Electron microscope

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Electron_microscope

A modern transmission electron microscope (TITAN)

An electron microscope is a microscope that uses a beam of electrons as a source of illumination. It uses electron optics that are analogous to the glass lenses of an optical light microscope to control the electron beam, for instance focusing it to produce magnified images or electron diffraction patterns. As the wavelength of an electron can be more than 100,000 times smaller than that of visible light, electron microscopes have a much higher resolution of about 0.1 nm, which compares to about 200 nm for light microscopes. Electron microscope may refer to:

• Transmission electron microscope (TEM) where swift electrons go through a thin sample
• Scanning transmission electron microscope (STEM) which is similar to TEM with a scanned electron probe
• Scanning electron microscope (SEM) which is similar to STEM, but with thick samples
• Electron microprobe similar to a SEM, but more for chemical analysis
• Low-energy electron microscope (LEEM), used to image surfaces
• Photoemission electron microscope (PEEM) which is similar to LEEM using electrons emitted from surfaces by photons

Additional details can be found in the above links. This article contains some general information mainly about transmission and scanning electron microscopes.

History

See also: Transmission electron microscopy § History

Many developments laid the groundwork of the electron optics used in microscopes. One significant step was the work of Hertz in 1883 who made a cathode-ray tube with electrostatic and magnetic deflection, demonstrating manipulation of the direction of an electron beam. Others were focusing of the electrons by an axial magnetic field by Emil Wiechert in 1899, improved oxide-coated cathodes which produced more electrons by Arthur Wehnelt in 1905 and the development of the electromagnetic lens in 1926 by Hans Busch. According to Dennis Gabor, the physicist Leó Szilárd tried in 1928 to convince him to build an electron microscope, for which Szilárd had filed a patent.

Reproduction of an early electron microscope constructed by Ernst Ruska in the 1930s

To this day the issue of who invented the transmission electron microscope is controversial. In 1928, at the Technische Hochschule in Charlottenburg (now Technische Universität Berlin), Adolf Matthias (Professor of High Voltage Technology and Electrical Installations) appointed Max Knoll to lead a team of researchers to advance research on electron beams and cathode-ray oscilloscopes. The team consisted of several PhD students including Ernst Ruska. In 1931, Max Knoll and Ernst Ruska successfully generated magnified images of mesh grids placed over an anode aperture. The device, a replicate of which is shown in the figure, used two magnetic lenses to achieve higher magnifications, the first electron microscope. (Max Knoll died in 1969, so did not receive a share of the 1986 Nobel prize for the invention of electron microscopes.)

Apparently independent of this effort was work at Siemens-Schuckert by Reinhold Rüdenberg. According to patent law (U.S. Patent No. 2058914 and 2070318, both filed in 1932), he is the inventor of the electron microscope, but it is not clear when he had a working instrument. He stated in a very brief article in 1932 that Siemens had been working on this for some years before the patents were filed in 1932, claiming that his effort was parallel to the university development. He died in 1961, so similar to Max Knoll, was not eligible for a share of the 1986 Nobel prize.

In the following year, 1933, Ruska and Knoll built the first electron microscope that exceeded the resolution of an optical (light) microscope. Four years later, in 1937, Siemens financed the work of Ernst Ruska and Bodo von Borries, and employed Helmut Ruska, Ernst's brother, to develop applications for the microscope, especially with biological specimens. Also in 1937, Manfred von Ardenne pioneered the scanning electron microscope. Siemens produced the first commercial electron microscope in 1938. The first North American electron microscopes were constructed in the 1930s, at the Washington State University by Anderson and Fitzsimmons  and at the University of Toronto by Eli Franklin Burton and students Cecil Hall, James Hillier, and Albert Prebus. Siemens produced a transmission electron microscope (TEM) in 1939. Although current transmission electron microscopes are capable of two million times magnification, as scientific instruments they remain similar but with improved optics.

