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Supramolecular Chemistry
Supramolecular chemistry refers to the area of chemistry that focuses on the noncovalent bonding interactions of molecules. While traditional chemistry focuses on the covalent bond, supramolecular chemistry examines the weaker and reversible noncovalent interactions between molecules. These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi-pi interactions and electrostatic effects. 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. 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.
Electrostatics
Electrostatics is the branch of science that deals with the phenomena arising from what seems to be stationary electric charges. Since ancient history it is known that some materials attract light particles after rubbing. The greek word for amber, (electron), gave name for many areas of natural science. Electrostatic phenomena arise from the forces that electric charges carry out on each other. Such forces are described by Coulomb's law. Electrostatic phenomena include such as simple as the attraction of plastic wrap to your hand after you remove it from a package to apparently spontaneous explosion of grain silos, to damage of electronic components during manufacturing, to the operation of photocopiers. Electrostatics involves the buildup of charge on the surface of objects due to contact with other surfaces. Although charge exchange happens whenever any two surfaces contact and separate, the effects of charge exchange are usually only noticed when at least one of the surfaces has a high resistance to electrical flow. This is because the charges that transfer to or from the highly resistive surface are more or less trapped there for a long enough time for their effects to be observed. These charges then remain on the object until they either bleed off to ground or are quickly neutralized by a discharge: e.g., the familiar phenomenon of a static 'shock' is caused by the neutralization of charge built up in the body from contact with nonconductive surface
Host-guest chemistry
In supramolecular chemistry, host-guest chemistry describes complexes that are composed of two or more molecules or ions held together in unique structural relationships by hydrogen bonding or by ion pairing or by Van der Waals force other than those of full covalent bonds.
The host component is defined as an organic molecule or ion whose binding sites converge in the complex and the guest component is defined as any molecule or ion whose binding sites diverge in the complex.
History
The existence of intermolecular forces was first postulated by Johannes Diderik van der Waals in 1873. However, it is with Nobel laureate Hermann Emil Fischer that supramolecular chemistry has its philosophical roots. In 1890, Fischer suggested that enzyme-substrate interactions take the form of a "lock and key", pre-empting the concepts 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 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 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 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.
DNA
Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.
Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.
Within cells, DNA is organized into structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, and fungi) store their DNA inside the cell nucleus, while in prokaryotes (bacteria and archae) it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed
Photochemistry
Photochemistry, a sub-discipline of chemistry, is the study of the interactions between atoms, small molecules, and light (or electromagnetic radiation.
Like most scientific disciplines, photochemistry utilizes the SI or metric measurement system. Important units and constants that show up regularly include the meter (and variants such as centimeter, millimeter, micrometer, nanometer, etc.), seconds, hertz, joules, moles, the gas constant R, and the Boltzmann constant. These units and constants are also integral to the field of physical chemistry.
The first law of photochemistry, known as the Grotthuss-Draper law (for chemists Theodor Grotthuss and John W. Draper), states that light must be absorbed by a chemical substance in order for a photochemical reaction to take place.
The second law of photochemistry, the Stark-Einstein law, states that for each photon of light absorbed by a chemical system, only one molecule is activated for a photochemical reaction. This is also known as the photoequivalence law and was derived by Albert Einstein at the time when the quantum (photon) theory of light was being developed.
Photochemistry may also be introduced to laymen as a reaction that proceeds with the absorption of light. Normally a reaction (not just a photochemical reaction) occurs when a molecule gains the necessary activation energy to undergo change. A simple example can be the combustion of gasoline (a hydrocarbon) into carbon dioxide and water. This is a chemical reaction where one or more molecules/chemical species are converted into others. For this reaction to take place activation energy should be supplied. The activation energy is provided in the form of heat or a spark. In case of photochemical reactions light provides the activation energy.
Nanoparticle
A nanoparticle which historically has included nanopowder, nanocluster, and nanocrystal is a small particle with at least one dimension less than 100 nm. This definition can be fleshed out further in order to remove ambiguity from future nano nomenclature. A nanoparticle is an amorphous or semicrystalline zero dimensional (0D) nano structure with at least one dimension between 10 and 100nm and a relatively large (≥ 15%) size dispersion. A nanocluster is an amorphous/semicrystalline nanostructure with at least one dimension being between 1-10nm and a narrow size distribution.This distinction is an extension of the term "cluster" which is used in inorganic/organometallic chemistry to indicate small molecular cages of fixed sizes. A nanopowder is an agglomeration of noncrystalline nanostructural subunits with at least one dimention less than 100nm. A nanocrystal is any nanomaterial with at least one dimension ≤ 100nm and that is singlecrystalline. Any particle which exhibits regions of crystallinity should be termed nanoparticle or nanocluster based on dimensions. Nanoparticle research is currently an area of intense scientific research, due to a wide variety of potential applications in biomedical, optical, and electronic fields. The National Nanotechnology Initiative of the United States government has driven huge amounts of state funding exclusively for nanoparticle research.
Chemical equilibrium
In a chemical process, chemical equilibrium is the state in which the chemical activities or concentrations of the reactants and products have no net change over time. Usually, this would be the state that results when the forward chemical process proceeds at the same rate as their reverse reaction. The reaction rates of the forward and reverse reactions are generally not zero but, being equal, there are no net changes in any of the reactant or product concentrations. This process is called dynamic equilibrium
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 tem
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 cease to operate entirely outside a very narrow termperature 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 machine
A molecular machine has been defined as a discrete number of molecular components that have been designed to perform mechanical-like movements in response to specific stimuli It is often applied more generally to molecules that simply mimic functions at the macroscopic level. The term is also common in nanotechnology and a number of highly complex molecular machines have been proposed towards the goal of constructing a molecular assembler. Molecular machines can be divided into two broad categories: synthetic and biological. Molecular systems that are able to shift a chemical or mechanical process away from equilibrium represent a potentially important branch of chemistry and nanotechnology. By definition these types of systems are examples of molecular machinery, as the gradient generated from this process is able to perform useful work.
