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Self-Assembly and Self-Organization

Michael F. Geer and Linda S. Shimizu
University of South Carolina, Columbia, SC, USA

1 Introduction
2 Key Players in Self-Assembly
3 Assembly in Solution to Yield Discrete Structures
4 Summary and Conclusions
References

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INTRODUCTION

Physicists, biologists, chemists, and material scientists have
all observed the ability of small units to self-organize into
larger defined entities long before this process was officially
named. Self-assembly describes the formation of discrete
architectures from building blocks that can range in size
from atoms and molecules up to macroscopic units without
help or guidance from an exterior source.1 The formation
of a more ordered ensemble from less ordered components seems counterintuitive from an entropy perspective.
Yet, atoms, molecules, and parts of macromolecules do
self-assemble into discrete soluble architectures including
folded structures, dimers, trimers, and so on. These small
assemblies may further associate into monolayers, films,
and polymers up to macroscopic structures such as vesicles,2 liquid crystals,3 and crystals.4 On the macroscale,
spontaneous assembly has been humorously visualized on
YouTube by a pile of Legos miraculously assembling
into the Millennium Falcon through the magic of stopaction photography. In this case, we are fooled and the

guiding source is an unseen person; however, even children can observe self-assembly in every day life as they
grow rock candy crystals and watch the formation of soap
bubbles.
Supramolecular structures have the potential to extend
to very complex extended structures. Nature has provided inspirational examples of functional assemblies.
In the tobacco mosaic virus, 2130 identical protein
units self-assemble around an RNA strand to form the
∼300 nm × 18 nm rod structure (Figure 1).5 Amazingly,
this structure can be dismantled, isolated as its component parts, and reconstituted in vitro to afford the intact
assembled virus.6 Early work distinguished the terms
self-assembly and self-organization by thermodynamics,
with self-assembly implying a spontaneous, reversible
process that reaches equilibrium while self-organization
required energy to afford a nonequilibrium state.7, 8 The
tobacco mosaic virus is an example of a spontaneous selfassembling system. Most people now use these terms interchangeably, although Lehn9 and others typically reserve
self-organization for multistable dynamic systems and this
term is most often encountered in the biological area.10, 11
Since no outside force is required for this spontaneous
assembly, the directions and driving force must be embedded in the building blocks themselves and influenced by the
surrounding environment. We are still far from elucidating
general rules that guide self-assembly at size scales that
range eight orders of magnitude from angstroms to centimeters. The rules governing pattern formation over this
huge range appear to be similar but not identical.12–14 For
example, the balance of the forces that guide molecules into
three-dimensional crystals versus two-dimensional films
may have different relative strengths and contributions at
these different length scales.15, 16 Researchers often refer
to three distinct size ranges that include the molecular,

Supramolecular Chemistry: From Molecules to Nanomaterials, Online  2012 John Wiley & Sons, Ltd.
This article is  2012 John Wiley & Sons, Ltd.
This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons, Ltd.
DOI: 10.1002/9780470661345.smc012

