A molecular switch is a
molecule
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioch ...
that can be
reversibly shifted between two or more stable states. The molecules may be shifted between the states in response to environmental stimuli, such as changes in pH, light, temperature, an electric current, microenvironment, or in the presence of ions and other
ligand
In coordination chemistry, a ligand is an ion or molecule (functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's electr ...
s. In some cases, a combination of stimuli is required. The oldest forms of synthetic molecular switches are
pH indicator
A pH indicator is a halochromic chemical compound added in small amounts to a solution so the pH (acidity or basicity) of the solution can be determined visually or spectroscopically by changes in absorption and/or emission properties. Hence, ...
s, which display distinct colors as a function of
pH. Currently synthetic molecular switches are of interest in the field of nanotechnology for application in
molecular computer
DNA computing is an emerging branch of unconventional computing which uses DNA, biochemistry, and molecular biology hardware, instead of the traditional electronic computing. Research and development in this area concerns theory, experiments, a ...
s or responsive drug delivery systems. Molecular switches are also important in
biology
Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary i ...
because many biological functions are based on it, for instance
allosteric regulation
In biochemistry, allosteric regulation (or allosteric control) is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site.
The site to which the effector binds is termed the ''allosteric site ...
and
vision
Vision, Visions, or The Vision may refer to:
Perception Optical perception
* Visual perception, the sense of sight
* Visual system, the physical mechanism of eyesight
* Computer vision, a field dealing with how computers can be made to gain un ...
. They are also one of the simplest examples of
molecular machine
A molecular machine, nanite, or nanomachine is a molecular component that produces quasi-mechanical movements (output) in response to specific stimuli (input). In cellular biology, macromolecular machines frequently perform tasks essential for l ...
s.
Biological molecular switches
In cellular biology, proteins act as intracellular signaling molecules by activating another protein in a signaling pathway. In order to do this, proteins can switch between active and inactive states, thus acting as molecular switches in response to another signal. For example, phosphorylation of proteins can be used to activate or inactivate proteins. The external signal flipping the 'molecular switch' could be a protein kinase, which adds a phosphate group to the protein, or a protein phosphatase, which removes phosphates.
Acidochromic molecular switches
The capacity of some compounds to change in function of the
pH was known since the sixteenth century. This effect was even known before the discovery of the acidity/basicity concept. Those are found in a wide range of plants like roses, cornflowers, primroses and violets.
Robert Boyle
Robert Boyle (; 25 January 1627 – 31 December 1691) was an Anglo-Irish natural philosopher, chemist, physicist, alchemist and inventor. Boyle is largely regarded today as the first modern chemist, and therefore one of the founders of ...
was the first person to describe this effect, employing plant juices (in the forms of solution and impregnated paper).
The most common use of these compounds is the pH indicators, which are molecules with acid/basic properties and whereas the different forms present different colors. When an acid or a base is added, the equilibrium between the two forms will be displaced.
Photochromic molecular switches
A widely studied class are
photochromic
Photochromism is the reversible transformation of a chemical species (photoswitch) between two forms by the absorption of electromagnetic radiation (photoisomerization), where the two forms have different absorption spectra. In plain language, th ...
compounds which are able to switch between electronic configurations when irradiated by light of a specific wavelength. Each state has a specific absorption maximum which can then be read out by
UV-VIS spectroscopy. Members of this class include
azobenzene
Azobenzene is a photoswitchable chemical compound composed of two phenyl rings linked by a N=N double bond. It is the simplest example of an aryl azo compound. The term 'azobenzene' or simply 'azo' is often used to refer to a wide class of simi ...
s,
diarylethene Diarylethene is the general name of a class of chemical compounds that have aromatic functional groups bonded to each end of a carbon–carbon double bond. The simplest example is stilbene, which has two geometric isomers, E and Z.
Under the influ ...
s,
dithienylethenes,
fulgides,
stilbene Stilbene may refer to one of the two stereoisomers of 1,2-diphenylethene:
* (''E'')-Stilbene (''trans'' isomer)
* (''Z'')-Stilbene (''cis'' isomer)
See also
* Stilbenoids, a class of molecules found in plants
* 1,1-Diphenylethylene
1,1-Diphenyl ...
s,
spiropyran A spiropyran is a type of organic chemical compound, known for photochromic properties that provide this molecule with the ability of being used in medical and technological areas. Spiropyrans were discovered in the early twentieth century. However, ...
s and phenoxynaphthacene quinones.