Protein Design
Protein design is the design of new protein molecules from scratch, or the deliberate design of a new molecule by making calcuated variations on a known structure. The number of possible amino acid sequences is infinite, but only a subset of these sequences will fold reliably and quickly to a single native state. Protein design involves identifying such sequences, in particular those with a physiologically active native state. Protein design is a rational design technique used in protein engineering. Protein design requires an understanding of the process by which proteins fold. In a sense it is the reverse of structure prediction: a tertiary structure is specified, and a primary sequence is identified which will fold to it. Protein design is also referred to as inverse folding. From a physical point of view, the native state conformation of a protein is the free energy minimum for the protein chain, at least at biological temperatures (i.e. at temperatures between zero and a hundred degrees Celsius). Hence, designing a new protein involves the identification of the sequences which have the chosen structure as free energy minimum. This can be done by use of computer models, which, while simplifying the problem, are able to generate sequences to fold on the desired structure. The design of minimalist computer models of proteins (lattice proteins), and the secondary structural modification of real proteins, began in the mid-1990s. The de novo design of real proteins became possible shortly afterwards, and the 21st century has seen the creation of small proteins with real biological function including catalysis and antiviral behaviour. There is great hope that the design of these and larger proteins will have application in medicine and bioengineering. Computational protein design algorithms seek to identify amino acid sequences that have low energies for target structures. While the sequence-conformation space that needs to be searched is large, the most challenging requirement for computational protein design is a fast, yet accurate, energy function that can distinguish optimal sequences from similar suboptimal ones. Using computational methods, a protein with a novel fold has been designed, as well as sensors for un-natural molecules. On the other hand, it is widely believed that not all possible protein structures are designable, which means that there are compact configurations of the chain on which no sequences can fold to. In particular, conformations which are poor in secondary structures are unlikely to be designable. The designability of given structures is still an issue that is poorly understood.
Molecular Barromean 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 Borromean rings was reported in 2004 by the group of J. Fraser Stoddart is made up of macrocycles formed from 2,6-diformylpyridine and diamine compounds complexed with zinc.
In Chemistry
In chemistry a molecular knot (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. Lactoferrin has an unusual biochemical reactivity compared to its linear analogue. Other synthetic molecular knots have a distinct globular shape and nanometer sized dimensions that make it potential building blocks in nanotechnology. Molecular knots are also referred to by some chemists as "knotanes".
A 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". They are conceptually related to other mechanically-interlocked molecular architectures, such as rotaxanes, molecular knots or molecular Borromean rings. Recently the terminology "mechanical bond" has been coined that describes the connection between the macrocycles of a catenane.
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. Stereochemistry is a hugely important facet of chemistry and the study of stereochemical problems spans the entire range of organic, inorganic, biological, physical and supramolecular chemistries. Stereochemistry includes methods for determining and describing these relationships; the effect on the physical or biological properties these relationships impart upon the molecules in question, and the manner in which these relationships influence the reactivity of the molecules in question (dynamic stereochemistry). Louis Pasteur could rightly be described as the first stereochemist, having observed in 1849 that salts of tartaric acid collected from wine production vessels could rotate plane polarized light, but that salts from other sources did not. This property, the only physical property in which the two types of tartrate salts differed, is due to optical isomerism. In 1874, Jacobus Henricus van 't Hoff and Joseph Le Bel explained optical activity in terms of the tetrahedral arrangement of the atoms bound to carbon. One of the most infamous demonstrations of the significance of stereochemistry was the thalidomide disaster. Thalidomide is a drug, first prepared in 1957 in Germany, prescribed for treating morning sickness in pregnant women. The drug however was discovered to cause deformation in babies. It was discovered that one optical isomer of the drug was safe while the other had teratogenic effects, causing serious genetic damage to early embryonic growth and development. In the human body, thalidomide undergoes racemization: even if only one of the two stereoisomers is ingested, the other one is produced. Thalidomide is currently used as a treatment for leprosy and must be used with contraceptives in women to prevent pregnancy related deformations. This disaster was a driving force behind requiring strict testing of drugs before making them available to the public. Cahn-Ingold-Prelog priority rules are part of a system for describing a molecule's stereochemistry. They rank the atoms around a stereocenter in a standard way, allowing the relative position of these atoms in the molecule to be described unambiguously. A Fischer projection is a simplified way to depict the stereochemistry around a stereocenter.
Activation Energy
Activation Energy also called threshold energy, is a term introduced in 1889 by Svante Arrhenius that is defined as the energy that must be overcome in order for a chemical reaction to occur. Activation energy may otherwise be denoted as the minimum energy necessary for a specific chemical reaction to occur.The activation energy of a reaction is usually denoted by Ea, and given in units of kilojoules per mole.Usually one can think of the activation energy as the height of the potential barrier (sometimes called the energy barrier) separating two minima of potential energy (of the reactants and of the products of reaction). For a chemical reaction to have noticeable rate, there should be noticeable number of molecules with the energy equal or greater than the activation energy.
Bipyridines
Bipyridinesform a family of chemical compounds with the formula. They are derived by the coupling of two pyridine rings. Six isomers of bipyridine exist. Two isomers are prominent: bipyridine is a popular ligand in coordination chemistry and 4,4'-bipyridine is a precursor to the herbicide paraquat. The bipyridines are colourless solids, which are soluble in organic solvents and slightly soluble in water.Inamrinone and Milrinone are used occasionally for short term. They inhibit phosphodiesterase by increasing cAMP, exerting positive inotropy and causing vasodilation. Amrinone causes thrombocytopenia; Milrinone decreases survival in heart failure.
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, and molecular Borromean rings.
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 cannot be separated without breaking the loop. On the molecular level the interlocked molecules cannot be separated without significant distortion of the covalent bonds that make up the conjoined molecules. Examples of mechanically-interlocked molecular architectures include catenanes, rotaxanes, molecular knots, and molecular Borromean rings.
