Supramolecular chemistry - AbsoluteAstronomy.com

Supramolecular chemistry refers to the area of chemistry

Chemistry

Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....

beyond the molecules and 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. While traditional chemistry focuses on the covalent bond

Covalent bond

A covalent bond is a form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms. The stable balance of attractive and repulsive forces between atoms when they share electrons is known as covalent bonding....

, supramolecular chemistry examines the weaker and reversible noncovalent interactions between molecules. These forces include hydrogen bond

Hydrogen bond

A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...

ing, metal coordination, hydrophobic forces

Hydrophobic effect

The hydrophobic effect is the observed tendency of nonpolar substances to aggregate in aqueous solution and exclude water molecules. The name, literally meaning "water-fearing," describes the segregation and apparent repulsion between water and nonpolar substances...

, van der Waals force

Van der Waals force

In physical chemistry, the van der Waals force , named after Dutch scientist Johannes Diderik van der Waals, is the sum of the attractive or repulsive forces between molecules other than those due to covalent bonds or to the electrostatic interaction of ions with one another or with neutral...

s, pi-pi interactions and electrostatic effects. Important concepts that have been demonstrated by supramolecular chemistry include molecular self-assembly

Molecular self-assembly

Molecular self-assembly is the process by which molecules adopt a defined arrangement without guidance or management from an outside source. There are two types of self-assembly, intramolecular self-assembly and intermolecular self-assembly...

, folding

Folding (chemistry)

In chemistry, folding is the process by which a molecule assumes its shape or conformation. The process can also be described as intramolecular self-assembly where the molecule is directed to form a specific shape through noncovalent interactions, such as hydrogen bonding, metal coordination,...

, molecular recognition

Molecular recognition

The term molecular recognition refers to the specific interaction between two or more molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π-π interactions, electrostatic and/or electromagnetic effects...

, host-guest chemistry

Host-guest chemistry

In supramolecular chemistry, host-guest chemistry describes complexes that are composed of two or more molecules or ions that are held together in unique structural relationships by forces other than those of full covalent bonds. Host-guest chemistry encompasses the idea of molecular recognition...

, mechanically-interlocked molecular architectures

Mechanically-interlocked molecular architectures

Mechanically interlocked molecular architectures are connections of molecules not through traditional bonds, but instead as a consequence of their topology. This connection of molecules is analogous to keys on a key chain loop. The keys are not directly connected to the key chain loop but they...

, and dynamic covalent chemistry

Dynamic covalent chemistry

In supramolecular chemistry, dynamic covalent chemistry is a strategy that aims at synthesizing large complex molecules. In it a reversible reaction is under thermodynamic reaction control and a specific reaction product out of many is captured...

. The study of non-covalent interactions

Noncovalent bonding

A noncovalent bond is a type of chemical bond, typically between macromolecules, that does not involve the sharing of pairs of electrons, but rather involves more dispersed variations of electromagnetic interactions. The noncovalent bond is the dominant type of bond between supermolecules in...

is crucial to understanding many biological processes from cell structure to vision that rely on these forces for structure and function. Biological systems

Systems biology

Systems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...

are often the inspiration for supramolecular research.

History

The existence of intermolecular forces was first postulated by Johannes Diderik van der Waals

Johannes Diderik van der Waals

Johannes Diderik van der Waals was a Dutch theoretical physicist and thermodynamicist famous for his work on an equation of state for gases and liquids....

in 1873. However, it is with Nobel laureate Hermann Emil Fischer

Hermann Emil Fischer

Hermann Emil Fischer, Emil Fischer was a German chemist and 1902 recipient of the Nobel Prize in Chemistry. He discovered the Fischer esterification. He developed the Fischer projection, a symbolic way of drawing asymmetric carbon atoms.-Early years:Fischer was born in Euskirchen, near Cologne,...

that supramolecular chemistry has its philosophical roots. In 1890, Fischer suggested that enzyme-substrate interactions

Enzyme catalysis

Enzyme catalysis is the catalysis of chemical reactions by specialized proteins known as enzymes. Catalysis of biochemical reactions in the cell is vital due to the very low reaction rates of the uncatalysed reactions....