:
![Dithienylethene](https://upload.wikimedia.org/wikipedia/commons/d/d0/Dithienylethene.svg)
Chiroptical molecular switches are a specific subgroup with photochemical switching taking place between an
enantiomeric pairs. In these compounds the readout is by
circular dichroism rather than by ordinary spectroscopy. Hindered alkenes such as the one depicted below change their
helicity (see:
planar chirality Planar chirality, also known as 2D chirality, is the special case of chirality for two dimensions.
Most fundamentally, planar chirality is a mathematical term, finding use in chemistry, physics and related physical sciences, for example, in astrono ...
) as response to irradiation with right or left-handed
circularly polarized light
:
![HinderedAlkeneMolecularSwitch](https://upload.wikimedia.org/wikipedia/commons/d/da/HinderedAlkeneMolecularSwitch.png)
Chiroptical molecular switches that show directional motion are considered
synthetic molecular motors
Synthetic molecular motors are molecular machines capable of continuous directional rotation under an energy input. Although the term "molecular motor" has traditionally referred to a naturally occurring protein that induces motion (via protein d ...
:
:
Host–guest molecular switches
In
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 che ...
the bistable states of molecular switches differ in their affinity for guests. Many early examples of such systems are based on
crown ether
In organic chemistry, crown ethers are cyclic chemical compounds that consist of a ring containing several ether groups (). The most common crown ethers are cyclic oligomers of ethylene oxide, the repeating unit being ethyleneoxy, i.e., . Impo ...
chemistry. The first switchable host is described in 1978 by Desvergne & Bouas-Laurent who create a crown ether via photochemical
anthracene
Anthracene is a solid polycyclic aromatic hydrocarbon (PAH) of formula C14H10, consisting of three fused benzene rings. It is a component of coal tar. Anthracene is used in the Economic production, production of the red dye alizarin and other dyes ...
dimerization. Although not strictly speaking switchable the compound is able to take up cations after a photochemical trigger and exposure to
acetonitrile
Acetonitrile, often abbreviated MeCN (methyl cyanide), is the chemical compound with the formula and structure . This colourless liquid is the simplest organic nitrile (hydrogen cyanide is a simpler nitrile, but the cyanide anion is not clas ...
gives back the open form.
:
![AnthraceneCrownDesvergne1978](https://upload.wikimedia.org/wikipedia/commons/b/be/AnthraceneCrownDesvergne1978.png)
In 1980 Yamashita et al. construct a crown ether already incorporating the anthracene units (an anthracenophane) and also study ion uptake vs photochemistry.
:
![AnthraceneCrownMisumi1980](https://upload.wikimedia.org/wikipedia/commons/3/36/AnthraceneCrownMisumi1980.png)
Also in 1980 Shinkai throws out the anthracene unit as photoantenna in favor of an
azobenzene
Azobenzene is a photoswitchable chemical compound composed of two phenyl rings linked by a N=N double bond. It is the simplest example of an aryl azo compound. The term 'azobenzene' or simply 'azo' is often used to refer to a wide class of simi ...
moiety and for the first time envisions the existence of molecules with an on-off switch. In this molecule light triggers a
trans-cis isomerization of the azo group which results in ring expansion. Thus in the trans form the crown binds preferentially to
ammonium
The ammonium cation is a positively-charged polyatomic ion with the chemical formula or . It is formed by the protonation of ammonia (). Ammonium is also a general name for positively charged or protonated substituted amines and quaternary a ...
,
lithium
Lithium (from el, λίθος, lithos, lit=stone) is a chemical element with the symbol Li and atomic number 3. It is a soft, silvery-white alkali metal. Under standard conditions, it is the least dense metal and the least dense solid el ...
and
sodium
Sodium is a chemical element with the symbol Na (from Latin ''natrium'') and atomic number 11. It is a soft, silvery-white, highly reactive metal. Sodium is an alkali metal, being in group 1 of the periodic table. Its only stable iso ...
ions while in the cis form the preference is for
potassium
Potassium is the chemical element with the symbol K (from Neo-Latin ''kalium'') and atomic number19. Potassium is a silvery-white metal that is soft enough to be cut with a knife with little force. Potassium metal reacts rapidly with atmosphe ...
and
rubidium
Rubidium is the chemical element with the symbol Rb and atomic number 37. It is a very soft, whitish-grey solid in the alkali metal group, similar to potassium and caesium. Rubidium is the first alkali metal in the group to have a density higher ...