there are many examples of these assembly patterns that give rise to functional systems for practical applications. or peptide to fold into a more ordered complex structure. more complex systems two different building blocks could assemble. Figure 2 shows the schematic selfassembly of identical molecular building blocks that are wedges. ammonium salts. A combination of organic and inorganic building blocks can be used to construct two and three-dimensional networks that yield interpenetrated or porous coordination polymers or metal organic frameworks (MOFs). blocks. Here. 20 Small geometric changes in the relative size and shape of the building block are amplified in the assembly process and ultimately control the size and shape of the final complex pattern that emerges. 2 KEY PLAYERS IN SELF-ASSEMBLY Our conceptualization of the self-assembly/self-organization process requires us to consider all the components of the system that could influence the formation of ordered ensembles. The physical properties of these building blocks are also important as these molecules need to interact with themselves and with other building blocks during the assembly process. etc.17 are typically molecules. and reversibility of the intra. melting point. polymer. This chapter focuses primarily on identifying variables that are important to the assembly process in all ranges and examines some simple molecular examples of self-assembly.) may form strong directional interactions that are discussed in the next section. 30 also self-assemble into micelles. Thus. we take a closer look at these components. shape. directionality. These functional groups (carboxylates.1 Building blocks The building blocks used by chemists. Alternatively. In slightly Figure 2 Schematic assembly of building blocks with various shapes to form discrete supramolecular structures. geometry. or columnar structures. DOI: 10.21–24 Block copolymers25–28 and dendrimers29.smc012 . and physical properties (solubility.19. their location. Shape complementarity is an important design consideration in self-assembling systems. amides.5 nanoscale.and intramolecular contacts that are both possible and accessible. Other molecular attributes also influence this organization including the type and position of functional groups within these molecular building blocks. the size and shape of these building blocks have a marked effect on how they may assemble into more ordered structures. Ltd. halogens. melting points and solubility help govern their ability to mix freely in a melt or solution. which usually endows function.31 Supramolecular Chemistry: From Molecules to Nanomaterials. amines. Mobility is also a requirement for assembly. 2. melamine and barbituric acid derivatives form cyclic hexamers that are also called rosettes.and intermolecular forces or bonds. and macroscopic. and orientation within the assembly unit have a major impact on the inter. or disks to give cyclic hexamers. For example. The size. lamellar sheets. which include: (i) the molecular structure and physical properties of the building blocks. A physical chemist or material scientist might discuss this in terms of mass transport and mixing. Online  2012 John Wiley & Sons. which are also referred to as construction units or tectons. and microtubules. For example.18 Complexity builds quickly. This article is  2012 John Wiley & Sons. This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons.) of these building blocks must be considered. and (iii) the solvent or solid interfaces in the surrounding environment. Obviously. L-shapes. carboxylic acids. (ii) the strength.1002/9780470661345.2 Concepts Protein ‘‘building block’’ Building blocks Discrete structures Self assembly Viral RNA strand Figure 1 Cartoon representation of the assembly of the tobacco mosaic virus from its protein building blocks that self-assemble around the strand of viral RNA. etc. these interactions may drive intramolecular associations and cause the macromolecule. Ltd. Although seemingly simple. functional groups. Ltd.

The strength of these interactions covers a huge range from very weak. Ltd.and intramolecular interactions have been used to guide self-assembly. Individual hydrogen bonds. There are three key issues to consider in the use of a specific covalent or noncovalent interaction for supramolecular assembly: (i) strength.18. Pd(II). geometric features. and many can be context dependent.34 hydrogen bonding. 44 and dative bonds that are similar in strength to covalent bonds (60–190 kcal mol−1 ). Pt(II) often form local but not global order. The dynamic nature of these systems allows for “error checking. ranging from 5–40 kcal−1 . strengths. and donor– acceptor interactions up to strong ion–ion interactions43. the individual components cannot adjust or reorganize their structures to form the most stable lattices (Figure 3). The formation of these complexes is kinetically controlled and often results in noncrystalline solids and glasses. the origins. positioning. the number. such as complexes of Cr(III). Ltd. such as the formation of a C–C bond or an irreversible dative bond. the assembly/disassembly equilibrium allows for these structures to respond to their environment. (ii) reversibility. These interactions can be used alone or in concert to afford assemblies. This article is  2012 John Wiley & Sons.48 The energetics. it must be allowed to equilibrate and find the thermodynamic minimum. and (iii) directionality. in solvents that compete for hydrogen bonds such as water. and geometries of aryl-stacking interactions are still a very active area of fundamental research. 41 dipole–dipole.49–51 For a complete discussion of these interactions see Chirality.2 Intra. For example. a dynamic and reversible metallosupramolecular assembly could be postmodified by addition of a new ligand or a template. a stronger the association constant is usually indicative of a less reversible process. however.” which is a controlled disassembly of thermodynamically unstable structures that endows the process with inherent self-correction.Self-assembly and self-organization 2. for example. however.40.smc012 .45–47 A quadruple hydrogen bond array in 2-ureido-4-pyrimidone derivatives from Sijbesma et al. Concepts. The strengths of these interactions span a considerable range. 35–37 halogen bonding. 54 In the case of an irreversible interaction. This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons. they are very weak ∼0 kcal mol−1 .32 hydrophobic interactions. DOI: 10.and intermolecular forces: strength and directionality Inter. Online  2012 John Wiley & Sons. In a reversible process. Supramolecular Chemistry: From Molecules to Nanomaterials. Potentially. displays association constants of Kdim − 6 × 107 L mol−1 in CHCl3 . 39 arylstacking. Like a contractor building a house. are stronger in the gas phase or in nonpolar solvents. Noncovalent forces range in strength from weak interactions (0–40 kcal mol−1 ) that include van der Waals.38. Figure 3 compares a reversible process with an irreversible one. and relative contributions of some of these interactions is still under debate. the molecules associate and dissociate in a dynamic equilibrium. Ltd. Strong but poorly labile metal–ligand interactions. as compared to thermal energies.35 In systems with multiple hydrogen bond donors and acceptors. one would assume that the stronger mortar would afford a more stable assembled structure. since the molecular structure builds itself.52 For example.33 close packing. In general. to intermediate strength but reversible dative interactions to a special set of strong covalent bonds. This reversibility allows the individual building blocks to adjust their position and orientation and to eventually find the thermodynamic ordered structure.53. Ru(II).42 ion–dipole.1002/9780470661345. and separation distance can modulate the strengths of these interactions over several orders of magnitude. Os(II). It is conceivable that an More complex Reversible Structure can follow Error checking Irreversible ‘‘Trapped’’ Figure 3 3 Comparison of reversible and irreversible steps and their effects on the supramolecular assembly.