take the form of a "lock and key", pre-empting the concepts of molecular recognition

Molecular recognition

and host-guest chemistry

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

Protein structure

Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...

and other biological processes. For instance, the important breakthrough that allowed the elucidation of the double helical structure

Nucleic acid double helix

In molecular biology, the term double helix refers to the structure formed by double-stranded molecules of nucleic acids such as DNA and RNA. The double helical structure of a nucleic acid complex arises as a consequence of its secondary structure, and is a fundamental component in determining its...

of DNA

DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

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 micelle

Micelle

A micelle is an aggregate of surfactant molecules dispersed in a liquid colloid. A typical micelle in aqueous solution forms an aggregate with the hydrophilic "head" regions in contact with surrounding solvent, sequestering the hydrophobic single tail regions in the micelle centre. This phase is...

s and microemulsion

Microemulsion

Microemulsions are clear, thermodynamically stable, isotropic liquid mixtures of oil, water and surfactant, frequently in combination with a cosurfactant. The aqueous phase may contain salt and/or other ingredients, and the "oil" may actually be a complex mixture of different hydrocarbons and olefins...

s.

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 ether

Crown ether

Crown ethers are cyclic chemical compounds that consist of a ring containing several ether groups. The most common crown ethers are oligomers of ethylene oxide, the repeating unit being ethyleneoxy, i.e., -CH2CH2O-. Important members of this series are the tetramer , the pentamer , and the hexamer...

s by Charles J. Pedersen

Charles J. Pedersen

Charles John Pedersen was an American organic chemist best known for describing methods of synthesizing crown ethers. He shared the Nobel Prize in Chemistry in 1987 with Donald J. Cram and Jean-Marie Lehn...

. Following this work, other researchers such as Donald J. Cram

Donald J. Cram

Donald James Cram was an American chemist who shared the 1987 Nobel Prize in Chemistry with Jean-Marie Lehn and Charles J...

, Jean-Marie Lehn

Jean-Marie Lehn

Jean-Marie Lehn is a French chemist. He received the Nobel Prize together with Donald Cram and Charles Pedersen in 1987 for his work in Chemistry, particularly his synthesis of the cryptands...

and Fritz Vogtle 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

Nobel Prize

The Nobel Prizes are annual international awards bestowed by Scandinavian committees in recognition of cultural and scientific advances. The will of the Swedish chemist Alfred Nobel, the inventor of dynamite, established the prizes in 1895...

for Chemistry which was awarded to Donald J. Cram, Jean-Marie Lehn, and Charles J. Pedersen in recognition of their work in this area. 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

James Fraser Stoddart

Sir James Fraser Stoddart is a Scottish chemist currently at the Department of Chemistry at Northwestern University. He works in the area of supramolecular chemistry and nanotechnology...

developing molecular machinery and highly complex self-assembled

Self-assembly

Self-assembly is a term used to describe processes in which a disordered system of pre-existing components forms an organized structure or pattern as a consequence of specific, local interactions among the components themselves, without external direction...

structures, and Itamar Willner developing sensors and methods of electronic and biological interfacing. During this period, electrochemical

Electrochemistry

Electrochemistry is a branch of chemistry that studies chemical reactions which take place in a solution at the interface of an electron conductor and an ionic conductor , and which involve electron transfer between the electrode and the electrolyte or species in solution.If a chemical reaction is...

and photochemical

Photochemistry

Photochemistry, a sub-discipline of chemistry, is the study of chemical reactions that proceed with the absorption of light by atoms or molecules.. Everyday examples include photosynthesis, the degradation of plastics and the formation of vitamin D with sunlight.-Principles:Light is a type of...