In the 1940s, high-resolution electron microscopes were developed, enabling greater magnification and resolution. By 1965, Albert Crewe at the University of Chicago introduced the scanning transmission electron microscope using a field emission source, enabling scanning microscopes at high resolution. By the early 1980s improvements in mechanical stability as well as the use of higher accelerating voltages enabled imaging of materials at the atomic scale. In the 1980s, the field emission gun became common for electron microscopes, improving the image quality due to the additional coherence and lower chromatic aberrations. The 2000s were marked by advancements in aberration-corrected electron microscopy, allowing for significant improvements in resolution and clarity of images.

Types of electron microscopes

Transmission electron microscope (TEM)

Main article: Transmission electron microscope

Transmission Electron Microscope

The original form of the electron microscope, the transmission electron microscope (TEM), uses a high voltage electron beam to illuminate the specimen and create an image. An electron beam is produced by an electron gun, with the electrons typically having energies in the range 20 to 400 keV, focused by electromagnetic lenses, and transmitted through a thin specimen. When it emerges from the specimen, the electron beam carries information about the structure of the specimen that is then magnified by the lenses of the microscope. The spatial variation in this information (the "image") may be viewed by projecting the magnified electron image onto a detector. For example, the image may be viewed directly by an operator using a fluorescent viewing screen coated with a phosphor or scintillator material such as zinc sulfide. More commonly a high-resolution phosphor is coupled by means of a lens optical system or a fibre optic light-guide to the sensor of a digital camera. A different approach is to use a direct electron detector which has no scintillator, which addresses some of the limitations of scintillator-coupled cameras.

For many years the resolution of TEMs was limited by aberrations of the electron optics, primarily the spherical aberration. In most recent instruments hardware correctors can reduce spherical aberration and other aberrations, improving the resolution in high-resolution transmission electron microscopy (HRTEM) to below 0.5 angstrom (50 picometres), enabling magnifications of more than 50 million times. The ability of HRTEM to determine the positions of atoms within materials is useful for many areas of research and development.

Scanning electron microscope (SEM)

Main article: Scanning electron microscope

An SEM produces images by probing the specimen with a focused electron beam that is scanned across the specimen (raster scanning). When the electron beam interacts with the specimen, it loses energy and is scattered in different directions by a variety of mechanisms. These interactions lead to, among other events, emission of low-energy secondary electrons and high-energy backscattered electrons, light emission (cathodoluminescence) or X-ray emission. All of these signals carrying information about the specimen, such as the surface topography and composition. The image displayed when using an SEM shows the variation in the intensity of any of these signals as an image. In these each position in the image corresponding to a position of the beam on the specimen when the signal was generated.

TESCAN S8000X SEM

SEMs are different from TEMs in that they use electrons with much lower energy, generally below 20 keV, while TEMs generally use electrons with energies in the range of 80-300 keV. Thus, the electron sources and optics of the two microscopes have different designs, and they are normally separate instruments.

Scanning transmission electron microscope (STEM)

Main article: Scanning transmission electron microscopy

A STEM combines features of both a TEM and a SEM by rastering a focused incident probe across a specimen, but now mainly using the electrons which are transmitted through the sample. Many types of imaging are common to both TEM and STEM, but some such as annular dark-field imaging and other analytical techniques are much easier to perform with higher spatial resolutions in a STEM instrument. One drawback is that image data is acquired in serial rather than in parallel fashion.

Main operating modes

An image of an ant in an SEM

The most common methods of obtaining images in an electron microscope involve selecting different directions for the electrons that have been transmitted through a sample, and/or electrons of different energies. There are a very large number of methods of doing this, although not all are very common.

Secondary electrons

Electron–matter interaction volume and types of signal generated in a SEM

In a SEM the signals result from interactions of the electron beam with atoms within the sample. The most common mode is to use the secondary electrons (SE) to produce images. Secondary electrons have very low energies, on the order of 50 eV, which limits their mean free path in solid matter to a few nanometers below the sample surface. The electrons are detected by an Everhart–Thornley detector, which is a type of collector-scintillator-photomultiplier system. The signal from secondary electrons tends to be highly localized at the point of impact of the primary electron beam, making it possible to collect images of the sample surface with a resolution of better than 1 nm, and with specialized instruments at the atomic scale.