Ltd. Perhaps these are the underlying causes for the subtle differences between assembly on the molecular. 2. Challenges remain in identifying each of these forces and weighing their individual contributions for assembly at atomic to macroscale sizes. people can now actively study the nucleation process. In chemistry. and macroscopic size scales.4 Concepts irreversible interaction can drive the kinetic self-assembly to afford discrete structures.” which can then be subsequently closed to complete the synthesis of the rotaxane. This article is  2012 John Wiley & Sons.smc012 . In biology. 60 esters. there are many examples of such template-assisted assembly83–87 used to facilitate covalent bond formation. 70–73 The chapter Supramolecular Information/Programming from a Boolean Perspective. One such example is in the synthesis of threaded and interlocked linked compounds88–90 such as the synthesis of a rotaxane (Figure 4) through the clipping method. the formation of many small favorable associations during the growth phase work to overcome this initial deficit. However. One can manipulate the temperature and conditions so that the formation of stable imines.3 Surrounding environment In solution. this intriguing method for discovering polymorphs highlights the difficulty in determining the role of the environment in guiding “spontaneous” self-assembly. Such processes are often referred to as assisted or directed self-assembly. the very process of nucleation and growth on a surface may be different due to thermodynamics of adsorption.66. Indeed. molecular chaperones can assist the folding of a protein. The solvent can have interactions with the building blocks and can help or hinder the assembly process. Section 3 highlights a number of examples of designed building blocks that assemble into discrete structures using directional interactions. directional interactions are important for programming a building block to adopt a specific assembly. many individual forces and effects contribute to the stability of the final complex assembly.76. Like a cascade reaction.81.61–64 disulfides. Ltd. Some examples of these covalent self-assembled systems include disulfide hosts68. work that will hopefully yield new insights. Selfassembly brings the open ring around the “bar. In addition to the strength of these individual interactions. surface diffusion. solvent/solute. solid/solvent. and chemical binding that may occur before or at the same time as growth processes. 69 and covalent organic frameworks.74 is kinetically slower in comparison to weaker noncovalent interactions and often requires a catalyst. Like a covalent single bond. Schematic synthesis of rotaxanes through the clipping Supramolecular Chemistry: From Molecules to Nanomaterials. all bonds must form correctly as there is no way to correct a mistake.15. This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons. For example. ion–dipole. often referred to as dynamic covalent chemistry.55–58 relatively few structures have been built with strong covalent bonds. 82 It could be argued that this is no longer a case of spontaneous self-assembly as Matzger et al. Online  2012 John Wiley & Sons. DOI: 10. hydrogen bonding. An extreme example might also include the formation of carbon nanotubes and fullerenes.59. and solid/solute. and ion–ion interactions. In a cooperative process. While not spontaneous at room temperature. carbon vapor at high temperature does “assemble” to form these intricate and beautiful structures. in which the shared electrons are localized between the two atoms. Thus. one must also consider their directionality. propose and that the solid polymer aids in nucleation and may selectively stabilize one polymorphic form of a pharmaceutical over another. This is due to the fact that normal covalent bonds are not easily broken and reformed. some of the noncovalent interactions are directional in nature including dative bonds.66 and boronate esters67 is reversible. 77 Typically. However. nanoscale. Molecular motion is a requirement for these nucleation and growth processes. Ltd.65 hydrazones.78–80 These environmental effects give rise to a range of new interactions to consider: solvent/solvent. In comparison to abundant examples of noncovalent supramolecular assemblies. we need at the very least to consider the solvent in this process and often a solid interface as well. diluting a sample with a solvent might induce Figure 4 method. 16 A good example of the solid interface influencing assembly is the differential growth of crystals in the presence of insoluble polymers. Solid interfaces can also aid or hinder assembly.75 The nucleation step is typically thermodynamically unfavorable and an entropy deficit must be overcome. the assembly is carried out in a solution or in a melt to aid molecular motion. halogen bonding. donor–acceptor. The equilibration of these strong covalent bonds. With the advent of neutron scattering and X-ray crystallography. Concepts delves deeper into the reversible covalent bond toolbox. In the design step.1002/9780470661345. The dynamic nature of these structures can complicate their characterization as the act of sample preparation for different analytical techniques can promote disassembly. the process of spontaneous self-assembly is thought to follow a thermodynamic model where the building blocks form an aggregate in solution that gives rise to initial intermolecular interactions (nucleation) followed by growth.

