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supramolecular chemistry
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file:Supramolecular Assembly Lehn.jpg |Self-Assembly of a Circular Double HelicateJOURNAL, 10.1002/anie.199618381, Self-Assembly of a Circular Double Helicate, Angewandte Chemie International Edition in English, 35, 16, 1838–1840, 1996, Hasenknopf, B., Lehn, J. M., Kneisel, B. O., Baum, G., Fenske, D., Cucurbituril gyroscope AngewChemIntEd 2002 v41 p275 hires.png|Host-guest complex within another host (cucurbit[10]uril)JOURNAL, 10.1002/1521-3773(20020118)41:23.0.CO;2-M, A Cucurbituril-Based Gyroscane: A New Supramolecular Form, Angewandte Chemie International Edition, 41, 2, 275, 2002, Day, A. I., Blanch, R. J., Arnold, A. P., Lorenzo, S., Lewis, G. R., Dance, I., Rotaxane Crystal Structure EurJOrgChem page2565 year1998.png|mechanically-interlocked molecular architectures|mechanically interlocked molecules (rotaxane)JOURNAL, 10.1002/(SICI)1099-0690(199811)1998:113.0.CO;2-8, High Yielding Template-Directed Syntheses of [2]Rotaxanes, European Journal of Organic Chemistry, 1998, 11, 2565–2571, 1998, Bravo, J. A., Raymo, F. I. M., Stoddart, J. F., White, A. J. P., Williams, D. J., Host Guest Complex Porphyrin Sanders AngewChemIntEdEngl 1995 1096.jpg|An example of a host-guest chemistryJOURNAL, 10.1002/anie.199510961, Assembly and Crystal Structure of a Photoactive Array of Five Porphyrins, Angewandte Chemie International Edition in English, 34, 10, 1096–1099, 1995, Anderson, S., Anderson, H. L., Bashall, A., McPartlin, M., Sanders, J. K. M., Cucurbit-6-uril ActaCrystallB-Stru 1984 382.jpg|host-guest complex with a p-xylylenediammonium bound within a cucurbiturilJOURNAL, 10.1107/S0108768184002354, Structures of thep-xylylenediammonium chloride and calcium hydrogensulfate adducts of the cavitand 'cucurbituril', C36H36N24O12, Acta Crystallographica Section B, 40, 4, 382–387, 1984, Freeman, W. A., Lehn Beautiful Foldamer HelvChimActa 1598 2003.jpg|Intramolecular self-assembly of a foldamer.JOURNAL, 10.1002/hlca.200390137, Helicity-Encoded Molecular Strands: Efficient Access by the Hydrazone Route and Structural Features, Helvetica Chimica Acta, 86, 5, 1598–1624, 2003, Schmitt, J. L., Stadler, A. M., Kyritsakas, N., Lehn, J. M., Silsesquioxane 3D interpenetrated network Dalton Transactions 2016 12312.png|3D interpenetrated network in the crystal structure of silsesquioxane.JOURNAL, Janeta, Mateusz, John, Łukasz, Ejfler, Jolanta, Lis, Tadeusz, Szafert, Sławomir, 2016-08-02, Multifunctional imine-POSS as uncommon 3D nanobuilding blocks for supramolecular hybrid materials: synthesis, structural characterization, and properties,weblink Dalton Transactions, en, 45, 31, 10.1039/C6DT02134D, 1477-9234, 12312–12321, Supramolecular chemistry is the domain of chemistry beyond that of molecules that focuses on the chemical systems made up of a discrete number of assembled molecular subunits or components. The forces responsible for the spatial organization may vary from weak (intermolecular forces, electrostatic or hydrogen bonding) to strong (covalent bonding), provided that the degree of electronic coupling between the molecular component remains small with respect to relevant energy parameters of the component.JOURNAL, 10.1126/science.8511582, 8511582, Supramolecular chemistry, Science, 260, 5115, 1762–3, 1993, Lehn, J., 1993Sci...260.1762L, Lehn, J.-M. (1995) Supramolecular Chemistry. Wiley-VCH. {{ISBN|978-3-527-29311-7}} While traditional chemistry focuses on the covalent bond, supramolecular chemistry examines the weaker and reversible noncovalent interactions between molecules.Schneider, H.-J. Binding mechanisms in supramolecular complexes Angew. Chem. Int. Ed. Engl. 2009, 48, 3924 – 3977.weblink These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi-pi interactions and electrostatic effects.Biedermann,F.; Schneider, H.-J. : Experimental Binding Energies in Supramolecular Complexes ... Chem. Rev., 2016, 116 , 5216–5300. weblink Important concepts that have been demonstrated by supramolecular chemistry include molecular self-assembly, folding, molecular recognition, host-guest chemistry, mechanically-interlocked molecular architectures, and dynamic covalent chemistry.JOURNAL, 10.1002/anie.200602815, Supramolecular Chemistry in Water, Angewandte Chemie International Edition, 46, 14, 2366–93, 2007, Oshovsky, G. V., Reinhoudt, D. N., Verboom, W., 17370285, The study of non-covalent interactions is crucial to understanding many biological processes from cell structure to vision that rely on these forces for structure and function. Biological systems are often the inspiration for supramolecular research.Supermolecules are to molecules and the intermolecular bond what molecules are to atoms and the covalent bond.

