Supramolecular chemistry 1

Supramolecular chemistry

An example of a supramolecular assembly.[1]

Supramolecular complex of a chloride ion,cucurbit[5]uril, and cucurbit[10]uril.[2]

An example of a mechanically-interlocked moleculararchitecture in this case a rotaxane.[3]

Supramolecular chemistry refers to the area of chemistry beyondthe molecules and focuses on the chemical systems made up of adiscrete number of assembled molecular subunits or components.The forces responsible for the spatial organization may vary fromweak (intermolecular forces, electrostatic or hydrogen bonding) tostrong (covalent bonding), provided that the degree of electroniccoupling between the molecular component remains small withrespect to relevant energy parameters of the component.[7] [8]

While traditional chemistry focuses on the covalent bond,supramolecular chemistry examines the weaker and reversiblenoncovalent interactions between molecules. These forces includehydrogen bonding, metal coordination, hydrophobic forces, vander Waals forces, pi-pi interactions and electrostatic effects.Important concepts that have been demonstrated bysupramolecular chemistry include molecular self-assembly,folding, molecular recognition, host-guest chemistry,mechanically-interlocked molecular architectures, and dynamiccovalent chemistry.[9] The study of non-covalent interactions iscrucial to understanding many biological processes from cellstructure to vision that rely on these forces for structure andfunction. Biological systems are often the inspiration forsupramolecular research.

History

The existence of intermolecular forces was first postulated byJohannes Diderik van der Waals in 1873. However, it is withNobel laureate Hermann Emil Fischer that supramolecularchemistry has its philosophical roots. In 1890, Fischer suggestedthat enzyme-substrate interactions take the form of a "lock andkey", pre-empting the concepts of molecular recognition andhost-guest chemistry. In the early twentieth century noncovalentbonds were understood in gradually more detail, with thehydrogen bond being described by Latimer and Rodebush in 1920.

The use of these principles led to an increasing understanding ofprotein structure and other biological processes. For instance, theimportant breakthrough that allowed the elucidation of the doublehelical structure of DNA occurred when it was realized that thereare two separate strands of nucleotides connected throughhydrogen bonds. The use of noncovalent bonds is essential to replication because they allow the strands to beseparated and used to template new double stranded DNA. Concomitantly, chemists

Supramolecular chemistry 2

An example of a host-guest chemistry.[4]

host-guest complex with a p-xylylenediammoniumbound within a cucurbituril.[5]

began to recognize and study synthetic structures based onnoncovalent interactions, such as micelles and microemulsions.

Eventually, chemists were able to take these concepts and applythem to synthetic systems. The breakthrough came in the 1960swith the synthesis of the crown ethers by Charles J. Pedersen.Following this work, other researchers such as Donald J. Cram,Jean-Marie Lehn and Fritz Vogtle became active in synthesizingshape- and ion-selective receptors, and throughout the 1980sresearch in the area gathered a rapid pace with concepts such asmechanically-interlocked molecular architectures emerging.

The importance of supramolecular chemistry was established bythe 1987 Nobel Prize for Chemistry which was awarded to DonaldJ. Cram, Jean-Marie Lehn, and Charles J. Pedersen in recognitionof their work in this area.[10] The development of selective"host-guest" complexes in particular, in which a host moleculerecognizes and selectively binds a certain guest, was cited as animportant contribution.

In the 1990s, supramolecular chemistry became even moresophisticated, with researchers such as James Fraser Stoddartdeveloping molecular machinery and highly complexself-assembled structures, and Itamar Willner developing sensorsand methods of electronic and biological interfacing. During thisperiod, electrochemical and photochemical motifs becameintegrated into supramolecular systems in order to increasefunctionality, research into synthetic self-replicating system began,and work on molecular information processing devices began. Theemerging science of nanotechnology also had a strong influenceon the subject, with building blocks such as fullerenes,nanoparticles, and dendrimers becoming involved in synthetic systems.