The synthesis of such entangled architectures has been made efficient through the combination of supramolecular chemistry with traditional covalent synthesis, however mechanically-interlocked molecular architectures have properties that differ from both “supramolecular assemblies” and “covalently-bonded molecules”. Recently the terminology "mechanical bond" has been coined to describe the connection between the components of mechanically-interlocked molecular architectures. Although research into mechanically-interlocked molecular architectures is primarily focused on artificial compounds many examples have been found in biological systems including: cystine knots, cyclotides or lasso-peptides such as microcin J25 are protein, and a variety of peptides. There is a great deal of interest in mechanically-interlocked molecular architectures to develop molecular machines by manipulating the relative position of the components.
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, and molecular Borromean rings.
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 cannot be separated without breaking the loop. On the molecular level the interlocked molecules cannot be separated without significant distortion of the covalent bonds that make up the conjoined molecules. Examples of mechanically-interlocked molecular architectures include catenanes, rotaxanes, molecular knots, and molecular Borromean rings.
The synthesis of such entangled architectures has been made efficient through the combination of supramolecular chemistry with traditional covalent synthesis, however mechanically-interlocked molecular architectures have properties that differ from both “supramolecular assemblies” and “covalently-bonded molecules”. Recently the terminology "mechanical bond" has been coined to describe the connection between the components of mechanically-interlocked molecular architectures. Although research into mechanically-interlocked molecular architectures is primarily focused on artificial compounds many examples have been found in biological systems including: cystine knots, cyclotides or lasso-peptides such as microcin J25 are protein, and a variety of peptides. There is a great deal of interest in mechanically-interlocked molecular architectures to develop molecular machines by manipulating the relative position of the components.
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.
Dynamic covalent chemistry
is a strategy in supramolecular chemistry with the aim to synthesise large complex molecules. In it a reversible reaction is under thermodynamic reaction control and a specific reaction product out of many possible reaction products is captured. Because all the components in the reaction mixture are able to equilibrate quickly, (according to its advocates) some degree of error checking and proof reading is enabled. The concept of dynamic Dynamic covalent chemistry is a strategy in supramolecular chemistry with the aim to synthesise large complex molecules. In it a reversible reaction is under thermodynamic reaction control and a specific reaction product out of many possible reaction products is captured. Because all the components in the reaction mixture are able to equilibrate quickly, (according to its advocates) some degree of error checking and proof reading is enabled. The concept of dynamic covalent chemistry was demonstrated in the development of specific molecular Borromean rings.
The concept is also demonstrated in a reaction sequence involving polyacetal macrocycles. The cyclophane C2 can be prepared by the irreversible highly diluted reaction of a diol with chlorobromomethane in the presence of sodium hydride. The dimer however is part of series of equilibria between polyacetal macrocycles of different size brought about by acid catalyzed (triflic acid) transacetalization. This particular type of transacetalization goes by the name of formal metathesis because it is reminiscent of olefin metathesis but then with formaldehyde. Regardless of the starting material, C2, C4 or a high molar mass product, the equilibrium will eventually produce an identical product distribution. In this system it is also possible to amplify the presence of C2 in the mixture when the catalyst is silver triflate because the silver ion fits ideally and irreversibly in its cavity.was demonstrated in the development of specific molecular Borromean rings.
The concept is also demonstrated in a reaction sequence involving polyacetal macrocycles. The cyclophane C2 can be prepared by the irreversible highly diluted reaction of a diol with chlorobromomethane in the presence of sodium hydride. The dimer however is part of series of equilibria between polyacetal macrocycles of different size brought about by acid catalyzed (triflic acid) transacetalization. This particular type of transacetalization goes by the name of formal metathesis because it is reminiscent of olefin metathesis but then with formaldehyde. Regardless of the starting material, C2, C4 or a high molar mass product, the equilibrium will eventually produce an identical product distribution. In this system it is also possible to amplify the presence of C2 in the mixture when the catalyst is silver triflate because the silver ion fits ideally and irreversibly in its cavity.
Dynamic covalent chemistry
is a strategy in supramolecular chemistry with the aim to synthesise large complex molecules. In it a reversible reaction is under thermodynamic reaction control and a specific reaction product out of many possible reaction products is captured. Because all the components in the reaction mixture are able to equilibrate quickly, (according to its advocates) some degree of error checking and proof reading is enabled. The concept of dynamic Dynamic covalent chemistry is a strategy in supramolecular chemistry with the aim to synthesise large complex molecules. In it a reversible reaction is under thermodynamic reaction control and a specific reaction product out of many possible reaction products is captured. Because all the components in the reaction mixture are able to equilibrate quickly, (according to its advocates) some degree of error checking and proof reading is enabled. The concept of dynamic covalent chemistry was demonstrated in the development of specific molecular Borromean rings.
The concept is also demonstrated in a reaction sequence involving polyacetal macrocycles. The cyclophane C2 can be prepared by the irreversible highly diluted reaction of a diol with chlorobromomethane in the presence of sodium hydride. The dimer however is part of series of equilibria between polyacetal macrocycles of different size brought about by acid catalyzed (triflic acid) transacetalization. This particular type of transacetalization goes by the name of formal metathesis because it is reminiscent of olefin metathesis but then with formaldehyde. Regardless of the starting material, C2, C4 or a high molar mass product, the equilibrium will eventually produce an identical product distribution. In this system it is also possible to amplify the presence of C2 in the mixture when the catalyst is silver triflate because the silver ion fits ideally and irreversibly in its cavity.was demonstrated in the development of specific molecular Borromean rings.
The concept is also demonstrated in a reaction sequence involving polyacetal macrocycles. The cyclophane C2 can be prepared by the irreversible highly diluted reaction of a diol with chlorobromomethane in the presence of sodium hydride. The dimer however is part of series of equilibria between polyacetal macrocycles of different size brought about by acid catalyzed (triflic acid) transacetalization. This particular type of transacetalization goes by the name of formal metathesis because it is reminiscent of olefin metathesis but then with formaldehyde. Regardless of the starting material, C2, C4 or a high molar mass product, the equilibrium will eventually produce an identical product distribution. In this system it is also possible to amplify the presence of C2 in the mixture when the catalyst is silver triflate because the silver ion fits ideally and irreversibly in its cavity.