History

The existence of intermolecular forces was first postulated by Johannes Diderik van der Waals in 1873. However, Nobel laureate Hermann Emil Fischer developed supramolecular chemistry's philosophical roots. In 1894,JOURNAL, 10.1002/cber.18940270364, Einfluss der Configuration auf die Wirkung der Enzyme, Berichte der deutschen chemischen Gesellschaft, 27, 3, 2985–2993, 1894, Fischer, E., Fischer suggested that enzyme-substrate interactions take the form of a "lock and key", the fundamental principles of molecular recognition and host-guest chemistry. In the early twentieth century noncovalent bonds were understood in gradually more detail, with the hydrogen bond being described by Latimer and Rodebush in 1920.The use of these principles led to an increasing understanding of protein structure and other biological processes. For instance, the important breakthrough that allowed the elucidation of the double helical structure of DNA occurred when it was realized that there are two separate strands of nucleotides connected through hydrogen bonds. The use of noncovalent bonds is essential to replication because they allow the strands to be separated and used to template new double stranded DNA. Concomitantly, chemists began to recognize and study synthetic structures based on noncovalent interactions, such as micelles and microemulsions.Eventually, chemists were able to take these concepts and apply them to synthetic systems. The breakthrough came in the 1960s with 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 Vögtle became active in synthesizing shape- and ion-selective receptors, and throughout the 1980s research in the area gathered a rapid pace with concepts such as mechanically interlocked molecular architectures emerging.The importance of supramolecular chemistry was established by the 1987 Nobel Prize for Chemistry which was awarded to Donald J. Cram, Jean-Marie Lehn, and Charles J. Pedersen in recognition of their work in this area.Schmeck, Harold M. Jr. (October 15, 1987) "Chemistry and Physics Nobels Hail Discoveries on Life and Superconductors; Three Share Prize for Synthesis of Vital Enzymes". New York Times The development of selective "host-guest" complexes in particular, in which a host molecule recognizes and selectively binds a certain guest, was cited as an important contribution.In the 1990s, supramolecular chemistry became even more sophisticated, with researchers such as James Fraser Stoddart developing molecular machinery and highly complex self-assembled structures, and Itamar Willner developing sensors and methods of electronic and biological interfacing. During this period, electrochemical and photochemical motifs became integrated into supramolecular systems in order to increase functionality, research into synthetic self-replicating system began, and work on molecular information processing devices began. The emerging science of nanotechnology also had a strong influence on the subject, with building blocks such as fullerenes, nanoparticles, and dendrimers becoming involved in synthetic systems.