Control of supramolecular chemistry

Thermodynamics

Supramolecular chemistry deals with subtle interactions, and consequently control over the processes involved canrequire great precision. In particular, noncovalent bonds have low energies and often no activation energy forformation. As demonstrated by the Arrhenius equation, this means that, unlike in covalent bond-forming chemistry,the rate of bond formation is not increased at higher temperatures. In fact, chemical equilibrium equations show thatthe low bond energy results in a shift towards the breaking of supramolecular complexes at higher temperatures.

Supramolecular chemistry 3

Intramolecular self-assembly of a foldamer.[6]

However, low temperatures can also be problematic tosupramolecular processes. Supramolecular chemistry can requiremolecules to distort into thermodynamically disfavoredconformations (e.g. during the "slipping" synthesis of rotaxanes),and may include some covalent chemistry that goes along with thesupramolecular. In addition, the dynamic nature of supramolecularchemistry is utilized in many systems (e.g. molecular mechanics),and cooling the system would slow these processes.

Thus, thermodynamics is an important tool to design, control, andstudy supramolecular chemistry. Perhaps the most strikingexample is that of warm-blooded biological systems, which ceaseto operate entirely outside a very narrow temperature range.

Environment

The molecular environment around a supramolecular system isalso of prime importance to its operation and stability. Manysolvents have strong hydrogen bonding, electrostatic, andcharge-transfer capabilities, and are therefore able to become involved in complex equilibria with the system, evenbreaking complexes completely. For this reason, the choice of solvent can be critical.

Concepts in supramolecular chemistry

Molecular self-assemblyMolecular self-assembly is the construction of systems without guidance or management from an outside source(other than to provide a suitable environment). The molecules are directed to assemble through noncovalentinteractions. Self-assembly may be subdivided into intermolecular self-assembly (to form a supramolecularassembly), and intramolecular self-assembly (or folding as demonstrated by foldamers and polypeptides). Molecularself-assembly also allows the construction of larger structures such as micelles, membranes, vesicles, liquid crystals,and is important to crystal engineering.[11]

Molecular recognition and complexationMolecular recognition is the specific binding of a guest molecule to a complementary host molecule to form ahost-guest complex. Often, the definition of which species is the "host" and which is the "guest" is arbitrary. Themolecules are able to identify each other using noncovalent interactions. Key applications of this field are theconstruction of molecular sensors and catalysis.[12] [13] [14]

Template-directed synthesisMolecular recognition and self-assembly may be used with reactive species in order to pre-organize a system for a chemical reaction (to form one or more covalent bonds). It may be considered a special case of supramolecular catalysis. Noncovalent bonds between the reactants and a "template" hold the reactive sites of the reactants close together, facilitating the desired chemistry. This technique is particularly useful for situations where the desired reaction conformation is thermodynamically or kinetically unlikely, such as in the preparation of large macrocycles. This pre-organization also serves purposes such as minimizing side reactions, lowering the activation energy of the reaction, and producing desired stereochemistry. After the reaction has taken place, the template may remain in place, be forcibly removed, or may be "automatically" decomplexed on account of the different recognition

Supramolecular chemistry 4

properties of the reaction product. The template may be as simple as a single metal ion or may be extremelycomplex.

Mechanically-interlocked molecular architecturesMechanically-interlocked molecular architectures consist of molecules that are linked only as a consequence of theirtopology. Some noncovalent interactions may exist between the different components (often those that were utilizedin the construction of the system), but covalent bonds do not. Supramolecular chemistry, and template-directedsynthesis in particular, is key to the efficient synthesis of the compounds. Examples of mechanically-interlockedmolecular architectures include catenanes, rotaxanes, molecular knots, and molecular Borromean rings.[15]

Dynamic covalent chemistryIn dynamic covalent chemistry covalent bonds are broken and formed in a reversible reaction under thermodynamiccontrol. While covalent bonds are key to the process, the system is directed by noncovalent forces to form the lowestenergy structures.[16]