Ltd. In the case of supramolecular polymers. dilution would be expected to lower the degree of polymerization. Ltd. peptides.Self-assembly and self-organization an equilibration of the material to afford an average smaller assembly. Ltd. and peptides amphiphiles have been assembled into nanostructured fibrals reminiscent of the extracellular matrix. van der Waal’s. and in light harvesting applications. DNA-based materials. While conceptually simple.smc012 . In this section.1 Dimeric structures and capsules An early example from the Cram group takes advantage of dipole–dipole. we highlight selected symmetrical self-assembled systems to illustrate how different N 5 intermolecular interactions can be used cooperatively to afford discrete structures that are of interest for molecular recognition.91 Section 2 in this volume focuses on the different techniques that have been used to probe these self-assembled structures. (c) Nolte’s molecular clips assemble into dimers through aryl-stacking and entropic effects. (b) Rebek’s “softball” dimers assembled through H-bonding99–102 . aryl–aryl stacking. and entropic effects97.97 These velcraplexes are cyclic aryl systems that incorporate quinoxoline “flaps” in an equatorial position to the aryl ring reminiscent of an octopus with four legs setting on the ocean floor (Figure 5a). 3. 3 ASSEMBLY IN SOLUTION TO YIELD DISCRETE STRUCTURES Self-assembly is used to organize molecules into amazing and complex structures. for sensing. a large number of aesthetically pleasing and functional structures have been synthesized that form dimers.92 Dendrimers. A minimalist would consider the association of two identical molecules together to form dimeric structures or capsules as a good model of selfassembly. Small molecular weight molecules can be assembled into structures of varying degrees from dimers and trimers all the way up to and including supramolecular polymers. This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons. and solvophobic interactions to drive assembly of two identical units into dimers.1002/9780470661345. Online  2012 John Wiley & Sons.93–96 Obviously. This article is  2012 John Wiley & Sons. DOI: 10. 98 .1 Simple amphiphiles form micelles and vesicles.103 Supramolecular Chemistry: From Molecules to Nanomaterials. we cannot cover here even a fraction of the creative and functional assembled systems reported. as nanoreactors. The dimers are formed from the “stacking” of the faces (the bottom side of the analogous octopus) of two of the monomers so that the axial facing methyl groups on the inner aryl cycle sit toward the face N O O N N O O C3H11 C3H11 C3H11 C3H11 O O N N O O N N Dimers (a) Ar H N H N O O N N Ar HO OH N N O O O O N N OH HO Ar N N O O N H (b) Ar N H (c) Figure 5 Examples of self-complementary molecules that yield dimeric assemblies: (a) Cartoon representation of velcrand dimers that assemble through CH-pi.