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.
Bionics
(also known as biomimetics, biognosis, biomimicry, or bionical creativity engineering) is the application of biological methods and systems found in nature to the study and design of engineering systems and modern technology. The word 'bionic' was coined by Jack E. Steele in 1958, possibly originating from the Greek word "βίον", pronounced "bion", meaning "unit of life" and the suffix -ic, meaning "like" or "in the manner of", hence "like life". Some dictionaries, however, explain the word as being formed from "biology" + "electronics"
The transfer of technology between lifeforms and synthetic constructs is, according to proponents of bionic technology, desirable because evolutionary pressure typically forces living organisms, including fauna and flora, to become highly optimized and efficient. A classical example is the development of dirt- and water-repellent paint (coating) from the observation that the surface of the lotus flower plant is practically unsticky for anything (the lotus effect). Examples of bionics in engineering include the hulls of boats imitating the thick skin of dolphins; sonar, radar, and medical ultrasound imaging imitating the echolocation of bats.
In the field of computer science, the study of bionics has produced artificial neurons, artificial neural networks, and swarm intelligence. Evolutionary computation was also motivated by bionics ideas but it took the idea further by simulating evolution in silico and producing well-optimized solutions that had never appeared in nature.
It is estimated by Julian Vincent, professor of biomimetics at the University of Bath in the UK, that "at present there is only a 10% overlap between biology and technology in terms of the mechanisms used".
Bionics
(also known as biomimetics, biognosis, biomimicry, or bionical creativity engineering) is the application of biological methods and systems found in nature to the study and design of engineering systems and modern technology. The word 'bionic' was coined by Jack E. Steele in 1958, possibly originating from the Greek word "βίον", pronounced "bion", meaning "unit of life" and the suffix -ic, meaning "like" or "in the manner of", hence "like life". Some dictionaries, however, explain the word as being formed from "biology" + "electronics"
The transfer of technology between lifeforms and synthetic constructs is, according to proponents of bionic technology, desirable because evolutionary pressure typically forces living organisms, including fauna and flora, to become highly optimized and efficient. A classical example is the development of dirt- and water-repellent paint (coating) from the observation that the surface of the lotus flower plant is practically unsticky for anything (the lotus effect). Examples of bionics in engineering include the hulls of boats imitating the thick skin of dolphins; sonar, radar, and medical ultrasound imaging imitating the echolocation of bats.
In the field of computer science, the study of bionics has produced artificial neurons, artificial neural networks, and swarm intelligence. Evolutionary computation was also motivated by bionics ideas but it took the idea further by simulating evolution in silico and producing well-optimized solutions that had never appeared in nature.
It is estimated by Julian Vincent, professor of biomimetics at the University of Bath in the UK, that "at present there is only a 10% overlap between biology and technology in terms of the mechanisms used".
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 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.
In chemistry, molecular imprinting is a technique to create template-shaped cavities in polymer matrices with memory of the template molecules. This technique is based on the system used by enzymes for substrate recognition, which is called the "lock and key" model. The active binding site of an enzyme has a unique geometric structure that is particularly suitable for a substrate. A substrate that has a corresponding shape to the site is recognized by selectively binding to the enzyme, while an incorrectly shaped molecule that does not fit the binding site is not recognized.
In a similar way, molecularly imprinted materials are prepared using a template molecule and functional monomers that assemble around the template and subsequently get crosslinked to each other. The functional monomers, which are self-assembled around the template molecule by interaction between functional groups on both the template and monomers, are polymerized to form an imprinted matrix.
Then the template molecule is removed from the matrix under certain conditions, leaving behind a cavity complementary in size and shape to the template. The obtained cavity can work as a selective binding site for a specific template molecule.
In chemistry, molecular imprinting is a technique to create template-shaped cavities in polymer matrices with memory of the template molecules. This technique is based on the system used by enzymes for substrate recognition, which is called the "lock and key" model. The active binding site of an enzyme has a unique geometric structure that is particularly suitable for a substrate. A substrate that has a corresponding shape to the site is recognized by selectively binding to the enzyme, while an incorrectly shaped molecule that does not fit the binding site is not recognized.
In a similar way, molecularly imprinted materials are prepared using a template molecule and functional monomers that assemble around the template and subsequently get crosslinked to each other. The functional monomers, which are self-assembled around the template molecule by interaction between functional groups on both the template and monomers, are polymerized to form an imprinted matrix.
Then the template molecule is removed from the matrix under certain conditions, leaving behind a cavity complementary in size and shape to the template. The obtained cavity can work as a selective binding site for a specific template molecule.
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.
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.
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.
Bipyridines
form a family of chemical compounds with the formula. They are derived by the coupling of two pyridine rings. Six isomers of bipyridine exist. Two isomers are prominent: bipyridine is a popular ligand in coordination chemistry and 4,4'-bipyridine is a precursor to the herbicide paraquat. The bipyridines are colourless solids, which are soluble in organic solvents and slightly soluble in water.
Inamrinone and Milrinone are used occasionally for short term. They inhibit phosphodiesterase by increasing cAMP, exerting positive inotropy and causing vasodilation. Amrinone causes thrombocytopenia; Milrinone decreases survival in heart failure.
Silver
has been known since ancient times and has long been valued as a precious metal, used to make ornaments, jewellery, high-value tableware and utensils (hence the term "silverware") and currency coins. Today, silver metal is used in electrical contacts and conductors, in mirrors and in catalysis of chemical reactions. Its compounds are used in photographic film and dilute solutions of silver nitrate and other silver compounds are used as disinfectants. Although the antimicrobial uses of silver have largely been supplanted by the use of antibiotics, its antiseptic properties are still a useful tool in the prevention and treatment of sepsis and infections caused by antibiotic-resistant microorganisms such as MRSA.
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.