The brightness of the signal depends on the number of secondary electrons reaching the detector. If the beam enters the sample perpendicular to the surface, then the electrons come out symmetrically about the axis of the beam. As the angle of incidence increases, the interaction volume from which they cone increases and the "escape" distance from one side of the beam decreases, resulting in more secondary electrons being emitted from the sample. Thus steep surfaces and edges tend to be brighter than flat surfaces, which results in images with a well-defined, three-dimensional appearance that is similar to a reflected light image.

Backscattered electrons

Backscattered electrons (BSE) are those emitted back out from the specimen due to beam-specimen interactions where the electrons undergo elastic and inelastic scattering. They are conventionally defined as having energies from 50 eV up to the energy of the primary beam. Backscattered electrons can be used for both imaging and to form an electron backscatter diffraction (EBSD) image, the latter can be used to determine the crystallography of the specimen.

Electron backscatter diffraction pattern for (001) single crystal silicon crystals taken at 20kV using Oxford S2 detector

Heavy elements (high atomic number) backscatter electrons more strongly than light elements (low atomic number), and thus appear brighter in the image, BSE images can therefore be used to detect areas with different chemical compositions. To optimize the signal, dedicated backscattered electron detectors are positioned above the sample in a "doughnut" type arrangement, concentric with the electron beam, maximizing the solid angle of collection. BSE detectors are usually either scintillator or semiconductor types. When all parts of the detector are used to collect electrons symmetrically about the beam, atomic number contrast is produced. However, strong topographic contrast is produced by collecting back-scattered electrons from one side above the specimen using an asymmetrical, directional BSE detector; the resulting contrast appears as if there was illumination of the topography from that side. Semiconductor detectors can be made in radial segments that can be switched in or out to control the type of contrast produced and its directionality.

Diffraction contrast imaging

Diffraction contrast uses the variation in either or both the direction of diffracted electrons or their amplitude as a function of position as the contrast mechanism. It is one of the simplest ways to image in a transmission electron microscope, and widely used.

The idea is to use an objective aperture below the sample and select only one or a range of different diffracted directions, then use these to form an image. When the aperture includes the incident beam direction the images are called bright field, since in the absence of any sample the field of view would be uniformly bright. When the aperture excludes the incident beam the images are called dark field, since similarly without a sample the image would be uniformly dark. One variant of this is called weak-beam dark-field microscopy, and can be used to obtain high resolution images of defects such as dislocations.

High resolution imaging

Main articles: High-resolution transmission electron microscopy and Annular dark-field imaging

CuTe High resolution image

In high-resolution transmission electron microscopy (also sometimes called high-resolution electron microscopy) a number of different diffracted beams are allowed through the objective aperture. These interfere, leading to images which represent the atomic structure of the material. These can include the incident beam direction, or with scanning transmission electron microscopes they typically are for a range of diffracted beams excluding the incident beam. Depending upon how thick the samples are and the aberrations of the microscope, these images can either be directly interpreted in terms of the positions of columns of atoms, or require a more careful analysis using calculations of the multiple scattering of the electrons and the effect of the contrast transfer function of the microscope.

Main articles: Electron holography and 4D STEM

There are many other imaging variants that can also to lead to atomic level information. Electron holography uses the interference of electrons which have been through the sample and a reference beam. 4D STEM collects diffraction data at each point using a scanning instrument, then processes them to produce different types of images.

X-ray microanalysis

Main article: Energy-dispersive X-ray spectroscopy

EDS spectrum of the mineral crust of the vent shrimp Rimicaris exoculata Most of these peaks are K-alpha and K-beta lines. One peak is from the L shell of iron.