these aryl–aryl interactions are considered to be less directional.” and “softballs” from the Rebek group. (d) Rebek’s cavitands take advantage of H bonds for self assembly.99–102 Figure 5(b) illustrates the assembly of two long and curved polycyclic units into large “softballs.99–102 and range of internal volumes. and what the Nolte group calls “cavity filling effects. This article is  2012 John Wiley & Sons.” “tennis balls.105 and triphenelene. DOI: 10.100. These C-shaped clips are formed from a bisimidazolidine core decorated with four aryl groups. clips with long alkane tails form well-ordered lamellar thin films and may have use in liquid crystalline applications. Concepts for a discussion of solvation. 125 . Examples of self-assembled dimers stabilized by hydrogen bonds are the “baseballs. Ltd. Like their covalent carcerand and hemicarcerand counterparts.107 selfassembled capsules are of interest for drug delivery and as containers for stabilizing reactive intermediates and for inducing selectivity in reactions. Online  2012 John Wiley & Sons. Ltd. 101 Symmetric molecular clips from the Nolte group rely on size and shape complementarity and aryl–aryl stacking interactions. Polar solvents also help to facilitate the formation of these dimers. from 60 to 300 A have been shown to exchange their guest molecules through O OO O OO O O HO OH HO O O O O H O HO O O O O H HO HO O O O O O H H O OH O OH (a) R2 R2 R2 R2 R1 (b) (c) R1 R1 R1 + − = SO3 Na = C(NH2)2+Cl− R1 = OCH2CH2CH3 R2 = OCH2CH2OCH2CH3 (d) Figure 6 Examples of self-assembled capsules: (a) Gibbs water-soluble cavitands forms a capsule in the presence of hydrophobic ˚ 3 130 .106 Egg-shaped or spherical capsules can be formed by the assembly of two halves or hemispheres. (c) Cavitands from the Reinhoudt molecules124. Capsules have been of the opposing aryl rings that are equatorial directed of the second monomer. These are formed from self-complementary curved pieces that are comprised of two glycouril units separated by different spacers such as durene. These systems have a wide ˚ 3 .103 This molecule forms a C-shaped clip that dimerizes in solution by interlocking the aryl groups (Figure 5c) through aryl–aryl stacking.1002/9780470661345.132.” which are knit together with eight pairs of hydrogen bonds. The exchange of solvent guests for larger molecules like adamantanes and ferrocene displays stabilizing effects of approximately 1–3 kcal mol−1 .” Typically. and the quinoline groups are offset from one another in a typical aryl–aryl offset stack. (b) Atwood cavitand that forms a hexameric cavitand with a volume of ∼1400 A 131 group employ ionic interactions. 133 Supramolecular Chemistry: From Molecules to Nanomaterials. The −G values for the formation of these dimers was shown to vary greatly from <1 to >9 kcal mol−1 . Yet. Ltd. These dimers are held together by CHpi stacking.smc012 .6 Concepts an entropic process.98 See Introduction to Surfactant Self-Assembly. This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons.104 quinone.