Bipyridines
form a family of chemical compounds with the formula. They are derived by the coupling of two pyridine rings. Six isomers of bipyridine exist. Two isomers are prominent: bipyridine is a popular ligand in coordination chemistry and 4,4'-bipyridine is a precursor to the herbicide paraquat. The bipyridines are colourless solids, which are soluble in organic solvents and slightly soluble in water.
Inamrinone and Milrinone are used occasionally for short term. They inhibit phosphodiesterase by increasing cAMP, exerting positive inotropy and causing vasodilation. Amrinone causes thrombocytopenia; Milrinone decreases survival in heart failure.
Silver
has been known since ancient times and has long been valued as a precious metal, used to make ornaments, jewellery, high-value tableware and utensils (hence the term "silverware") and currency coins. Today, silver metal is used in electrical contacts and conductors, in mirrors and in catalysis of chemical reactions. Its compounds are used in photographic film and dilute solutions of silver nitrate and other silver compounds are used as disinfectants. Although the antimicrobial uses of silver have largely been supplanted by the use of antibiotics, its antiseptic properties are still a useful tool in the prevention and treatment of sepsis and infections caused by antibiotic-resistant microorganisms such as MRSA.
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 synthesized to provide more taliored recognition properties.
Cyclodextrins
make up a family of cyclic oligosaccharides, composed of 5 or more α-D-glucopyranoside units linked, as in amylose. The 5-membered macrocycle is not natural. Recently, the largest well-characterized cyclodextrin contains 32 anhydroglucopyranoside units, while as a poorly characterized mixture, even at least 150-membered cyclic oligosaccharides are also known. Typical cyclodextrins contain a number of glucose monomers ranging from six to eight units in a ring, creating a cone shape. thus denoting:
Cyclodextrins
are produced from starch by means of enzymatic conversion. Over the last few years they have found a wide range of applications in food, pharmaceutical and chemical industries as well as agriculture and environmental engineering. It is also the chief active compound found in Procter and Gamble's deodorizing product "Febreze".
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 synthesized to provide more taliored recognition properties.
Cyclodextrins
make up a family of cyclic oligosaccharides, composed of 5 or more α-D-glucopyranoside units linked, as in amylose. The 5-membered macrocycle is not natural. Recently, the largest well-characterized cyclodextrin contains 32 anhydroglucopyranoside units, while as a poorly characterized mixture, even at least 150-membered cyclic oligosaccharides are also known. Typical cyclodextrins contain a number of glucose monomers ranging from six to eight units in a ring, creating a cone shape. thus denoting:
Cyclodextrins
are produced from starch by means of enzymatic conversion. Over the last few years they have found a wide range of applications in food, pharmaceutical and chemical industries as well as agriculture and environmental engineering. It is also the chief active compound found in Procter and Gamble's deodorizing product "Febreze".
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, 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.
A nanoparticle
which historically has included nanopowder, nanocluster, and nanocrystal is a small particle with at least one dimension less than 100 nm. This definition can be fleshed out further in order to remove ambiguity from future nano nomenclature. A nanoparticle is an amorphous or semicrystalline zero dimensional nano structure with at least one dimension between 10 and 100nm and a relatively large size dispersion.
A nanocluster is an amorphous/semicrystalline nanostructure with at least one dimension being between 1-10nm and a narrow size distribution.
This distinction is an extension of the term "cluster" which is used in inorganic/organometallic chemistry to indicate small molecular cages of fixed sizes. A nanopowder is an agglomeration of noncrystalline nanostructural subunits with at least one dimention less than 100nm.
A nanocrystal is any nanomaterial with at least one dimension ≤ 100nm and that is singlecrystalline.
Any particle which exhibits regions of crystallinity should be termed nanoparticle or nanocluster based on dimensions. Nanoparticle research is currently an area of intense scientific research, due to a wide variety of potential applications in biomedical, optical, and electronic fields. The National Nanotechnology Initiative of the United States government has driven huge amounts of state funding exclusively for nanoparticle research.
Surface science
is the study of physical and chemical phenomena that occur at the interface of two phases, including solid-liquid interfaces, solid-gas interfaces, solid-vacuum interfaces, and liquid-gas interfaces. It includes the fields of surface chemistry and surface physics.
Some related practical applications are classed as surface engineering. The science encompasses concepts such as heterogeneous catalysis, semiconductor device fabrication, fuel cells, self-assembled monolayers and adhesives. Surface science is closely related with Interface and Colloid Science.
Interfacial chemistry and physics are common subjects for both. Methods are different. In addition, Interface and Colloid Science studies macroscopic phenomena that occur in heterogeneous systems due to peculiarities of interfaces.
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.
A nanoparticle
which historically has included nanopowder, nanocluster, and nanocrystal is a small particle with at least one dimension less than 100 nm. This definition can be fleshed out further in order to remove ambiguity from future nano nomenclature. A nanoparticle is an amorphous or semicrystalline zero dimensional nano structure with at least one dimension between 10 and 100nm and a relatively large size dispersion.
A nanocluster is an amorphous/semicrystalline nanostructure with at least one dimension being between 1-10nm and a narrow size distribution.
This distinction is an extension of the term "cluster" which is used in inorganic/organometallic chemistry to indicate small molecular cages of fixed sizes. A nanopowder is an agglomeration of noncrystalline nanostructural subunits with at least one dimention less than 100nm.
A nanocrystal is any nanomaterial with at least one dimension ≤ 100nm and that is singlecrystalline.
Any particle which exhibits regions of crystallinity should be termed nanoparticle or nanocluster based on dimensions. Nanoparticle research is currently an area of intense scientific research, due to a wide variety of potential applications in biomedical, optical, and electronic fields. The National Nanotechnology Initiative of the United States government has driven huge amounts of state funding exclusively for nanoparticle research.
Surface science
is the study of physical and chemical phenomena that occur at the interface of two phases, including solid-liquid interfaces, solid-gas interfaces, solid-vacuum interfaces, and liquid-gas interfaces. It includes the fields of surface chemistry and surface physics.