Control

Thermodynamics

Supramolecular chemistry deals with subtle interactions, and consequently control over the processes involved can require great precision. In particular, noncovalent bonds have low energies and often no activation energy for formation. 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 that the low bond energy results in a shift towards the breaking of supramolecular complexes at higher temperatures.However, low temperatures can also be problematic to supramolecular processes. Supramolecular chemistry can require molecules to distort into thermodynamically disfavored conformations (e.g. during the "slipping" synthesis of rotaxanes), and may include some covalent chemistry that goes along with the supramolecular. In addition, the dynamic nature of supramolecular chemistry 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, and study supramolecular chemistry. Perhaps the most striking example is that of warm-blooded biological systems, which entirely cease to operate outside a very narrow temperature range.

Environment

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

Concepts

Molecular self-assembly

Molecular 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 noncovalent interactions. Self-assembly may be subdivided into intermolecular self-assembly (to form a supramolecular assembly), and intramolecular self-assembly (or folding as demonstrated by foldamers and polypeptides). Molecular self-assembly also allows the construction of larger structures such as micelles, membranes, vesicles, liquid crystals, and is important to crystal engineering.JOURNAL, 10.1088/1468-6996/9/1/014109, Challenges and breakthroughs in recent research on self-assembly, Science and Technology of Advanced Materials, 9, 014109, 2008, Ariga, K., Hill, J. P., Lee, M. V., Vinu, A., Charvet, R., Acharya, S., 2008STAdM...9a4109A, 27877935, 5099804, {{open access}}

Molecular recognition and complexation

Molecular recognition is the specific binding of a guest molecule to a complementary host molecule to form a host-guest complex. Often, the definition of which species is the "host" and which is the "guest" is arbitrary. The molecules are able to identify each other using noncovalent interactions. Key applications of this field are the construction of molecular sensors and catalysis.JOURNAL, 10.1088/1468-6996/9/1/014103, Metallo-supramolecular modules as a paradigm for materials science, Science and Technology of Advanced Materials, 9, 014103, 2008, Kurth, D. G., 2008STAdM...9a4103G, {{Open access}}JOURNAL, 10.1039/C2SC20583A, Supramolecular hosts that recognize methyllysines and disrupt the interaction between a modified histone tail and its epigenetic reader protein, Chemical Science, 3, 2695, 2012, Daze, K., JOURNAL, 10.1088/1468-6996/9/1/014108, Chemistry and application of flexible porous coordination polymers, Science and Technology of Advanced Materials, 9, 014108, 2008, Bureekaew, S., Shimomura, S., Kitagawa, S., 2008STAdM...9a4108B, 27877934, 5099803, {{Open access}}JOURNAL, 10.1002/anie.199013041, Perspectives in Supramolecular Chemistry—From Molecular Recognition towards Molecular Information Processing and Self-Organization, Angewandte Chemie International Edition in English, 29, 11, 1304–1319, 1990, Lehn, J. M.,

Template-directed synthesis

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

Mechanically interlocked molecular architectures

Mechanically interlocked molecular architectures consist of molecules that are linked only as a consequence of their topology. Some noncovalent interactions may exist between the different components (often those that were utilized in the construction of the system), but covalent bonds do not. Supramolecular chemistry, and template-directed synthesis in particular, is key to the efficient synthesis of the compounds. Examples of mechanically interlocked molecular architectures include catenanes, rotaxanes, molecular knots, molecular Borromean ringsJOURNAL, 10.1088/1468-6996/9/1/014104, Electrochromic materials using mechanically interlocked molecules, Science and Technology of Advanced Materials, 9, 014104, 2008, Ikeda, T., Stoddart, J. F., 2008STAdM...9a4104I, {{Open access}} and ravels.JOURNAL, 10.1038/ncomms1208, 21343923, Metallosupramolecular self-assembly of a universal 3-ravel, Nature Communications, 2, 205, 2011, Li, F., Clegg, J. K., Lindoy, L. F., MacQuart, R. B., Meehan, G. V., 2011NatCo...2E.205L,