For example. 123 and solvophobic interactions.150 In the presence of metal cations. This cage has been used to accelerate room temperature Diels–Alder reactions.” which occupied opposite faces of the octahedron and created a hydrophobic cavity (Figure 8a).smc012 . This article is  2012 John Wiley & Sons.151 By tuning the exterior functional groups on the tetramer to control repulsive and attractive interactions discrete assembled systems can be stabilized. and Pd salts.131 This entropy driven assembly displayed association constants in the range of 106 M−1 . directionality. the 8-aryl2 deoxyguanosine derivative from Rivera in Figure 8(b) Supramolecular Chemistry: From Molecules to Nanomaterials. one notes the self-complementary hydrogen bond donors and acceptors and the aromatic surfaces.4 -bis-platinum benzophenone has a geometry of 120◦ that opens the angles between the diacids and results in a hexagonal structure (Figure 7c).144 More recently. dodecamers. DOI: 10. Using isothermal titration calorimetery Sun. and Gibb found that the driving force for this complexation125 was the expulsion of a hydrophobic guest molecule from aqueous solution (solvophobic) as it was taken up in the cavity of the capsule and shielded from water. Alternately.134.127–129 and hydrocarbon separation. The octa-acid groups enhanced the solubility of these cavitand hosts in basic aqueous solution.136.1002/9780470661345. Ltd.138 Two porphyrins from separate trefoils assemble through dative bonds from zinc within the chlorophyll pieces to diazo bicyclooctane ligands that connect to neighboring trimers.132. 137 One example is Wasielewski’s trimers formed from three chlorophyll derivatives connected by a phenyl triethynelene in a trefoil-like structure (Figure 7a). The Gibb group provides an example that relies on solvophobic interactions. They synthesized cavitands based on resorcinarenes that were composed of 12 aryl systems that are functionalized with eight carboxylic acids. Sun et al. Gibb. and perhaps these are better viewed as trimeric or larger assemblies depending on the number of guests.22. This assembly is being studied for light harvesting capabilities and exhibits interesting dual singlet–singlet annihilation energy transfer processes that suggest two separate time scale energy transfers within the molecule. For example. where they were monomeric and unassembled (Figure 6a). two tetramers can assemble further into octomers.113–117 coordination chemistry.141 A water-soluble coordination cage was assembled via a tridentate tripyridyl-triazine ligand.146–148 Upon first inspection of guanosine derivatives. The reactive substrates appeared to be preorganized within the pocket.145 Hydrogen bonded guanosine tetramers (G-quartets) have a rich biological and materials chemistry.124 Other examples of capsules include the spherical molecular assemblies from Atwood’s group.108–112 and noncovalent interactions that include hydrogen bonds. has demonstrated the self-assembly of 24 metals and 48 ligands into amazingly large M24 L48 coordination spheres.140 The size and shape of the resulting structures are dependent on the geometries and bend angle of the platinum pieces. This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons.2 Trimers and larger functional assemblies Because of their strength.122.118–121 ionic interactions. hexadecamers. the 4. 3. 142 Stang’s group has capitalized on the directionality and the selective interaction of carboxylates with platinum to assemble neutral complexes. Most interesting was the ability of these capsules to open and close.6-bis-platinum phenanthrene takes on a 90◦ geometry that restricts the options for the diacid ligand and results in a tetragonal structure (Figure 7b). Several excellent reviews highlight the utility of these materials.130 The spontaneous self-assembly of six identical calix[4]resorcinarenes (Figure 6b) and eight water molecules gave a snub cube ˚ 3 . and selectivity.126 photochemistry. Ltd. The dative bond directs the porphyrins to stack one on top of another creating a pseudohexagonal shaped center cavity. thereby allowing exchange of guests or enabling the expulsion of products upon completion of a reaction. Ltd.125 The guest therefore played an integral role in the assembly process. These capsules could accommodate molecules of ∼600 A ˚ in length.Self-assembly and self-organization assembled from dynamic covalent bonds. enables one to probe the effects of this confinement on the physical properties and chemical reactivity of the guests. Gibbs and Ramamurthy demonstrated the utility of these assembled systems as reaction vessels for selective oxidation. two of the octa-acid hemispheres dimerized forming a capsule. Online  2012 John Wiley & Sons. It is not surprising that these units self-assemble into ribbons149 and tetrameric macrocycles. metal–ligand interactions are valuable for assembling large 7 functional structures. 125 Upon addition of a guest that was small and nonpolar. 133 The study of the assembly of relup to 22 A atively small organic capsules is advantageous as it allows one to follow the assembly/disassembly process and in the cases where guests are encapsulated. 3. The elongated capsules from Rebek and coworkers were assembled from derivations of calix[4]resorcinarene (Figure 6d) and use H-bond donors and acceptors to form cylindrical capsules with cavities ˚ 3 . which resulted in high stereoselectivity.139 Self-assembled coordination cages provide a fascinating and active research area with much promise for delivering active and functional materials. 135 A complex with an internal volume of ∼1375 A from the Reinhoudt group was formed from the 1:1 assembly of oppositely charged calix[4]arene building blocks in a polar mixture of CH3 OH/H2 O (Figure 6c).143 The Fujita group’s octahedral tetramer was formed from four triazines and six palladium atoms to form an octahedral tetramer with triazine “panels. and higher ordered structures known as G-quadruplexes.124.

