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9 Future Perspectives: Drawing Inspiration from the Complex System that is Nature

9 Future Perspectives: Drawing Inspiration from the Complex System that is Nature

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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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UK, 2010.

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Nature’s Most Successful Designs, Meghan Kiffer Press, Tampa, FL, 2008.

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Washington DC, 1994.

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and Appropriations Issues, Congressional Research Service, Washington DC, 2011.

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Bioinspired Self-Assembly I:

Self-Assembled Structures


School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia


School of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia


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.




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








Hydrogen bonding

Dipole interactions

Dispersion forces

π-Aromatic stacking

Hydrophobic effect

Figure 2.1




Shape (conformation)


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.



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:



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

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