Chemistry Reference
In-Depth Information
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 inter-
action 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.
The hydrogen bonded knot can also be synthesised by a step-wise route, which
helps determine the way in which it is formed in the one-step reaction [
40
]. A string-
like molecule was prepared in order to ascertain if indeed it is an intermediate on the
pathway to the knot (Fig.
12
). The reaction of this “pre-knot” with a di-acid chloride
generated the knot in 11% yield. The creative chemist will immediately have
realised that using the knot precursor as a reagent with different di-acid chlorides
is possible, and indeed this path leads to a variety of substituted knot molecules and
analogues, especially in combination with different [
41
,
42
] and quite exotic and
beautiful knotty structures [
43
]. The formation of compounds that contain various
knots was achieved by the functionalisation of the 5-position of the pyridine rings
with different functional groups, which makes possible selective reaction at
each external loop, which can be appreciated in the X-ray structure of the native
compound. To give just one case, the functionalisation of the knots with allyloxy
units facilitates the preparation of linear and branched oligomers of knots [
44
].
This section would not be complete without mention of the beautiful objects
prepared using DNA. Single-stranded DNA is a practical building block for the
preparation of topologically complex unnatural interlocked structures in awe-
inspiring manner [
45
]. Mutually compatible sequences of DNA (designed so as to
form interlocked structures) pair through the Watson-Crick code and allow precise
control of the ravelling necessary to form knots. A 4
1
knot has been made by precise
double helix formation and control of the directionality of the strands [
46
]. This
figure-eight knot has two positive and two negative nodes, defined as such by the
direction the strands cross each another. Defining the DNA direction as the 5
0
to 3
0
vector, the right-handed B-DNA double helix has only negative nodes, and the left-
handed Z-DNA double helix contains exclusively positive nodes. The type of DNA
encoded at each crossing results in the stereoselective formation of the knots, an
approach that is inspirational for the purely synthetic approach to knots. Indeed,
three knotted topologies can be achieved with a synthetic DNA molecule [
47
].
4 Molecular Knot Characteristics and Beauty
When a chemist working with molecules incorporating organic fragments makes an
object as beautiful as a knot, one might expect that the symmetry of this object be
reflected in some of its characteristic spectroscopic signatures, such as its nuclear
magnetic resonance spectrum. NMR spectra of apparently large and complex