X-ray microanalysis is a method of obtaining local chemical information within electron microscopes of all types, although it is most commonly used in scanning instruments. When high energy electrons interact with atoms they can knock out electrons, particularly those in the inner shells and core electrons. These are then filled by valence electron, and the energy difference between the valence and core states can be converted into an x-ray which is detected by a spectrometer. The energies of these x-rays is somewhat specific to the atomic species, so local chemistry can be probed.

EELS

Main article: Electron energy loss spectroscopy

Experimental electron energy loss spectrum, showing the major features: zero-loss peak, plasmon peaks and core loss edge.

Similar to X-ray microanalysis, the energies of electrons which have transmitted through a sample can be analyzed and yield information ranging from details of the local electronic structure to chemical information.

Electron diffraction

Main article: Electron diffraction

Transmission electron microscopes can be used in electron diffraction mode where a map of the angles of the electrons leaving the sample is produced. The advantages of electron diffraction over X-ray crystallography are primarily in the size of the crystals. In X-ray crystallography, crystals are commonly visible by the naked eye and are generally in the hundreds of micrometers in length. In comparison, crystals for electron diffraction must be less than a few hundred nanometers in thickness, and have no lower boundary of size. Additionally, electron diffraction is done on a TEM, which can also be used to obtain other types of information, rather than requiring a separate instrument.

Variations in CBED with thickness for Si (001)

Main articles: Convergent beam electron diffraction and Precession electron diffraction

There are many variants on electron diffraction, depending upon exactly what type of illumination conditions are used. If a parallel beam is used with an aperture to limit the region exposed to the electrons then sharp diffraction features are normally observed, a technique called selected area electron diffraction. This is often the main technique used. Another common approach uses conical illumination and is called convergent beam electron diffraction (CBED). This is good for determining the symmetry of materials. A third is precession electron diffraction, where a parallel beam is spun around a large angle, producing a type of average diffraction pattern. These often have less multiple scattering.

Other electron microscope techniques

• Cathodoluminescence - analysing photons due to the electron beam
• Charge contrast imaging - using how charging varies with position to produce images
• CryoEM - using frozen samples, almost always biological samples
• EBSD - using the back-scattered electrons, typically in a SEM
  • TKD - using the Kikuchi lines in diffraction patterns
• ECCI - using contrast due to electron channelling
• EBIC - measuring the current produced as a function of the position of a small beam
• Electron tomography - methods to produce 3D information by combining images
• FEM - technique to interrogate nanocrystalline materials
• Immune electron microscopy - the use of electron microscopy in immunology
• Geometric phase analysis - a method to analyze high-resolution images
• Serial block-face scanning electron microscopy - a way to produce 3D information from many images
• WDXS - higher precision detection of x-rays to analyze local chemistry

Aberration corrected instruments

Scanning transmission electron microscope equipped with a 3rd-order spherical aberration corrector

Main article: Aberration-corrected transmission electron microscopy

Aberration-corrected transmission electron microscopy (AC-TEM) is the general term for electron microscopes where electro optical components are introduced to reduce the aberrations that would otherwise limit the resolution of the images. Historically electron microscopes had quite severe aberrations, and until about the start of the 21st century the resolution was limited, able to image the atomic structure of materials if the atoms were far enough apart. Around the turn of the century the electron optical components were coupled with computer control of the lenses and their alignment, enabling correction of aberrations. The first demonstration of aberration correction in TEM mode was by Harald Rose and Maximilian Haider in 1998 using a hexapole corrector, and in STEM mode by Ondrej Krivanek and Niklas Dellby in 1999 using a quadrupole/octupole corrector.

As of 2025 correction of geometric aberrations is standard in many commercial electron microscopes, and they are extensively used in many different areas of science. Similar correctors have also been used at much lower energies for LEEM instruments.

Sample preparation

An insect coated in gold for viewing with a scanning electron microscope (SEM)

Main articles: TEM Sample preparation, Ultramicrotomy, Staining, Cryofixation, Chemical milling, and Sputtering

Samples for electron microscopes mostly cannot be observed directly. The samples need to be prepared to stabilize the sample and enhance contrast. Preparation techniques differ vastly in respect to the sample and its specific qualities to be observed as well as the specific microscope used. Details can be found in the relevant main articles listed above.

