co-workers, who made a knotane in 20% yield [39]. This amazing route (Fig. 11) was uncovered serendipitously during the synthesis of catenanes. The crystal structure of the compound was the definitive proof for the structure, because neither NMR nor mass spectrometry could tell it apart conclusively from the macrocycles that are also formed. 

Fig. 12 Representation of the synthetic pathway to a trefoil knot by hydrogen bond-mediated weaving...

A more accurate treatment requires to reduce the size of the system and to use model compounds. E.g. Schalley and coworkers [125, 126] carried out DFT calculations in order to gain insight into the details of the hydrogen bond patterns involved in the formation of mechanically interlocked species such as amide rotax-anes, catenanes, and knots. 

From rotaxanes to knots. Templating, hydrogen bond patterns, and cyclochirality 00PAC2223. 

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