Some related practical applications are classed as surface engineering. The science encompasses concepts such as heterogeneous catalysis, semiconductor device fabrication, fuel cells, self-assembled monolayers and adhesives. Surface science is closely related with Interface and Colloid Science.
Interfacial chemistry and physics are common subjects for both. Methods are different. In addition, Interface and Colloid Science studies macroscopic phenomena that occur in heterogeneous systems due to peculiarities of interfaces.
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 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.
Porphyrin
is a heterocyclic macrocycle derived from four pyrroline subunits interconnected via their α carbon atoms via methine bridges . Porphyrins are aromatic and they obey Huckel's rule for aromaticity in that they possess electrons which are delocalized over the macrocycle. The macrocycle, therefore, is a highly-conjugated system, and, as a consequence, is deeply coloured - the name porphyrin comes from a Greek word for purple. The macrocycle has 22 pi electrons.Many porphyrins occur in nature, such as in green leaves and red blood cells, and in bio-inspired synthetic catalysts and devices. The parent porphyrin is porphine, and substituted porphines are called porphyrins.
Benzidine
is the trivial name for 4,4'-diaminobiphenyl, a carcinogenic aromatic amine which has been used as part of a test for cyanide and also in the synthesis of dyes. It has been linked to bladder cancer and pancreatic cancer.
In common with benzidine some other aromatic amines such as 2-aminonaphthalene have been withdrawn from use in almost all industries because they are so carcinogenic.
In the past a common test for blood used benzidine but this has largely been replaced by tests using phenolphthalein / hydrogen peroxide and luminol. An enzyme in blood causes the benzidine to be oxidized to a polymer which is blue coloured. The test for cyanide uses similar chemistry to give the blue colour.
Photochromic and photoisomerizable groups have the ability to change their shapes and 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.
Porphyrin
is a heterocyclic macrocycle derived from four pyrroline subunits interconnected via their α carbon atoms via methine bridges . Porphyrins are aromatic and they obey Huckel's rule for aromaticity in that they possess electrons which are delocalized over the macrocycle. The macrocycle, therefore, is a highly-conjugated system, and, as a consequence, is deeply coloured - the name porphyrin comes from a Greek word for purple. The macrocycle has 22 pi electrons.Many porphyrins occur in nature, such as in green leaves and red blood cells, and in bio-inspired synthetic catalysts and devices. The parent porphyrin is porphine, and substituted porphines are called porphyrins.
Benzidine
is the trivial name for 4,4'-diaminobiphenyl, a carcinogenic aromatic amine which has been used as part of a test for cyanide and also in the synthesis of dyes. It has been linked to bladder cancer and pancreatic cancer.
In common with benzidine some other aromatic amines such as 2-aminonaphthalene have been withdrawn from use in almost all industries because they are so carcinogenic.
In the past a common test for blood used benzidine but this has largely been replaced by tests using phenolphthalein / hydrogen peroxide and luminol. An enzyme in blood causes the benzidine to be oxidized to a polymer which is blue coloured. The test for cyanide uses similar chemistry to give the blue colour.
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.
Avidin
is a glycoprotein found in the egg white and tissues of birds, reptiles and amphibians. It contains four identical subunits having a combined mass of 67,000-68,000 daltons. Each subunit consists of 128 amino acids and binds one molecule of biotin. The extent of glycosylation is very high. Carbohydrate accounts for about 10% of the total mass of avidin. Avidin has a basic isoelectric point (pI) of 10-10.5 and is stable over a wide range of pH and temperature. Extensive chemical modification has little effect on the activity of avidin, making it especially useful for protein purification. Because of its carbohydrate content and basic pI, avidin has relatively high nonspecific binding.
Enzymes
are biomolecules that catalyze chemical reactions.
Almost all enzymes are proteins. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, the products. Almost all processes in a biological cell need enzymes in order to occur at significant rates. Since enzymes are extremely selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell.
Like all catalysts, enzymes work by lowering the activation energy for a reaction, thus dramatically increasing the rate of the reaction. Most enzyme reaction rates are millions of times faster than those of comparable uncatalyzed reactions. As with all catalysts, enzymes are not consumed by the reactions they catalyze, nor do they alter the equilibrium of these reactions. However, enzymes do differ from most other catalysts by being much more specific. Enzymes are known to catalyze about 4,000 biochemical reactions.
A few RNA molecules called ribozymes catalyze reactions, with an important example being some parts of the ribosome.
Synthetic molecules called artificial enzymes also display enzyme-like catalysis.
Enzyme activity can be affected by other molecules. Inhibitors are molecules that decrease enzyme activity; activators are molecules that increase activity. Many drugs and poisons are enzyme inhibitors. Activity is also affected by temperature, chemical environment, and the concentration of substrate. Some enzymes are used commercially, for example, in the synthesis of antibiotics. In addition, some household products use enzymes to speed up biochemical reactions.
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.
Avidin
is a glycoprotein found in the egg white and tissues of birds, reptiles and amphibians. It contains four identical subunits having a combined mass of 67,000-68,000 daltons. Each subunit consists of 128 amino acids and binds one molecule of biotin. The extent of glycosylation is very high. Carbohydrate accounts for about 10% of the total mass of avidin. Avidin has a basic isoelectric point (pI) of 10-10.5 and is stable over a wide range of pH and temperature. Extensive chemical modification has little effect on the activity of avidin, making it especially useful for protein purification. Because of its carbohydrate content and basic pI, avidin has relatively high nonspecific binding.
Enzymes
are biomolecules that catalyze chemical reactions.
Almost all enzymes are proteins. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, the products. Almost all processes in a biological cell need enzymes in order to occur at significant rates. Since enzymes are extremely selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell.
Like all catalysts, enzymes work by lowering the activation energy for a reaction, thus dramatically increasing the rate of the reaction. Most enzyme reaction rates are millions of times faster than those of comparable uncatalyzed reactions. As with all catalysts, enzymes are not consumed by the reactions they catalyze, nor do they alter the equilibrium of these reactions. However, enzymes do differ from most other catalysts by being much more specific. Enzymes are known to catalyze about 4,000 biochemical reactions.