1002/9780470661345. shape. Ltd.172 Temperature studies in chloroform gave an estimated association constants of ∼2500 M−1 .174.8 Concepts Trimers O N N C10H21 C8H17 Zn N N O N O N C8H17 O O C10H21 O N N Zn N N N N N Zn N O O (a) C8H17 O C10H21 Tetramer O 22 22 Pt O Pt O O (b) O Hexamer O 33 Pt O Pt 33 O O O O (c) Figure 7 Examples of dative directed assemblies: (a) Wasielewski porphyrin trefoil that uses diazo-bicyclic octane to form a trimer with a hexagonal center cavity138 . This article is  2012 John Wiley & Sons. Ltd. Ltd.3 Disk shaped building blocks Natural tubular assemblies show remarkable biological functions. For example. DOI: 10.141 exhibits selective stabilization of a dodecamer (94%) upon titration with 0. Given that simple self-assembling macrocycles and disks form assemblies reminiscent of these biological structures. assembled into robust columnar structures via amide hydrogen bonds. 177 Supramolecular Chemistry: From Molecules to Nanomaterials.171 such as the example from Ghadiri and coworkers (Figure 9b). drug delivery. 175 Columnar and nanotubular peptide structures show promise as functional bionanomaterials with potential applications as sensors. ion transport. This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons.154. it is not surprising that they have been a very active area of research.168 The spontaneous assembly process could be triggered by controlled acidification of a basic solution of the peptides to afford needle like crystals.164 These straw-shaped columns formed via the three-centered urea hydrogen bonding motif pack together to generate crystals with permanent porosity. Like the bis-ureas macrocycles. and tissue engineering.153 gelators.163 The macrocycles are relatively flat with the ureas preorganized perpendicular to the plane of the macrocycles. electronics. 155 and for molecular electronics. tubular shaped channels aid the transport of materials in and out of cells. 167 Cyclic peptides with alternating D.176. and interior functionality of the channels are controlled by the single macrocyclic unit used in their construction.166. such as the bis-urea in Figure 9(a). (b) Stang’s tetrameric structures are formed by the assembly of two bis-platinum phenanthrenes and 2 disodium carboxylates140 .and L-amino acids.157–162 The stacking of macrocycles ureas.smc012 .156 3. a conformation that aids columnar assembly (Figure 9a).7 equivalent of KI in CD3 CN. cyclic peptides that can adopt flat structures with the amide oriented perpendicular to the macrocycles readily assemble into tubular structures.152 Assembled guanosine derivatives are of interest as anticancer agents. The size. Online  2012 John Wiley & Sons.173 Cyclic peptides have been made from a wide range of natural and unnatural amino acids. quickly generates tubular shaped structures with homogeneous channels.165 Such homogeneous porous solids can be used to facilitate selective photocycloadditions. (c) Three bis-platinum benzophenone units and three disodium carboxylates organize to form hexagonal structures.