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

Nanotechnology

Nanotechnology is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with developing materials, devices, or other structures possessing at least one dimension sized from 1 to 100 nanometres...

also had a strong influence on the subject, with building blocks such as fullerene

Fullerene

A fullerene is any molecule composed entirely of carbon, in the form of a hollow sphere, ellipsoid, or tube. Spherical fullerenes are also called buckyballs, and they resemble the balls used in association football. Cylindrical ones are called carbon nanotubes or buckytubes...

s, nanoparticle

Nanoparticle

In nanotechnology, a particle is defined as a small object that behaves as a whole unit in terms of its transport and properties. Particles are further classified according to size : in terms of diameter, coarse particles cover a range between 10,000 and 2,500 nanometers. Fine particles are sized...

s, and dendrimer

Dendrimer

Dendrimers are repetitively branched molecules. The name comes from the Greek word "δένδρον" , which translates to "tree". Synonymous terms for dendrimer include arborols and cascade molecules. However, dendrimer is currently the internationally accepted term. A dendrimer is typically symmetric...

s becoming involved in synthetic systems.

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

Activation energy

In chemistry, activation energy is a term introduced in 1889 by the Swedish scientist Svante Arrhenius that is defined as the energy that must be overcome in order for a chemical reaction to occur. Activation energy may also be defined as the minimum energy required to start a chemical reaction...

for formation. As demonstrated by the Arrhenius equation

Arrhenius equation

The Arrhenius equation is a simple, but remarkably accurate, formula for the temperature dependence of the reaction rate constant, and therefore, rate of a chemical reaction. The equation was first proposed by the Dutch chemist J. H. van 't Hoff in 1884; five years later in 1889, the Swedish...

, this means that, unlike in covalent bond-forming chemistry, the rate of bond formation is not increased at higher temperatures. In fact, chemical equilibrium

Chemical equilibrium

In a chemical reaction, chemical equilibrium is the state in which the concentrations of the reactants and products have not yet changed with time. It occurs only in reversible reactions, and not in irreversible reactions. Usually, this state results when the forward reaction proceeds at the same...

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

Chemical structure

A chemical structure includes molecular geometry, electronic structure and crystal structure of molecules. Molecular geometry refers to the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together. Molecular geometry can range from the very simple, such as...

(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

Molecular mechanics

Molecular mechanics uses Newtonian mechanics to model molecular systems. The potential energy of all systems in molecular mechanics is calculated using force fields...

), and cooling the system would slow these processes.

Thus, thermodynamics

Thermodynamics

Thermodynamics is a physical science that studies the effects on material bodies, and on radiation in regions of space, of transfer of heat and of work done on or by the bodies or radiation...

is an important tool to design, control, and study supramolecular chemistry. Perhaps the most striking example is that of warm-blooded

Warm-blooded

The term warm-blooded is a colloquial term to describe animal species which have a relatively higher blood temperature, and maintain thermal homeostasis primarily through internal metabolic processes...

biological systems, which cease to operate entirely 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.

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

Supramolecular assembly

A supramolecular assembly or "supermolecule" is a well defined complex of molecules held together by noncovalent bonds. While a supramolecular assembly can be simply composed of two molecules , it is more often used to denote larger complexes of molecules that form sphere-, rod-, or sheet-like...

), and intramolecular self-assembly (or folding

Folding (chemistry)

as demonstrated by foldamers

Foldamers

A foldamer, is a discrete chain molecule or oligomer that adopts a secondary structure stabilized by noncovalent interactions. They are artificial molecules that mimic the ability of proteins, nucleic acids, and polysaccharides to fold into well-defined conformations, such as helices and β-sheets...

and polypeptides). Molecular self-assembly also allows the construction of larger structures such as micelles, membranes

Cell membrane

The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. It basically protects the cell...

, vesicles

Vesicle (biology)

A vesicle is a bubble of liquid within another liquid, a supramolecular assembly made up of many different molecules. More technically, a vesicle is a small membrane-enclosed sack that can store or transport substances. Vesicles can form naturally because of the properties of lipid membranes , or...

, liquid crystals, and is important to crystal engineering

Crystal engineering

Crystal engineering is the design and synthesis of molecular solid-state structures with desired properties, based on an understanding and exploitation of intermolecular interactions. The two main strategies currently in use for crystal engineering are based on hydrogen bonding and coordination...

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

Host-guest chemistry

. 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 sensor

Molecular sensor

A molecular sensor or chemosensor is a molecule that interacts with an analyte to produce a detectable change. Molecular sensors combine molecular recognition with some form of reporter so the presence of the guest can be observed...

s and catalysis

Catalysis

Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....

