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9 Future Perspectives: Drawing Inspiration from the Complex System that is Nature
INTRODUCTION: THE CONCEPT OF BIOMIMICRY AND BIOINSPIRATION IN CHEMISTRY
phenomenon of “economic growth”). As such, they offer the prospect of unifying
science and improving the human experience.
This book provides a perspective on how the study of Nature has had a profound
impact on the disciplines of chemistry and materials science. It is a story that is
thousands of years old, yet we are still in the introductory chapter. The inspiration
that will be gleaned from the earthly biosphere over the coming years is vast and
we may never discover all of its secrets, much less elucidate the web of synergistic
interactions that makes it all work. It is breathtaking to realize that our world is
but one among a vast number of likely worlds, many of which will surely have
evolved their own biospheres with their own unique materials and interconnected
processes. In the fullness of time bioinspiration and biomimicry may ultimately
grow to encompass an interplanetary aspect. Perhaps this will one day turn out to
be the best justiﬁcation for humankind to reach for the stars.
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Bioinspired Self-Assembly I:
LEONARD F. LINDOY
School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
School of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia
JACK K. CLEGG
School of Chemistry and Molecular Biosciences, The University of Queensland,
Brisbane St Lucia, QLD 4072, Australia
Self-assembly processes are ubiquitous in Nature where, typically, multifunctional
building blocks are assembled into larger molecular entities showing considerable
sophistication in both their function and form. These natural self-assembly processes are often of exquisite subtlety and include, among many others, protein
folding, the assembly of DNA, and the formation of bilayers, micelles, and vesicles. In this chapter we discuss selected self-assembled synthetic structures, in
general prepared by the “bottom–up” approach. These structures mimic or were
inspired to a greater or lesser degree by aspects of natural systems. This discussion
is intended, in part, to introduce the reader to certain of the structural types that
will be discussed in greater detail in later chapters.
Since the rise of supramolecular chemistry as a deﬁned subdiscipline of chemistry over the past four decades or so—recognized by the award of the Nobel
Prize to D. J. Cram, J.-M. Lehn, and C. J. Pedersen in 1987—there has been
steady progress in understanding the rules involved in self-assembly processes and
applying them to the construction of synthetic assemblies. This has led to generally
increased appreciation of the latent steric and electronic information inherent in a
wide range of molecular or ionic building blocks that are either already available
Bioinspiration and Biomimicry in Chemistry: Reverse-Engineering Nature, First Edition.
Edited by Gerhard F. Swiegers.
© 2012 John Wiley & Sons, Inc. Published 2012 by John Wiley & Sons, Inc.
BIOINSPIRED SELF-ASSEMBLY I: SELF-ASSEMBLED STRUCTURES
or are able to be synthesized. A large number of structures incorporating metal ions
as structural elements have now been reported. This is perhaps not surprising since
each metal ion type may be considered to be a package of structural and electronic
information whose unique identity can potentially be harnessed to achieve a particular supramolecular outcome. As for natural systems, the bottom–up approach
has been successful in constructing a range of new nanoscale materials displaying
a wide range of properties, often related to those of Nature’s materials.
As in Nature, the “glue” between the ionic and/or molecular building blocks
in these synthetic assemblies consists of weaker noncovalent interactions. These
include hydrogen bonding, dispersion forces, π -π stacking, π -cation and π -anion
interactions, as well as the full complement of electrostatic (ion–ion, ion–dipole,
dipole–dipole) interactions. Metal-donor atom coordination bonds of generally
moderate strength can also be employed (giving rise to metallosupramolecular
systems).1, 2 Overall, hydrogen bonding is a key interaction across many selfassembled systems, reﬂecting the directionality and speciﬁcity of this interaction
type. This is not surprising in the case of Nature’s assemblies since classical natural building blocks such as the carbohydrates, amino acids, and nucleic acids all
incorporate numerous hydrogen bond donors and acceptors.
While the level of complexity generally achieved so far for synthetic systems
falls considerably short of that routinely exhibited by natural systems,3 steady
progress toward more complex systems is being made. Since the same rules apply
to Nature’s assemblies as for synthetic systems, there is every reason to anticipate continuing progress in this respect in the future. Nevertheless, there can be
no doubt that the design and preparation of more complex, functional synthetic
systems remains a considerable challenge at both the intellectual and the practical
level—requiring not only the appropriate choice of building blocks but also keen
insight into the skilled application of the weak noncovalent interactions mentioned
above. A good measure of creativity on the part of the practitioners is also clearly
an important ingredient!
Supramolecular assemblies, whether natural or synthetic, show a common feature in being capable of self-repair, implying inherent reversibility with respect
to their formation processes. This is a direct consequence of the use of weak (or
moderate, in the case of metal-donor) interactions in their construction. Apart from
providing a mechanism for error correction during their formation (see below), such
reversibility is also sometimes crucial to the function of the resulting assembly.