Dynamic covalent chemistry

In dynamic covalent chemistry covalent bonds are broken and formed in a reversible reaction under thermodynamic control. While covalent bonds are key to the process, the system is directed by noncovalent forces to form the lowest energy structures.JOURNAL, 10.1002/1521-3773(20020315)41:63.0.CO;2-E, Dynamic Covalent Chemistry, Angewandte Chemie International Edition, 41, 6, 898–952, 2002, Rowan, S. J., Cantrill, S. J., Cousins, G. R. L., Sanders, J. K. M., Stoddart, J. F.,

Biomimetics

Many synthetic supramolecular systems are designed to copy functions of biological systems. These biomimetic architectures can be used to learn about both the biological model and the synthetic implementation. Examples include photoelectrochemical systems, catalytic systems, protein design and self-replication.JOURNAL, 10.1038/nbt874, 14520402, Fabrication of novel biomaterials through molecular self-assembly, Nature Biotechnology, 21, 10, 1171–8, 2003, Zhang, S.,

Imprinting

Molecular imprinting describes a process by which a host is constructed from small molecules using a suitable molecular species as a template. After construction, the template is removed leaving only the host. The template for host construction may be subtly different from the guest that the finished host binds to. In its simplest form, imprinting utilizes only steric interactions, but more complex systems also incorporate hydrogen bonding and other interactions to improve binding strength and specificity.JOURNAL, 10.1016/S0165-9936(98)00123-X, Molecular imprinting in chemical sensing, TrAC Trends in Analytical Chemistry, 18, 3, 192–199, 1999, Dickert, F.,

Molecular machinery

Molecular machines are molecules or molecular assemblies that can perform functions such as linear or rotational movement, switching, and entrapment. These devices exist at the boundary between supramolecular chemistry and nanotechnology, and prototypes have been demonstrated using supramolecular concepts.JOURNAL, 10.1021/ar970340y, Molecular Machines, Accounts of Chemical Research, 31, 7, 405–414, 1998, Balzani, V., Gómez-López, M., Stoddart, J. F., Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Feringa shared the 2016 Nobel Prize in Chemistry for the 'design and synthesis of molecular machines'.WEB,weblink The Nobel Prize in Chemistry 2016, Nobelprize.org, Nobel Media AB 2014, 14 January 2017,

Building blocks

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

Synthetic recognition motifs

Macrocycles

Macrocycles are very useful in supramolecular chemistry, as they provide whole cavities that can completely surround 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 synthesised to provide more tailored recognition properties.
  • Supramolecular metallocycles are macrocyclic aggregates with metal ions in the ring, often formed from angular and linear modules. Common metallocycle shapes in these types of applications include triangles, squares, and pentagons, each bearing functional groups that connect the pieces via "self-assembly."JOURNAL, 10.1021/ar700216n, 18271561, Chiral Metallocycles: Rational Synthesis and Novel Applications, Accounts of Chemical Research, 41, 4, 521–37, 2008, Lee, S. J., Lin, W.,
  • Metallacrowns are metallomacrocycles generated via a similar self-assembly approach from fused chelate-rings.

Structural units

Many supramolecular systems require their components to have suitable spacing and conformations relative to each other, and therefore easily employed structural units are required.BOOK,weblink Comprehensive supramolecular chemistry II, Atwood, J. L.,, Gokel, George W., 1946-, Barbour, Leonard J.,, 9780128031995, Amsterdam, Netherlands, 992802408, 46,
  • 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 and multilayers.
  • The understanding of intermolecular interactions in solids has undergone a major renaissance via inputs from different experimental and computational methods in the last decade. This includes high-pressure studies in solids and in situ crystallization of compounds which are liquids at room temperature along with the utilization of electron density analysis, crystal structure prediction and DFT calculations in solid state to enable a quantitative understanding of the nature, energetics and topological properties associated with such interactions in crystals.{| title = Understanding Intermolecular Interactions in the Solid State: Approaches and Techniques; edited by Dr D.Chopra, RSC | year = 2018|}

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 been utilized in supramolecular electrochemical devices.