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

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

Activation energy

of the reaction, and producing desired stereochemistry

Stereochemistry

Stereochemistry, a subdiscipline of chemistry, involves the study of the relative spatial arrangement of atoms within molecules. An important branch of stereochemistry is the study of chiral molecules....

. 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

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 catenane

Catenane

A catenane is a mechanically-interlocked molecular architecture consisting of two or more interlocked macrocycles. The interlocked rings cannot be separated without breaking the covalent bonds of the macrocycles. Catenane is derived from the Latin catena meaning "chain"...

s, rotaxane

Rotaxane

A rotaxane is a mechanically-interlocked molecular architecture consisting of a "dumbbell shaped molecule" which is threaded through a "macrocycle" . The name is derived from the Latin for wheel and axle...

s, molecular knot

Molecular knot

In chemistry, a molecular knot, or knotane, is a mechanically-interlocked molecular architecture that is analogous to a macroscopic knot. A molecular knot in a trefoil knot configuration is chiral, having at least two enantiomers. Examples of naturally formed knotanes are DNA and certain proteins....

s, and molecular Borromean rings

Molecular Borromean rings

Molecular Borromean rings are an example of a mechanically-interlocked molecular architecture in which three macrocycles are interlocked in such a way that breaking any macrocycle allows the others to disassociate. They are the smallest examples of Borromean rings. The synthesis of molecular...

Dynamic covalent chemistry

In dynamic covalent chemistry

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.

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

Protein design

Protein design is the design of new protein molecules, either from scratch or by making calculated variations on a known structure. The use of rational design techniques for proteins is a major aspect of protein engineering....

and self-replication

Self-replication

Self-replication is any behavior of a dynamical system that yields construction of an identical copy of that dynamical system. Biological cells, given suitable environments, reproduce by cell division. During cell division, DNA is replicated and can be transmitted to offspring during reproduction...

Imprinting

Molecular imprinting

In chemistry, molecular imprinting is a technique to create template-shaped cavities in polymer matrices with memory of the template molecules to be used in molecular recognition . This technique is based on the system used by enzymes for substrate recognition, which is called the "lock and key"...

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 bind. 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.

Molecular machinery

Molecular machine

A molecular machine, or nanomachine, is any discrete number of molecular components that produce quasi-mechanical movements in response to specific stimuli . The expression is often more generally applied to molecules that simply mimic functions that occur at the macroscopic level...

s 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

Nanotechnology

, and prototypes have been demonstrated using supramolecular concepts.

Building blocks of supramolecular chemistry

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

The pi-pi charge-transfer interactions
Stacking (chemistry)
In chemistry, pi stacking refers to attractive, noncovalent interactions between aromatic rings. These interactions are historically thought to be important in to base stacking of DNA nucleotides, protein folding, template-directed synthesis, materials science, and molecular recognition, although...

of bipyridinium with dioxyarenes or diaminoarenes have been used extensively for the construction of mechanically interlocked systems and in crystal engineering
Crystal engineering
Crystal engineering is the design and synthesis of molecular solid-state structures with desired properties, based on an understanding and exploitation of intermolecular interactions. The two main strategies currently in use for crystal engineering are based on hydrogen bonding and coordination...

.
The use of crown ether
Crown ether
Crown ethers are cyclic chemical compounds that consist of a ring containing several ether groups. The most common crown ethers are oligomers of ethylene oxide, the repeating unit being ethyleneoxy, i.e., -CH2CH2O-. Important members of this series are the tetramer , the pentamer , and the hexamer...

binding with metal or ammonium cations
Ammonium
The ammonium cation is a positively charged polyatomic cation with the chemical formula NH. It is formed by the protonation of ammonia...

is ubiquitous in supramolecular chemistry.
The formation of carboxylic acid
Carboxylic acid
Carboxylic acids are organic acids characterized by the presence of at least one carboxyl group. The general formula of a carboxylic acid is R-COOH, where R is some monovalent functional group...

dimers and other simple hydrogen bonding interactions.
The complexation of bipyridine
Bipyridine
Bipyridines are a family of chemical compounds with the formula 2, which are formed by the coupling of two pyridine rings. Six isomers of bipyridine exist, but two isomers are prominent: 2,2'-bipyridine is a popular ligand in coordination chemistry and 4,4'-bipyridine is a precursor to the...

s or tripyridines with ruthenium
Ruthenium
Ruthenium is a chemical element with symbol Ru and atomic number 44. It is a rare transition metal belonging to the platinum group of the periodic table. Like the other metals of the platinum group, ruthenium is inert to most chemicals. The Russian scientist Karl Ernst Claus discovered the element...