A few RNA molecules called ribozymes catalyze reactions, with an important example being some parts of the ribosome.
Synthetic molecules called artificial enzymes also display enzyme-like catalysis.
Enzyme activity can be affected by other molecules. Inhibitors are molecules that decrease enzyme activity; activators are molecules that increase activity. Many drugs and poisons are enzyme inhibitors. Activity is also affected by temperature, chemical environment, and the concentration of substrate. Some enzymes are used commercially, for example, in the synthesis of antibiotics. In addition, some household products use enzymes to speed up biochemical reactions.
Materials technology
Supramolecular chemistry and molecular self-assembly processes in particular 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.
Nanotechnology
refers broadly to a field of applied science and technology whose unifying theme is the control of matter on the atomic and molecular scale, generally 100 nanometers or smaller, and the fabrication of devices with critical dimensions that lie within that size range.
Molecular self-assembly
is an important aspect of bottom-up approaches to nanotechnology. Using molecular self-assembly the final (desired) structure is programmed in the shape and functional groups of the molecules. Self-assembly is referred to as a 'bottom-up' manufacturing technique in contrast to a 'top-down' technique such as lithography where the desired final structure is carved from a larger block of matter. In the speculative vision of molecular nanotechnology, microchips of the future might be made by molecular self-assembly. An advantage to constructing nanostructure using molecular self-assembly for biological materials is that they will degrade back into individual molecules that can be broken down by the body.
Nanotechnology
refers broadly to a field of applied science and technology whose unifying theme is the control of matter on the atomic and molecular scale, generally 100 nanometers or smaller, and the fabrication of devices with critical dimensions that lie within that size range.
Molecular self-assembly
is an important aspect of bottom-up approaches to nanotechnology. Using molecular self-assembly the final (desired) structure is programmed in the shape and functional groups of the molecules. Self-assembly is referred to as a 'bottom-up' manufacturing technique in contrast to a 'top-down' technique such as lithography where the desired final structure is carved from a larger block of matter. In the speculative vision of molecular nanotechnology, microchips of the future might be made by molecular self-assembly. An advantage to constructing nanostructure using molecular self-assembly for biological materials is that they will degrade back into individual molecules that can be broken down by the body.
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 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.
Catalysis is the process by which the rate of a chemical reaction (or biological process) is increased by means of the addition of a species known as a catalyst to the reaction. What makes a catalyst different from a chemical reagent is that whilst it participates in the reaction, is not consumed in the reaction. That is, the catalysts may undergo several chemical transformations during the reaction, but at the conclusion of the reaction, the catalyst is regenerated unchanged. As a catalyst is regenerated in a reaction, often only a very small amount is needed to increase the rate of the reaction.
Catalysis is the process by which the rate of a chemical reaction (or biological process) is increased by means of the addition of a species known as a catalyst to the reaction. What makes a catalyst different from a chemical reagent is that whilst it participates in the reaction, is not consumed in the reaction. That is, the catalysts may undergo several chemical transformations during the reaction, but at the conclusion of the reaction, the catalyst is regenerated unchanged. As a catalyst is regenerated in a reaction, often only a very small amount is needed to increase the rate of the reaction.
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 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 interactions that are important to cellular function.
Drug delivery
is a term that refers to the delivery of a pharmaceutical compound to humans or animals. Most common methods of delivery include the preferred non-invasive oral (through the mouth), nasal, pneumonial (inhalation), and rectal routes. Many medications, however, can not be delivered using these routes because they might be susceptible to degradation or are not incorporated efficiently. For this reason many protein and peptide drugs have to be delivered by injection. For example, many immunizations are based on the delivery of protein drugs and are often done by injection.
Current efforts in the area of drug delivery include the development of targeted delivery in which the drug is only active in the target area of the body (for example, in cancerous tissues) and sustained release formulations in which the drug is released over a period of time in a controlled manner from a formulation.
Current efforts in the area of drug delivery include the development of targeted delivery in which the drug is only active in the target area of the body (for example, in cancerous tissues) and sustained release formulations in which the drug is released over a period of time in a controlled manner from a formulation.
Protein-protein interactions
refer to the association of protein molecules and the study of these associations from the perspective of biochemistry, signal transduction and networks.
The interactions between proteins are important for many biological functions. For example, signals from the exterior of a cell are mediated to the inside of that cell by protein-protein interactions of the signaling molecules. This process, called signal transduction, plays a fundamental role in many biological processes and in many diseases (e.g. cancer). Proteins might interact for a long time to form part of a protein complex, a protein may be carrying another protein (for example, from cytoplasm to nucleus or vice versa in the case of the nuclear pore importins), or a protein may interact briefly with another protein just to modify it (for example, a protein kinase will add a phosphate to a target protein). This modification of proteins can itself change protein-protein interactions. For example, some proteins with SH2 domains only bind to other proteins when they are phosphorylated on the amino acid tyrosine. In conclusion, protein-protein interactions are of central importance for virtually every process in a living cell. Information about these interactions improves our understanding of diseases and can provide the basis for new therapeutic approaches.
The interactions between proteins are important for many biological functions. For example, signals from the exterior of a cell are mediated to the inside of that cell by protein-protein interactions of the signaling molecules. This process, called signal transduction, plays a fundamental role in many biological processes and in many diseases (e.g. cancer). Proteins might interact for a long time to form part of a protein complex, a protein may be carrying another protein (for example, from cytoplasm to nucleus or vice versa in the case of the nuclear pore importins), or a protein may interact briefly with another protein just to modify it (for example, a protein kinase will add a phosphate to a target protein). This modification of proteins can itself change protein-protein interactions. For example, some proteins with SH2 domains only bind to other proteins when they are phosphorylated on the amino acid tyrosine. In conclusion, protein-protein interactions are of central importance for virtually every process in a living cell. Information about these interactions improves our understanding of diseases and can provide the basis for new therapeutic approaches.