(both larger ions in same
alkali metal
The alkali metals consist of the chemical elements lithium (Li), sodium (Na), potassium (K),The symbols Na and K for sodium and potassium are derived from their Latin names, ''natrium'' and ''kalium''; these are still the origins of the names ...
group). In the dark the reverse isomerization takes place.
:
![MolecularSwitchShinkay1980](https://upload.wikimedia.org/wikipedia/commons/9/91/MolecularSwitchShinkay1980.png)
Shinkai employs this devices in actual ion transport mimicking the biochemical action of
monensin
Monensin is a polyether antibiotic isolated from '' Streptomyces cinnamonensis''. It is widely used in ruminant animal feeds.
The structure of monensin was first described by Agtarap et al. in 1967, and was the first polyether antibiotic to have ...
and
nigericin
Nigericin is an antibiotic derived from '' Streptomyces hygroscopicus''. Its isolation was described in the 1950s, and in 1968 the structure could be elucidated by X-ray crystallography. The structure and properties of nigericin are similar to th ...
: in a biphasic system ions are taken up triggered by light in one phase and deposited in the other phase in absence of light.
Mechanically-interlocked molecular switches
Some of the most advanced molecular switches are based on
mechanically-interlocked molecular architectures
In chemistry, mechanically-interlocked molecular architectures (MIMAs) are molecules that are connected as a consequence of their topology. This connection of molecules is analogous to keys on a keychain loop. The keys are not directly connected ...
where the bistable states differ in the position of the macrocycle. In 1991
Stoddart devices a
molecular shuttle
A molecular shuttle in supramolecular chemistry is a special type of molecular machine capable of shuttling molecules or ions from one location to another. This field is of relevance to nanotechnology in its quest for nanoscale electronic compone ...
based on a
rotaxane
In chemistry, a rotaxane () is a mechanically interlocked molecular architecture consisting of a dumbbell-shaped molecule which is threaded through a macrocycle (see graphical representation). The two components of a rotaxane are kinetically t ...
on which a molecular ''bead'' is able to shuttle between two ''docking stations'' situated on a molecular ''thread''. Stoddart predicts that when the stations are dissimilar with each of the stations addressed by a different external stimulus the shuttle becomes a molecular machine. In 1993 Stoddart is scooped by supramolecular chemistry pioneer Fritz Vögtle who actually delivers a switchable molecule based not on a rotaxane but on a related
catenane
In macromolecular chemistry, a catenane () is a mechanically interlocked molecular architecture consisting of two or more interlocked macrocycles, i.e. a molecule containing two or more intertwined rings. The interlocked rings cannot be se ...
This compound is based on two ring systems: one ring holds the photoswichable azobenzene ring and two
paraquat docking stations and the other ring is a polyether with to arene rings with binding affinity for the paraquat units. In this system
NMR spectroscopy
Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fiel ...
shows that in the azo trans-form the polyether ring is free to rotate around its partner ring but then when a light trigger activates the cis azo form this rotation mode is stopped
Kaifer and Stoddart in 1994 modify their
molecular shuttle
A molecular shuttle in supramolecular chemistry is a special type of molecular machine capable of shuttling molecules or ions from one location to another. This field is of relevance to nanotechnology in its quest for nanoscale electronic compone ...
such a way that an electron-poor tetracationic cyclophane bead now has a choice between two docking stations: one
biphenol
In organic chemistry, a biphenol refers to compounds with the formula (C6H4OH)2. Such compounds formally result from the coupling of two phenols.
{{short description, Chemical compound
Three symmetrical isomer
In chemistry, isomers are mol ...
and one
benzidine unit. In solution at room temperature
NMR spectroscopy
Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fiel ...
reveals that the bead shuttles at a rate comparable to the NMR timescale, reducing the temperature to 229K resolves the signals with 84% of the population favoring the benzidine station. However, on addition of
trifluoroacetic acid
Trifluoroacetic acid (TFA) is an organofluorine compound with the chemical formula CF3CO2H. It is a structural analogue of acetic acid with all three of the acetyl group's hydrogen atoms replaced by fluorine atoms and is a colorless liquid with a ...
, the benzidine nitrogen atoms are protonated and the bead is fixed permanently on the biphenol station. The same effect is obtained by
electrochemical
Electrochemistry is the branch of physical chemistry concerned with the relationship between electrical potential difference, as a measurable and quantitative phenomenon, and identifiable chemical change, with the potential difference as an outco ...
oxidation (forming the benzidine
radical ion
In organic chemistry, a radical anion is a free radical species that carries a negative charge. Radical anions are encountered in organic chemistry as reduced derivatives of polycyclic aromatic compounds, e.g. sodium naphthenide. An example of a ...