, silver
Silver
Silver is a metallic chemical element with the chemical symbol Ag and atomic number 47. A soft, white, lustrous transition metal, it has the highest electrical conductivity of any element and the highest thermal conductivity of any metal...

or other metal ions is of great utility in the construction of complex architectures of many individual molecules.
The complexation of porphyrin
Porphyrin
Porphyrins are a group of organic compounds, many naturally occurring. One of the best-known porphyrins is heme, the pigment in red blood cells; heme is a cofactor of the protein hemoglobin. Porphyrins are heterocyclic macrocycles composed of four modified pyrrole subunits interconnected at...

s or phthalocyanine
Phthalocyanine
Phthalocyanine is an intensely blue-green coloured macrocyclic compound that is widely used in dyeing. Phthalocyanines form coordination complexes with most elements of the periodic table...

s around metal ions gives access to catalytic, photochemical and electrochemical properties as well as complexation. These units are used a great deal by nature.

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.

Cyclodextrin
Cyclodextrin
Cyclodextrins are a family of compounds made up of sugar molecules bound together in a ring ....

s, calixarene
Calixarene
A calixarene is a macrocycle or cyclic oligomer based on a hydroxyalkylation product of a phenol and an aldehyde. The word calixarene is derived from calix or chalice because this type of molecule resembles a vase and from the word arene that refers to the aromatic building block...

s, cucurbituril
Cucurbituril
Cucurbiturils are methylene-linked macrocyclic molecules made of glycoluril [=C4H2N4O2=] monomers. The oxygen atoms are located along the edges of the band and are tilted inwards, forming a partly enclosed cavity...

s and crown ether
Crown ether
Crown ethers are cyclic chemical compounds that consist of a ring containing several ether groups. The most common crown ethers are oligomers of ethylene oxide, the repeating unit being ethyleneoxy, i.e., -CH2CH2O-. Important members of this series are the tetramer , the pentamer , and the hexamer...

s are readily synthesized in large quantities, and are therefore convenient for use in supramolecular systems.
More complex cyclophane
Cyclophane
A cyclophane is a hydrocarbon consisting of an aromatic unit and an aliphatic chain that forms a bridge between two non-adjacent positions of the aromatic ring. More complex derivatives with multiple aromatic units and bridges forming cagelike structures are also known...

s, and cryptand
Cryptand
Cryptands are a family of synthetic bi- and polycyclic multidentate ligands for a variety of cations. The Nobel Prize for Chemistry in 1987 was given to Donald J. Cram, Jean-Marie Lehn, and Charles J. Pedersen for their efforts in discovering and determining uses of cryptands and crown ethers,...

s 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, and pentagons, each bearing functional group
Functional group
In organic chemistry, functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction regardless of the size of the molecule it is a part of...

s that connect the pieces via "self-assembly."
Metallacrown
Metallacrown
thumb|300px|right|Figure showing the metallacrown analogy to the organic crown ether. Ligand substituents are omitted for clarity. a) 12-crown-4 b)12-MCFeN-4 c) 15-crown-5 d) 15-MCCuN-5...

s are metallamacrocycles generated via a similar self-assembly
Self-assembly
Self-assembly is a term used to describe processes in which a disordered system of pre-existing components forms an organized structure or pattern as a consequence of specific, local interactions among the components themselves, without external direction...

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.

Commonly used spacers and connecting groups include polyether chains, biphenyl
Biphenyl
Biphenyl is an organic compound that forms colorless crystals. It has a distinctively pleasant smell. Biphenyl is an aromatic hydrocarbon with a molecular formula 2...

s 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 monolayer
Self-assembled monolayer
A self assembled monolayer is an organized layer of amphiphilic molecules in which one end of the molecule, the “head group” shows a specific, reversible affinity for a substrate...

s and multilayers.