Protein-protein interaction network visualization
Visualization of protein-protein interaction networks is a popular application of scientific visualization techniques. Although protein interaction diagrams are common in textbooks, diagrams of whole cell protein interaction networks were not as common since the level of complexity made them difficult to generate. One example of a manually produced molecular interaction map is Kurt Kohn's 1999 map of cell cycle control Drawing on Kohn's map, in 2000 Schwikowski, Uetz, and Fields published a paper on protein-protein interactions in yeast, linking together 1,548 interacting proteins determined by two-hybrid testing. They used a force-directed (Sugiyama) graph drawing algorithm to automatically generate an image of their network.
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.
Green Chemistry
Research in supramolecular chemistry also has application in green chemistry 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.
Green chemistry also called sustainable chemistry, is a chemical philosophy encouraging the design of products and processes that reduce or eliminate the use and generation of hazardous substances. Whereas environmental chemistry is the chemistry of the natural environment, and of pollutant chemicals in nature, green chemistry seeks to reduce and prevent pollution at its source. In 1990 the Pollution Prevention Act was passed in the United States. This act helped create a modus operandi for dealing with pollution in an original and innovative way.
As a chemical philosophy, green chemistry derives from organic chemistry, inorganic chemistry, biochemistry, analytical chemistry, and even physical chemistry. However, the philosophy of green chemistry tends to focus on industrial applications. Contrast this with click chemistry which tends to favor academic applications, although industrial applications are possible. The focus is on minimizing the hazard and maximizing the efficiency of any chemical choice. It is distinct from environmental chemistry which focuses on chemical phenomena in the environment.
In 2005 Ryoji Noyori identified three key developments in green chemistry: use of supercritical carbon dioxide as green solvent, aqueous hydrogen peroxide for clean oxidations and the use of hydrogen in asymmetric synthesis.
As a chemical philosophy, green chemistry derives from organic chemistry, inorganic chemistry, biochemistry, analytical chemistry, and even physical chemistry. However, the philosophy of green chemistry tends to focus on industrial applications. Contrast this with click chemistry which tends to favor academic applications, although industrial applications are possible. The focus is on minimizing the hazard and maximizing the efficiency of any chemical choice. It is distinct from environmental chemistry which focuses on chemical phenomena in the environment.
In 2005 Ryoji Noyori identified three key developments in green chemistry: use of supercritical carbon dioxide as green solvent, aqueous hydrogen peroxide for clean oxidations and the use of hydrogen in asymmetric synthesis.
Examples of applied green chemistry are supercritical water oxidation, on water reactions and dry media reactions.
Bioengineering is also seen as a promising technique for achieving green chemistry goals. A number of important process chemicals can be synthesized in engineered organisms, such as shikimate, a Tamiflu precursor which is fermented by Roche in bacteria.
Bioengineering is also seen as a promising technique for achieving green chemistry goals. A number of important process chemicals can be synthesized in engineered organisms, such as shikimate, a Tamiflu precursor which is fermented by Roche in bacteria.
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 properties, light responsiveness, self-healing polymers, molecular sensors, etc. Supramolecular research has been applied to develop high-tech sensors, processes to treat radioactive waste, and contrast agents for CAT scans.
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.
The term supramolecular analytical chemistry has recently been coined to describe the application of molecular sensors to analytical chemistry.
Early examples of molecular sensors are crown ethers with large affinity for sodium ions but not for potassium and forms of metal detection by so-called complexones which are traditional pH indicators retrofitted with molecular groups sensitive to metals. This receptor-spacer-reporter concept is a recurring theme often with the reporter displaying photoinduced electron transfer.
One example is a sensor sensitive to heparin.
Other receptors are sensitive not to a specific molecule but to a molecular compound class. One example is the grouped analysis of several tannic acids that accumulate in ageing scotch whiskey in oak barrels. The grouped results demonstrated a correlation with the age but the individual components did not. A similar receptor can be used to analyze tartrates in wine.
The compound saxitoxin is a neurotoxin found in shellfish and a chemical weapon. An experimental sensor for this compound is again based on PET. Interaction of saxitoxin with the sensor's crown ether moiety kills its PET process towards the fluorophore and fluorescence is switched from off to on.
The unusual boron moiety makes sure the fluorescence takes place in the visible light part of the electromagnetic spectrum
In another strategy called indicator-displacement assay (IDA) an analyte such as citrate or phosphate ions displace a fluorescent indicator in an indicator-host complex. The so-called UT taste chip (University of Texas) is a prototype electronic tongue and combines supramolecular chemistry with charge-coupled devices based on silicon wafers and immobilized receptor molecules.
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.
The term supramolecular analytical chemistry has recently been coined to describe the application of molecular sensors to analytical chemistry.
Early examples of molecular sensors are crown ethers with large affinity for sodium ions but not for potassium and forms of metal detection by so-called complexones which are traditional pH indicators retrofitted with molecular groups sensitive to metals. This receptor-spacer-reporter concept is a recurring theme often with the reporter displaying photoinduced electron transfer.
One example is a sensor sensitive to heparin.
Other receptors are sensitive not to a specific molecule but to a molecular compound class. One example is the grouped analysis of several tannic acids that accumulate in ageing scotch whiskey in oak barrels. The grouped results demonstrated a correlation with the age but the individual components did not. A similar receptor can be used to analyze tartrates in wine.
The compound saxitoxin is a neurotoxin found in shellfish and a chemical weapon. An experimental sensor for this compound is again based on PET. Interaction of saxitoxin with the sensor's crown ether moiety kills its PET process towards the fluorophore and fluorescence is switched from off to on.
The unusual boron moiety makes sure the fluorescence takes place in the visible light part of the electromagnetic spectrum
In another strategy called indicator-displacement assay (IDA) an analyte such as citrate or phosphate ions displace a fluorescent indicator in an indicator-host complex. The so-called UT taste chip (University of Texas) is a prototype electronic tongue and combines supramolecular chemistry with charge-coupled devices based on silicon wafers and immobilized receptor molecules.
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