BiomimeticsMany synthetic supramolecular systems are designed to copy functions of biological systems. These biomimeticarchitectures can be used to learn about both the biological model and the synthetic implementation. Examplesinclude photoelectrochemical systems, catalytic systems, protein design and self-replication.[17]

ImprintingMolecular imprinting describes a process by which a host is constructed from small molecules using a suitablemolecular species as a template. After construction, the template is removed leaving only the host. The template forhost construction may be subtly different from the guest that the finished host bind. In its simplest form, imprintingutilizes only steric interactions, but more complex systems also incorporate hydrogen bonding and other interactionsto improve binding strength and specificity.[18]

Molecular machineryMolecular machines are molecules or molecular assemblies that can perform functions such as linear or rotationalmovement, switching, and entrapment. These devices exist at the boundary between supramolecular chemistry andnanotechnology, and prototypes have been demonstrated using supramolecular concepts.[19]

Building blocks of supramolecular chemistrySupramolecular systems are rarely designed from first principles. Rather, chemists have a range of well-studiedstructural and functional building blocks that they are able to use to build up larger functional architectures. Many ofthese exist as whole families of similar units, from which the analog with the exact desired properties can be chosen.

Supramolecular chemistry 5

Synthetic recognition motifs• The pi-pi charge-transfer interactions of bipyridinium with dioxyarenes or diaminoarenes have been used

extensively for the construction of mechanically interlocked systems and in crystal engineering.• The use of crown ether binding with metal or ammonium cations is ubiquitous in supramolecular chemistry.• The formation of carboxylic acid dimers and other simple hydrogen bonding interactions.• The complexation of bipyridines or tripyridines with ruthenium, silver or other metal ions is of great utility in the

construction of complex architectures of many individual molecules.• The complexation of porphyrins or phthalocyanines around metal ions gives access to catalytic, photochemical

and electrochemical properties as well as complexation. These units are used a great deal by nature.

MacrocyclesMacrocycles are very useful in supramolecular chemistry, as they provide whole cavities that can completelysurround guest molecules and may be chemically modified to fine-tune their properties.• Cyclodextrins, calixarenes, cucurbiturils and crown ethers are readily synthesized in large quantities, and are

therefore convenient for use in supramolecular systems.• More complex cyclophanes, and cryptands can be synthesized to provide more tailored recognition properties.• Supramolecular metallacycles are macrocyclic aggregates with metal ions in the ring, often formed from angular

and linear modules. Common metallacycle shapes in these types of applications include triangles, squares, andpentagons, each bearing functional groups that connect the pieces via "self-assembly."[20]

• Metallacrowns are metallamacrocycles generated via a similar self-assembly approach from fused chelate-rings.

Structural unitsMany supramolecular systems require their components to have suitable spacing and conformations relative to eachother, and therefore easily-employed structural units are required.• Commonly used spacers and connecting groups include polyether chains, biphenyls and triphenyls, and simple

alkyl chains. The chemistry for creating and connecting these units is very well understood.• nanoparticles, nanorods, fullerenes and dendrimers offer nanometer-sized structure and encapsulation units.• Surfaces can be used as scaffolds for the construction of complex systems and also for interfacing electrochemical

systems with electrodes. Regular surfaces can be used for the construction of self-assembled monolayers andmultilayers.

Photo-/electro-chemically active units• Porphyrins, and phthalocyanines have highly tunable photochemical and electrochemical activity as well as the

potential for forming complexes.• Photochromic and photoisomerizable groups have the ability to change their shapes and properties (including

binding properties) upon exposure to light.• TTF and quinones have more than one stable oxidation state, and therefore can be switched with redox chemistry

or electrochemistry. Other units such as benzidine derivatives, viologens groups and fullerenes, have also beenutilized in supramolecular electrochemical devices.

Supramolecular chemistry 6

Biologically-derived units• The extremely strong complexation between avidin and biotin is instrumental in blood clotting, and has been used

as the recognition motif to construct synthetic systems.• The binding of enzymes with their cofactors has been used as a route to produce modified enzymes, electrically

contacted enzymes, and even photoswitchable enzymes.• DNA has been used both as a structural and as a functional unit in synthetic supramolecular systems.