Photo-/electro-chemically active units

Porphyrin
Porphyrin
Porphyrins are a group of organic compounds, many naturally occurring. One of the best-known porphyrins is heme, the pigment in red blood cells; heme is a cofactor of the protein hemoglobin. Porphyrins are heterocyclic macrocycles composed of four modified pyrrole subunits interconnected at...

s, and phthalocyanine
Phthalocyanine
Phthalocyanine is an intensely blue-green coloured macrocyclic compound that is widely used in dyeing. Phthalocyanines form coordination complexes with most elements of the periodic table...

s 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
Tetrathiafulvalene
Tetrathiafulvalene is a organosulfur compound with the formula 2. Studies on this heterocyclic compound contributed to the development of molecular electronics. TTF is related to the hydrocarbon fulvalene, 2, by replacement of four CH groups with sulfur atoms...

and quinone
Quinone
A quinone is a class of organic compounds that are formally "derived from aromatic compounds [such as benzene or naphthalene] by conversion of an even number of –CH= groups into –C– groups with any necessary rearrangement of double bonds," resulting in "a fully conjugated cyclic dione structure."...

s have more than one stable oxidation state
Oxidation state
In chemistry, the oxidation state is an indicator of the degree of oxidation of an atom in a chemical compound. The formal oxidation state is the hypothetical charge that an atom would have if all bonds to atoms of different elements were 100% ionic. Oxidation states are typically represented by...

, and therefore can be switched with redox
Redox
Redox reactions describe all chemical reactions in which atoms have their oxidation state changed....

chemistry or electrochemistry. Other units such as benzidine
Benzidine
Benzidine, the trivial name for 4,4'-diaminobiphenyl, is the solid organic compound with the formula 2. This aromatic amine is a component of a test for cyanide and also in the production of dyes...

derivatives, viologen
Viologen
Viologens are toxic bipyridinium derivatives of 4,4'-bipyridyl. The name is because this class of compounds is easily reduced to the radical mono cation, which is intensely blue coloured....

s groups and fullerene
Fullerene
A fullerene is any molecule composed entirely of carbon, in the form of a hollow sphere, ellipsoid, or tube. Spherical fullerenes are also called buckyballs, and they resemble the balls used in association football. Cylindrical ones are called carbon nanotubes or buckytubes...

s, have also been utilized in supramolecular electrochemical devices.

Biologically-derived units

The extremely strong complexation between avidin
Avidin
Avidin is a tetrameric biotin-binding protein produced in the oviducts of birds, reptiles and amphibians deposited in the whites of their eggs. In chicken egg white, avidin makes up approximately 0.05% of total protein...

and biotin
Biotin
Biotin, also known as Vitamin H or Coenzyme R, is a water-soluble B-complex vitamin discovered by Bateman in 1916. It is composed of a ureido ring fused with a tetrahydrothiophene ring. A valeric acid substituent is attached to one of the carbon atoms of the tetrahydrothiophene ring...

is instrumental in blood clotting, and has been used as the recognition motif to construct synthetic systems.
The binding of enzymes with their cofactors
Cofactor (biochemistry)
A cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. These proteins are commonly enzymes, and cofactors can be considered "helper molecules" that assist in biochemical transformations....

has been used as a route to produce modified enzymes, electrically contacted enzymes, and even photoswitchable enzymes.
DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

has been used both as a structural and as a functional unit in synthetic supramolecular systems.

Materials technology

Supramolecular chemistry and molecular self-assembly

Molecular self-assembly

processes in particular have been applied to the development of new materials. Large structures can be readily accessed using bottom-up

Top-down and bottom-up design

Top–down and bottom–up are strategies of information processing and knowledge ordering, mostly involving software, but also other humanistic and scientific theories . In practice, they can be seen as a style of thinking and teaching...

synthesis as they are composed of small molecules requiring fewer steps to synthesize. Thus most of the bottom-up approaches to nanotechnology

Nanotechnology

are based on supramolecular chemistry.