the need for one-dimensional electronically active materials also expands. trinitrotoluene) at the part-per-trillion scale. The macrocyclic columnar structures such as arylene ethynylene macrocycles (AEMs) from Moore’s group (Figure 9b) are potentially simple building blocks for controlled one-dimensional assembly. This article is  2012 John Wiley & Sons. (b) Guanine derivatives assemble into planar tetramers that can use a metal coordinate to stack into more complex structures. Online  2012 John Wiley & Sons.178 These fibrils showed polarized emission parallel to the aryl-stacking of the cycles.1002/9780470661345. These macrocyclic systems displayed liquid crystalline phases in seven different solvents. These systems can be cyclized in high yield through an alkyne metathesis process. Because of their aggregation properties and possible Pt–Pt interactions these structures are being probed for the possible liquid crystal applications and conductive nanotubes. This together with the electron donating capability of the AEM and the porous structure of the nanofibrils deposited on a surface enabled the detection of oxidative molecules (such as TNT. which indicated an intermolecular delocalization of the π clouds. Ltd.170 This platinum–Schiff base complex was synthesized in a onepot reaction with salicylaldimine proligands in basic DMSO (dimethyl sulfoxide).smc012 .Self-assembly and self-organization 9 Pd NN N NN NN N N 12+ NN N N NN N Pd Pd N N NN N N PdN NN N N NN N N N N N NN N N N N N NN N N (a) Pd NN NN Pd O O O O N O N N N N H N H H O N N H O O N N H N N N N O N H H O H O O O O N O O O N H M+ N O O O H O H N O H H N O N N N N O N N N O H N N H O N O O O O (b) Figure 8 Coordination driven assembly to discrete structures: (a) Fujita group’s assembly with four tridentate ligands and six palladium atoms forms a tetrameric cage143 . The ligands assembled in a head-totail manner to yield cyclic structures. This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons. They also showed birefringence and an uncommon aggregation in solution of concentrations even as low as 10−6 mol L−1 . Supramolecular Chemistry: From Molecules to Nanomaterials.169 Casting of AEMs with linear alkyl side chains on carbon films afforded entangled nanofibrils via aryl-stacking interactions and side chain interdigitation. Ltd.152 As the demand for smaller and smaller electronic devices grows. DOI: 10. The delocalization led to long range fluorescence quenching. synthesized a neutral macrocyclic complex (Figure 9d) with the goal of forming columnar structures through metal–metal interactions.179 Frischmann et al. Ltd.

smc012 . (b) cyclic peptides of Ghadiri et al.4 Specificity in the assembly process In nature.163 . and KAB ). KBB . This article is  2012 John Wiley & Sons. and (d) MacLachlan’s Pt4 rings. Online  2012 John Wiley & Sons. Ltd. They may also have some propensity to form heterodimers (AB) in a mixture. Each of these units has some preference to selfassemble and form homodimers (AA and BB) (Figure 10). for example.181 K AA A B B A BA A B A B A A K BB K AB Figure 10 Comparison of an assembly process that could afford both heterodimers (AA and BB) and homodimers (AB). (c) carbazole arylene ethynylene macrocycle (AEM) of Moore et al. selective self-assembly to afford exclusively homodimers is governed by the three equilibrium constants (KAA . monolayers. Ltd. This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons. Ltd. This spontaneous resolution of enantiomers was first observed in 1848 with Louis Pasteur’s physical separation of hemihedral crystals of two types of enantiopure tartaric acid.10 Concepts O O NH NH HN HN O O (a) R R H N O N N H N O N N O Pt t N P O O O N NH H H HN N H R R O O N t N P O N R (b) O N N O Pt N H O (c) C14H29.170 3. temperature. Consider. C(O)OC13H27 N (d) Figure 9 Examples of self-assembling stacking macrocycles: (a) bis-ureas from Shimizu et al. some assemblies form preferentially in the presence of mixtures of many other competitors.1002/9780470661345. a simple mixture with two assembly units (A and B). and supramolecular polymers and is likely controlled by subtle noncovalent interactions including crystal packing forces and crystallization kinetics. Obviously. which has been described by Lyle Isaacs as “the high-fidelity recognition of self from nonself. and the presence of competitors.169 . it would be both fascinating and extremely useful to be able to predict and control this process. The reasons for this preference are still under debate and the process is not yet predictable.168 . concentration. Supramolecular Chemistry: From Molecules to Nanomaterials.182 But spontaneous resolution can also afford chiral liquid crystals. Perhaps an extreme example of such a self-assembly process is the formation of enantiopure crystals from a racemic solution. DOI: 10.”180 One can imagine the homodimers continuing to grow selective and finally yield a crystal containing only As and a separate crystal containing only Bs. This selectivity for a component is often referred to as self-sorting. From a thermodynamic standpoint.

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