Applications

Materials technologySupramolecular chemistry and molecular self-assembly processes in particular have been applied to the developmentof new materials. Large structures can be readily accessed using bottom-up synthesis as they are composed of smallmolecules requiring fewer steps to synthesize. Thus most of the bottom-up approaches to nanotechnology are basedon supramolecular chemistry.

CatalysisA major application of supramolecular chemistry is the design and understanding of catalysts and catalysis.Noncovalent interactions are extremely important in catalysis, binding reactants into conformations suitable forreaction and lowering the transition state energy of reaction. Template-directed synthesis is a special case ofsupramolecular catalysis. Encapsulation systems such as micelles and dendrimers are also used in catalysis to createmicroenvironments suitable for reactions (or steps in reactions) to progress that is not possible to use on amacroscopic scale.

MedicineSupramolecular chemistry is also important to the development of new pharmaceutical therapies by understandingthe interactions at a drug binding site. The area of drug delivery has also made critical advances as a result ofsupramolecular chemistry providing encapsulation and targeted release mechanisms. In addition, supramolecularsystems have been designed to disrupt protein-protein interactions that are important to cellular function.

Data storage and processingSupramolecular chemistry has been used to demonstrate computation functions on a molecular scale. In many cases,photonic or chemical signals have been used in these components, but electrical interfacing of these units has alsobeen shown by supramolecular signal transduction devices. Data storage has been accomplished by the use ofmolecular switches with photochromic and photoisomerizable units, by electrochromic and redox-switchable units,and even by molecular motion. Synthetic molecular logic gates have been demonstrated on a conceptual level. Evenfull-scale computations have been achieved by semi-synthetic DNA computers.

Supramolecular chemistry 7

Green chemistryResearch in supramolecular chemistry also has application in green chemistry where reactions have been developedwhich proceed in the solid state directed by non-covalent bonding. Such procedures are highly desirable since theyreduce the need for solvents during the production of chemicals.

Other devices and functionsSupramolecular chemistry is often pursued to develop new functions that cannot appear from a single molecule.These functions also include magnetic properties, light responsiveness, self-healing polymers, synthetic ionchannels, molecular sensors, etc. Supramolecular research has been applied to develop high-tech sensors, processesto treat radioactive waste, and contrast agents for CAT scans.

References[1] Hasenknopf, Bernold; Lehn, Jean-Marie; Kneisel, Boris O.; Baum, Gerhard; Fenske, Dieter (1996). "Self-Assembly of a Circular Double

Helicate". Angewandte Chemie International Edition in English 35: 1838. doi:10.1002/anie.199618381.[2] Day, A. I. et al. (2002). "A Cucurbituril-Based Gyroscane: A New Supramolecular Form This research was supported by the Australian

Research Council and the University of New South Wales. G.R.L. acknowledges the award of a Royal Society Fellowship tenable inAustralia.". Angew. Chem. Int. Ed. 41: 275–277. doi:10.1002/1521-3773(20020118)41:2<275::AID-ANIE275>3.0.CO;2-M.

[3] Bravo, J. A. et al. (1998). "High Yielding Template-Directed Syntheses of [2]Rotaxanes". Eur. J. Org. Chem. 1998: 2565–2571.doi:10.1002/(SICI)1099-0690(199811)1998:11<2565::AID-EJOC2565>3.0.CO;2-8.

[4] Anderson, Sally; Anderson, Harry L.; Bashall, Alan; McPartlin, Mary; Sanders, Jeremy K. M. (1995). "Assembly and Crystal Structure of aPhotoactive Array of Five Porphyrins". Angewandte Chemie International Edition in English 34: 1096. doi:10.1002/anie.199510961.