Disadvantages

JEOL transmission and scanning electron microscope made in the mid-1970s

Electron microscopes are expensive to build and maintain. Microscopes designed to achieve high resolutions must be housed in stable buildings (sometimes underground) with special services such as magnetic field canceling systems and anti vibration mounts.

The samples largely have to be viewed in vacuum, as the molecules that make up air would scatter the electrons. An exception is liquid-phase electron microscopy using either a closed liquid cell or an environmental chamber, for example, in the environmental scanning electron microscope, which allows hydrated samples to be viewed in a low-pressure (up to 20 Torr or 2.7 kPa) wet environment. Various techniques for in situ electron microscopy of gaseous samples have also been developed.

Pleolipoviral virion (HRPV-6)

Samples of hydrated materials, including almost all biological specimens, have to be prepared in various ways to stabilize them, reduce their thickness (ultrathin sectioning) and increase their electron optical contrast (staining). These processes may result in artifacts, but these can usually be identified by comparing the results obtained by using radically different specimen preparation methods. Since the 1980s, analysis of cryofixed, vitrified specimens has also become increasingly used.

Many samples suffer from radiation damage which can change internal structures. This can be due to either or both radiolytic processes or ballistic, for instance with collision cascades. This can be a severe issue for biological samples.

Isomer

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Isomer

In chemistry, isomers are molecules or polyatomic ions with an identical molecular formula – that is, the same number of atoms of each element – but distinct arrangements of atoms in space. Isomerism refers to the existence or possibility of isomers.

Isomers do not necessarily share similar chemical or physical properties. Two main forms of isomerism are structural (or constitutional) isomerism, in which bonds between the atoms differ; and stereoisomerism (or spatial isomerism), in which the bonds are the same but the relative positions of the atoms differ.

Isomeric relationships form a hierarchy. Two chemicals might be the same constitutional isomer, but upon deeper analysis be stereoisomers of each other. Two molecules that are the same stereoisomer as each other might be in different conformational forms or be different isotopologues. The depth of analysis depends on the field of study or the chemical and physical properties of interest.

The English word "isomer" (/ˈaɪsəmər/) is a back-formation from "isomeric", which was borrowed through German isomerisch from Swedish isomerisk; which in turn was coined from Greek ἰσόμερoς isómeros, with roots isos = "equal", méros = "part".

Two broad types of isomers

Structural isomers

Main article: Structural isomer

Structural isomers have the same number of atoms of each element (hence the same molecular formula), but the atoms are connected in distinct ways.

Example: C
₃H
₈O

For example, there are three distinct compounds with the molecular formula ${\displaystyle {\text{C}}_3^{}{\text{H}}_8^{}\text{O}}$:

The first two isomers shown of ${\displaystyle {\text{C}}_3^{}{\text{H}}_8^{}\text{O}}$ are propanols, that is, alcohols derived from propane. Both have a chain of three carbon atoms connected by single bonds, with the remaining carbon valences being filled by seven hydrogen atoms and by a hydroxyl group ${\displaystyle -\text{OH}}$ comprising the oxygen atom bound to a hydrogen atom. These two isomers differ on which carbon the hydroxyl is bound to: either to an extremity of the carbon chain propan-1-ol (1-propanol, n-propyl alcohol, n-propanol; I) or to the middle carbon propan-2-ol (2-propanol, isopropyl alcohol, isopropanol; II). These can be described by the condensed structural formulas ${\displaystyle {\text{H}}_3^{}\text{C}-{\text{CH}}_2^{}-{\text{CH}}_2^{}\text{OH}}$ and ${\displaystyle {\text{H}}_3^{}\text{C}-\text{CH}(\text{OH})-{\text{CH}}_3^{}}$.