) and significantly both processes are reversible.
In 2007 molecular shuttles were utilized in an experimental
DRAM circuit.
[''A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre''
Jonathan E. Green, Jang Wook Choi1, Akram Boukai, Yuri Bunimovich, Ezekiel Johnston-Halperin, Erica DeIonno, Yi Luo, Bonnie A. Sheriff, Ke Xu, Young Shik Shin, Hsian-Rong Tseng, J. Fraser Stoddart and James R. Heath ]Nature
Nature, in the broadest sense, is the physics, physical world or universe. "Nature" can refer to the phenomenon, phenomena of the physical world, and also to life in general. The study of nature is a large, if not the only, part of science. ...
445, 414-417 (25 January 2007) , The device consists of 400 bottom
silicon
Silicon is a chemical element with the symbol Si and atomic number 14. It is a hard, brittle crystalline solid with a blue-grey metallic luster, and is a tetravalent metalloid and semiconductor. It is a member of group 14 in the periodic tab ...
nanowire
A nanowire is a nanostructure in the form of a wire with the diameter of the order of a nanometre (10−9 metres). More generally, nanowires can be defined as structures that have a thickness or diameter constrained to tens of nanometers or less ...
electrode
An electrode is an electrical conductor used to make contact with a nonmetallic part of a circuit (e.g. a semiconductor, an electrolyte, a vacuum or air). Electrodes are essential parts of batteries that can consist of a variety of materials de ...
s (16
nanometer
330px, Different lengths as in respect to the molecular scale.
The nanometre (international spelling as used by the International Bureau of Weights and Measures; SI symbol: nm) or nanometer (American and British English spelling differences#-re ...
(nm) wide at 33 nm intervals) crossed by another 400
titanium
Titanium is a chemical element with the symbol Ti and atomic number 22. Found in nature only as an oxide, it can be reduced to produce a lustrous transition metal with a silver color, low density, and high strength, resistant to corrosion in ...
top-nanowires with similar dimensions sandwiching a
monolayer A monolayer is a single, closely packed layer of atoms, molecules, or cells. In some cases it is referred to as a self-assembled monolayer. Monolayers of layered crystals like graphene and molybdenum disulfide are generally called 2D materials.
...
of a bistable rotaxane depicted below:
:
![MolecularSwitchInElectronicmemory](https://upload.wikimedia.org/wikipedia/commons/3/30/MolecularSwitchInElectronicmemory.png)
Each
bit
The bit is the most basic unit of information in computing and digital communications. The name is a portmanteau of binary digit. The bit represents a logical state with one of two possible values. These values are most commonly represente ...
in the device consists of a silicon and a titanium crossbar with around 100 rotaxane molecules filling in the space between them at perpendicular angles. The hydrophilic
diethylene glycol
Diethylene glycol (DEG) is an organic compound with the formula (HOCH2CH2)2O. It is a colorless, practically odorless, and hygroscopic liquid with a sweetish taste. It is a four carbon dimer of ethylene glycol. It is miscible in water, alcohol, ...
stopper on the left (gray) is specifically designed to anchor to the silicon wire (made hydrophilic by phosphorus doping) while the hydrophobic
tetraarylmethane stopper on the right does the same to the likewise hydrophobic titanium wire. In the ground state of the switch, the paraquat ring is located around a
tetrathiafulvalene
Tetrathiafulvalene is an organosulfur compound with the formula (. Studies on this heterocyclic compound contributed to the development of molecular electronics. TTF is related to the hydrocarbon fulvalene, , by replacement of four CH groups wi ...
unit (in red) but it moves to the
dioxynaphthyl unit (in green) when the fulvalene unit is oxidized by application of a current. When the fulvalene is reduced back a metastable high conductance '1' state is formed which relaxes back to the ground state with a
chemical half-life of around one hour. The problem of defects is circumvented by adopting a defect-tolerant architecture also found in the
Teramac project. In this way a circuit is obtained consisting of 160,000 bits on an area the size of a
white blood cell
White blood cells, also called leukocytes or leucocytes, are the cell (biology), cells of the immune system that are involved in protecting the body against both infectious disease and foreign invaders. All white blood cells are produced and de ...
translating into 10
11 bits per square centimeter.
References
{{reflist
Supramolecular chemistry
Molecular machines