Catalysis

A major application of supramolecular chemistry is the design and understanding of catalysts and catalysis

Catalysis

. Noncovalent interactions are extremely important in catalysis, binding reactants into conformations suitable for reaction and lowering the transition state

Transition state

The transition state of a chemical reaction is a particular configuration along the reaction coordinate. It is defined as the state corresponding to the highest energy along this reaction coordinate. At this point, assuming a perfectly irreversible reaction, colliding reactant molecules will always...

energy of reaction. Template-directed synthesis is a special case of supramolecular catalysis. Encapsulation systems

Molecular encapsulation

Molecular encapsulation in supramolecular chemistry is the confinement of a guest molecule inside the cavity of a supramolecular host molecule...

such as micelles and dendrimers 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

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

Drug delivery

Drug delivery is the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals. Drug delivery technologies modify drug release profile, absorption, distribution and elimination for the benefit of improving product efficacy and safety, as well...

has also made critical advances as a result of supramolecular chemistry providing encapsulation and targeted release mechanisms. In addition, supramolecular systems have been designed to disrupt protein-protein interaction

Protein-protein interaction

Protein–protein interactions occur when two or more proteins bind together, often to carry out their biological function. Many of the most important molecular processes in the cell such as DNA replication are carried out by large molecular machines that are built from a large number of protein...

s that are important to cellular function.

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

Signal transduction

Signal transduction occurs when an extracellular signaling molecule activates a cell surface receptor. In turn, this receptor alters intracellular molecules creating a response...

devices. Data storage

Data storage device

thumb|200px|right|A reel-to-reel tape recorder .The magnetic tape is a data storage medium. The recorder is data storage equipment using a portable medium to store the data....

has been accomplished by the use of molecular switch

Molecular switch

A molecular switch is a molecule that can be reversibly shifted between two or more stable states. The molecules may be shifted between the states in response to changes in e.g. pH, light, temperature, an electrical current, microenvironment, or the presence of a ligand. In some cases, a...

es with photochromic and photoisomerizable units, by electrochromic and redox

Redox

Redox reactions describe all chemical reactions in which atoms have their oxidation state changed....

-switchable units, and even by molecular motion. Synthetic molecular logic gate

Molecular logic gate

A molecular logic gate is a molecule that performs a logical operation on one or more logic inputs and produces a single logic output. Much academic research is dedicated to the development of these systems and several prototypes now exist...

s have been demonstrated on a conceptual level. Even full-scale computations have been achieved by semi-synthetic DNA computers.

Green chemistry

Research in supramolecular chemistry also has application in green chemistry

Green chemistry

Green chemistry, also called sustainable chemistry, is a philosophy of chemical research and engineering that encourages the design of products and processes that minimize the use and generation of hazardous substances...

where reactions have been developed which proceed in the solid state directed by non-covalent bonding. Such procedures are highly desirable since they reduce the need for solvents during the production of chemicals.

Other devices and functions

Supramolecular chemistry is often pursued to develop new functions that cannot appear from a single molecule. These functions also include magnetic

Magnetism

Magnetism is a property of materials that respond at an atomic or subatomic level to an applied magnetic field. Ferromagnetism is the strongest and most familiar type of magnetism. It is responsible for the behavior of permanent magnets, which produce their own persistent magnetic fields, as well...

properties, light responsiveness, self-healing polymers, synthetic ion channels

Synthetic ion channels

Synthetic ion channels are de novo chemical compounds that insert into lipid bilayers, form pores, and allow ions to flow from one side to the other. They are man-made analogues of natural ion channels, and are thus also known as artificial ion channels...

, molecular sensors

Molecular sensor

, etc. Supramolecular research has been applied to develop high-tech sensors

Biosensor

A biosensor is an analytical device for the detection of an analyte that combines a biological component with a physicochemical detector component.It consists of 3 parts:* the sensitive biological element A biosensor is an analytical device for the detection of an analyte that combines a biological...

, processes to treat radioactive waste

Radioactive waste

Radioactive wastes are wastes that contain radioactive material. Radioactive wastes are usually by-products of nuclear power generation and other applications of nuclear fission or nuclear technology, such as research and medicine...

, and contrast agents for CAT scans.

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 - Thematic Series in the Open Access Beilstein Journal of Organic Chemistry

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