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 technology

Supramolecular chemistry has found many applications,Schneider, H.-J. ( Ed.) (2012) Applications of Supramolecular Chemistry , CRC Press Taylor & Francis Boca Raton etc , weblink in particular molecular self-assembly processes have been applied to the development of new materials. Large structures can be readily accessed using bottom-up synthesis as they are composed of small molecules requiring fewer steps to synthesize. Thus most of the bottom-up approaches to nanotechnology are based on supramolecular chemistry.Gale, P.A. and Steed, J.W. (eds.) (2012) Supramolecular Chemistry: From Molecules to Nanomaterials. Wiley. {{ISBN|978-0-470-74640-0}} Many smart materials Smart Materials Book Series, Royal Soc. Chem. Cambridge UK .weblink are based on molecular recognition.Chemoresponsive Materials /Stimulation by Chemical and Biological Signals, Schneider, H.-J. ; Ed:, (2015)The Royal Society of Chemistry, Cambridgeweblink

Catalysis

A 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 for reaction and lowering the transition state energy of reaction. Template-directed synthesis is a special case of supramolecular catalysis. Encapsulation systems such as micelles, dendrimers, and cavitandsJOURNAL, 10.1021/jo301499t, Deep-Cavity Cavitand Octa Acid as a Hydrogen Donor: Photofunctionalization with Nitrenes Generated from Azidoadamantanes, The Journal of Organic Chemistry, 78, 5, 1824–1832, 2012, Choudhury, R., 22931185, are also used in catalysis to create microenvironments suitable for reactions (or steps in reactions) to progress that is not possible to use on a macroscopic scale.

Medicine

Design based on supramolecular chemistry has led to numerous applications in the creation of functional biomaterials and therapeutics.JOURNAL, Webber, Matthew J., Appel, Eric A., Meijer, E. W., Langer, Robert, Supramolecular biomaterials, Nature Materials, 18 December 2015, 15, 1, 13–26, 10.1038/nmat4474, 2016NatMa..15...13W, Supramolecular biomaterials afford a number of modular and generalizable platforms with tunable mechanical, chemical and biological properties. These include systems based on supramolecular assembly of peptides, host-guest macrocycles, high-affinity hydrogen bonding, and metal-ligand interactions.A supramolecular approach has been used extensively to create artificial ion channels for the transport of sodium and potassium ions into and out of cells.BOOK, Nuria, Rodríguez-Vázquez, Alberto, Fuertes, Manuel, Amorín, Juan R., Granja, Springer, 2016, Metal Ions in Life Sciences, 16, The Alkali Metal Ions: Their Role in Life, Astrid, Sigel, Helmut, Sigel, Roland K.O., Sigel, Chapter 14. Bioinspired Artificial Sodium and Potassium Ion Channels, 485–556, 10.1007/978-4-319-21756-7_14, Supramolecular chemistry is also important to the development of new pharmaceutical therapies by understanding the interactions at a drug binding site. The area of drug delivery has also made critical advances as a result of supramolecular chemistry providing encapsulation and targeted release mechanisms.Smart Materials for Drug Delivery: Complete Set (2013) Royal Soc. Chem. Cambridge UKweblink In addition, supramolecular systems have been designed to disrupt protein-protein interactions that are important to cellular function.JOURNAL, 10.1016/j.jconrel.2011.04.027, 21571017, New pharmaceutical applications for macromolecular binders, Journal of Controlled Release, 155, 2, 200–10, 2011, Bertrand, N., Gauthier, M. A., Bouvet, C. L., Moreau, P., Petitjean, A., Leroux, J. C., Leblond, J.,

Data storage and processing

Supramolecular 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 also been shown by supramolecular signal transduction devices. Data storage has been accomplished by the use of molecular 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. Even full-scale computations have been achieved by semi-synthetic DNA computers.

See also

References

{{Reflist|30em}}

External links

{{commons|Supramolecular chemistry}} {{BranchesofChemistry}}

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