[5] Freeman, W. A. (1984). "Structures of thep-xylylenediammonium chloride and calcium hydrogensulfate adducts of the cavitand 'cucurbituril',C36H36N24O12". Acta Crystallographica Section B Structural Science 40: 382. doi:10.1107/S0108768184002354.

[6] Schmitt, Jean-Louis; Stadler, Adrian-Mihail; Kyritsakas, Nathalie; Lehn, Jean-Marie (2003). "Helicity-Encoded Molecular Strands: EfficientAccess by the Hydrazone Route and Structural Features". Helvetica Chimica Acta 86: 1598. doi:10.1002/hlca.200390137.

[7] Lehn JM (1993). "Supramolecular chemistry". Science 260 (5115): 1762–3. doi:10.1126/science.8511582. PMID 8511582.[8] Supramolecular Chemistry, J.-M. Lehn, Wiley-VCH (1995) ISBN 978-3527293117[9] Gennady V. Oshovsky, Dr. Dr., David N. Reinhoudt, Prof. Dr. Ir., Willem Verboom, Dr. (2007). "Supramolecular Chemistry in Water".

Angewandte Chemie International Edition 46 (14): 2366–2393. doi:10.1002/anie.200602815. PMID 17370285.[10] "Chemistry and Physics Nobels Hail Discoveries on Life and Superconductors; Three Share Prize for Synthesis of Vital Enzymes" (http:/ /

query. nytimes. com/ gst/ fullpage. html?res=9B0DE0DB143DF936A25753C1A961948260& sec=& spon=& partner=permalink&exprod=permalink) Harold M. Schmeck Jr. New York Times October 15, 1987

[11] Ariga, Katsuhiko; Hill, Jonathan P; Lee, Michael V; Vinu, Ajayan; Charvet, Richard; Acharya, Somobrata (2008). "Challenges andbreakthroughs in recent research on self-assembly" (free-download review). Science and Technology of Advanced Materials 9: 014109.doi:10.1088/1468-6996/9/1/014109.

[12] G Kurth, Dirk (2008). "Metallo-supramolecular modules as a paradigm for materials science" (free-download review). Science andTechnology of Advanced Materials 9: 014103. doi:10.1088/1468-6996/9/1/014103.

[13] Bureekaew, Sareeya; Shimomura, Satoru; Kitagawa, Susumu (2008). "Chemistry and application of flexible porous coordination polymers"(free-download review). Science and Technology of Advanced Materials 9: 014108. doi:10.1088/1468-6996/9/1/014108.

[14] J. M. Lehn, (1990). "Perspectives in supramolecular chemistry - from molecular recognition towards molecular information-processing andself-organization". Angewandte Chemie-International Edition in English 29 (11): 1304–1319. doi:10.1002/anie.199013041.

[15] Ikeda, Taichi; Stoddart, James Fraser (2008). "Electrochromic materials using mechanically interlocked molecules" (free-download review).Science and Technology of Advanced Materials 9: 014104. doi:10.1088/1468-6996/9/1/014104.

[16] S. J. Rowan, S. J. Cantrill, G. R. L. Cousins, J. K. M. Sanders and J. F. Stoddart (2002). "Dynamic covalent chemistry". AngewandteChemie-International Edition in English 41 (6): 898–952. doi:10.1002/1521-3773(20020315)41:6<898::AID-ANIE898>3.0.CO;2-E.PMID 12491278.

[17] S. G. Zhang (2003). "Fabrication of novel biomaterials through molecular selfassembly". Nature Biotechnology 21 (10): 1171–1178.doi:10.1038/nbt874. PMID 14520402.

[18] F. L. Dickert and O. Hayden (1999). "Molecular imprinting in chemical sensing". Trac-Trends in Analytical Chemistry 18 (3): 192–199.doi:10.1016/S0165-9936(98)00123-X.

[19] V. Balzani, M. Gomez-Lopez and J. F. Stoddart (1998). "Molecular machines". Accounts of Chemical Research 31 (7): 405–414.doi:10.1021/ar970340y.