For example, in molecular and ionic transport processes the host (receptor) entity
must ﬁrst take up the substrate, then release it under the inﬂuence of an external
stimulus (such as a pH change or the presence of a concentration differential).
Hence, strong thermodynamic binding of a suitable guest molecule or ion in such
cases is not necessarily advantageous.
Electronic and steric complementarity is another feature of importance in the
design and assembly of supramolecular systems. Such complementarity may be
considered to act at two levels. First, it may refer to the complementarity between
adjacent building blocks in constructing a given molecular assembly. Second,
on a larger scale, a degree of host–guest complementarity between a cleft- or
MOLECULAR CLEFTS, CAPSULES, AND CAGES
Functional group types
Functional group orientation
Parameters that may inﬂuence molecular and ionic complementarity.
cavity-containing assembly and its potential guest is necessary for guest encapsulation to occur. A range of parameters, including appropriate use of selected
noncovalent weak intermolecular interactions of the types mentioned above, may
typically contribute to achieving such complementarity (see Figure 2.1).
The preparation of bioinspired systems has, so far, proceeded along two general
lines. First, fully synthetic components have been constructed and assembled into
systems that mimic, at least in part, particular functions of the natural systems. A
large number of published structures fall into this category. Second, there have been
a smaller number of studies that employ naturally occurring molecules, with their
built-in propensities for self-assembly (and in some cases functionality), to produce
new synthetic molecular assemblies that “borrow” some of their characteristics
from the natural systems. Particularly notable in the latter case is the use of DNAcontaining synthetic assemblies, often displaying aesthetic nuances, as exempliﬁed
by the research of the Seeman group.4 In addition to being very challenging science,
the results of such a hybrid approach have so far been quite impressive.
MOLECULAR CLEFTS, CAPSULES, AND CAGES
Nature makes good use of molecular (and ionic) encapsulation in a range of
important biological systems that include enzymes, proteasomes, and viral capsids. Natural cage and cleft systems are typically characterized by the presence of
deep cavity-like structures whose biological function is associated with the encapsulation of guest species. Such an inclusion process may be associated with some
combination of the following:
BIOINSPIRED SELF-ASSEMBLY I: SELF-ASSEMBLED STRUCTURES
Selective guest uptake (sometimes associated with chiral recognition)
Induced high catalytic activity
Concentration and guest storage of particular guests (including toxic species)
Molecular/ionic guest transport processes
The guest can range from a single molecule (or ion) to considerably larger
entities. In many cases, where guest uptake occurs, this involves transfer from the
bulk surroundings into the microenvironment in the host’s cavity. Such enclosure
typically has a marked effect on the guest, with inclusion generally resulting in a
range of altered properties. In a good many instances this has been demonstrated
to include a marked alteration of guest reactivity (even when the cavities lack
speciﬁcally tailored functional groups of the type present at the active sites of
enzymes).6, 8, 13, 16–20 To give just one example, a carboxylate group is unable to
hydrolyze a polysaccharide in water but can do so when enclosed at the active site
of lysozyme since in the latter case the “protecting” solvating water shell has been
effectively stripped in the hydrophobic pocket of the enzyme, effectively enhancing
the nucleophilicity of the carboxylate group.
The spontaneous and often selective inclusion of numerous neutral and charged
(both cationic and anionic) guests in the cavities of a wide range of cage-like
synthetic hosts (often referred to as “container” molecules or assemblies)9, 11 – 14
has now, of course, been the subject of a vast number of studies, with many
systems of this type showing parallels in their behavior and properties to those
observed in Nature’s encapsulating systems.15 For example, like particular natural cage and cage-like systems, the reaction of molecules held in the restricted
cage environments of particular synthetic hosts has been documented to differ signiﬁcantly from their reaction in bulk solution.6, 8, 13, 16 – 20 Encapsulations giving
rise to novel stereo- and regioselective reactions are well documented; for example,
Diels–Alder reactions displaying unusual regioselectivities have been demonstrated
under such conditions.16 Once again, factors such as the degree of complementarity
present between host and guest together with solvation/desolvation differences, the
restriction of possible guest conformations in the cavity, and the forced presence
of reagent proximity may all contribute to such a reactivity difference.
Over the past two decades there has been increased effort to devise syntheses for larger cage-like molecules and assemblies, a number of which exhibit
polyhedral shapes corresponding to those of Platonic or Archimedean solids.21
While the majority of these larger structures fall within the realm of metallosupramolecular chemistry,22 – 27 a range of such larger metal-free structures has
now also been reported.8, 14, 28–32 A number of the larger polyhedral structures28, 33
mirror the shapes of particular naturally occurring systems such as the virus capsids and the protein enzyme lumazine synthase. The capsids represent a welldeﬁned group of biostructures34 that serve as the protein shells of viruses and
consist of oligomeric structural subunits that enclose the genetic material of the
virus. Collectively, they are assembled from common protein building blocks
whose shapes and connection points give rise to their shell-like structures. The
faces of these unusual cages are composed of one or more proteins and are held