[20] Lee, S.J.; Lin, W. (2008). "Chiral metallocycles: Rational synthesis and novel applications". Acc. Chem. Res. 41 (9): 521–37.doi:10.1021/ar700216n. PMID 18271561.

Supramolecular chemistry 8

External links• 2D and 3D Models of Dodecahedrane and Cuneane Assemlies (http:/ / www. wikinfo. org/ index. php/

2D_and_3D_Models_of_Dodecahedrane_and_Cuneane_Assemblies)• Supramolecular Chemistry (http:/ / www. beilstein-journals. org/ bjoc/ browse/ singleSeries. htm?sn=6) -

Thematic Series in the Open Access Beilstein Journal of Organic Chemistry

Article Sources and Contributors 9

Article Sources and ContributorsSupramolecular chemistry  Source: http://en.wikipedia.org/w/index.php?oldid=425730963  Contributors: *drew, Agilemolecule, Ahm 123, Albacore, Avathar, Breakyunit, Calvero JP, Contrib,D6, Dirac66, El C, Epolk, Ghutchis, Giftlite, Hbent, Headbomb, Hugo-cs, Itub, Jankolov, Jared81, Jeremiah, Jkwchui, Junkyardprince, Karol Langner, M stone, Masakim, Materialscientist,Mayumashu, Mipah, Mrestko, Nick Number, PaddyM, Passw0rd, Pearle, Peterebun, Pizza1512, Prateekdongare, Rjwilmsi, SBunnage, Sadi Carnot, Shropshire, Sikkema, Smokefoot,Teleomorph, Telf, TestPilot, TheBendster, Tomgally, V8rik, Van helsing, Vsmith, WikiUserPedia, Woohookitty, 43 anonymous edits

Image Sources, Licenses and ContributorsImage:Supramolecular Assembly Lehn.jpg  Source: http://en.wikipedia.org/w/index.php?title=File:Supramolecular_Assembly_Lehn.jpg  License: GNU Free Documentation License Contributors: Original uploader was M stone at en.wikipediaImage:Cucurbituril gyroscope AngewChemIntEd 2002 v41 p275 hires.png  Source:http://en.wikipedia.org/w/index.php?title=File:Cucurbituril_gyroscope_AngewChemIntEd_2002_v41_p275_hires.png  License: GNU Free Documentation License  Contributors: Originaluploader was M stone at en.wikipedia Later version(s) were uploaded by Mahahahaneapneap at en.wikipedia.Image:Rotaxane Crystal Structure EurJOrgChem page2565 year1998.jpg  Source:http://en.wikipedia.org/w/index.php?title=File:Rotaxane_Crystal_Structure_EurJOrgChem_page2565_year1998.jpg  License: GNU Free Documentation License  Contributors: Original uploaderwas M stone at en.wikipediaImage:Host Guest Complex Porphyrin Sanders AngewChemIntEdEngl 1995 1096.jpg  Source:http://en.wikipedia.org/w/index.php?title=File:Host_Guest_Complex_Porphyrin_Sanders_AngewChemIntEdEngl_1995_1096.jpg  License: unknown  Contributors: Original uploader was Mstone at en.wikipediaImage:Cucurbit-6-uril ActaCrystallB-Stru 1984 382.jpg  Source: http://en.wikipedia.org/w/index.php?title=File:Cucurbit-6-uril_ActaCrystallB-Stru_1984_382.jpg  License: GNU FreeDocumentation License  Contributors: Original uploader was M stone at en.wikipediaImage:Lehn Beautiful Foldamer HelvChimActa 1598 2003.jpg  Source: http://en.wikipedia.org/w/index.php?title=File:Lehn_Beautiful_Foldamer_HelvChimActa_1598_2003.jpg  License:GNU Free Documentation License  Contributors: Original uploader was M stone at en.wikipedia

LicenseCreative Commons Attribution-Share Alike 3.0 Unportedhttp:/ / creativecommons. org/ licenses/ by-sa/ 3. 0/