The third isomer of ${\displaystyle {\text{C}}_3^{}{\text{H}}_8^{}\text{O}}$ is the ether methoxyethane (ethyl-methyl-ether; III). Unlike the other two, it has the oxygen atom connected to two carbons, and all eight hydrogens bonded directly to carbons. It can be described by the condensed formula ${\displaystyle {\text{H}}_3^{}\text{C}-{\text{CH}}_2^{}-\text{O}-{\text{CH}}_3^{}}$.

The alcohol "3-propanol" is not another isomer, since the difference between it and 1-propanol is the result of a choice in the direction of numbering the carbons along the chain. For the same reason, "ethoxymethane" is the same molecule as methoxyethane, not another isomer.

1-Propanol and 2-propanol are examples of positional isomers, which differ by the position at which certain features, such as double bonds or functional groups, occur on a "parent" molecule (propane, in that case).

Example: C
₃H
₄

There are also three structural isomers of the hydrocarbon ${\displaystyle {\text{C}}_3^{}{\text{H}}_4^{}}$:

I Propadiene	II Propyne	III Cyclopropene

In two of the isomers, the three carbon atoms are connected in an open chain, but in one of them (propadiene or allene; I) the carbons are connected by two double bonds, while in the other (propyne or methylacetylene; II) they are connected by a single bond and a triple bond. In the third isomer (cyclopropene; III) the three carbons are connected into a ring by two single bonds and a double bond. In all three, the remaining valences of the carbon atoms are satisfied by the four hydrogens.

Again, note that there is only one structural isomer with a triple bond, because the other possible placement of that bond is just drawing the three carbons in a different order. For the same reason, there is only one cyclopropene, not three.

Tautomers

Tautomers are structural isomers which readily interconvert, so that two or more species co-exist in equilibrium such as

${\displaystyle \text{H}-\text{X}-\text{Y}=\text{Z}\stackrel{-\rightharpoonup }{\leftharpoondown -}\text{X}=\text{Y}-\text{Z}-\text{H}}$.

Important examples are keto-enol tautomerism and the equilibrium between neutral and zwitterionic forms of an amino acid.

Stereoisomers

Two kinds of stereoisomers

Main article: Stereoisomerism

Stereoisomers have the same atoms or isotopes connected by bonds of the same type, but differ in the relative positions of those atoms in space. Two broad types of stereoisomers exist, enantiomers and diastereomers. Enantiomers have identical physical properties but diastereomers do not.

Enantiomers

Two compounds are said to be enantiomers if their molecules are mirror images of each other and cannot be made to coincide only by rotations or translations – like a left hand and a right hand. The two shapes are said to be chiral.

A classic example is bromochlorofluoromethane (${\displaystyle \text{CHFClBr}}$). The two enantiomers can be distinguished, for example, by whether the path ${\displaystyle \text{F}⟶\text{Cl}⟶\text{Br}}$ turns clockwise or counterclockwise as seen from the hydrogen atom. In order to change one conformation to the other, at some point those four atoms would have to lie on the same plane – which would require severely straining or breaking their bonds to the carbon atom. The corresponding energy barrier between the two conformations is so high that there is practically no conversion between them at room temperature, and they can be regarded as different configurations.

The compound chlorofluoromethane ${\displaystyle {\text{CH}}_2^{}\text{ClF}}$, in contrast, is not chiral; the mirror image of its molecule is also obtained by a half-turn about a suitable axis.

(R)-2,3-Pentadiene

Another example of a chiral compound is 2,3-pentadiene ${\displaystyle {\text{H}}_3^{}\text{C}-\text{CH}=\text{C}=\text{CH}-{\text{CH}}_3^{}}$, a hydrocarbon that contains two overlapping double bonds. The double bonds are such that the three middle carbons are in a straight line, while the first three and last three lie on perpendicular planes. The molecule and its mirror image are not superimposable, even though the molecule has an axis of symmetry. The two enantiomers can be distinguished, for example, by the right-hand rule. This type of isomerism is called axial isomerism.

Enantiomers behave identically in chemical reactions, except when reacting with chiral compounds or in the presence of chiral catalysts, such as most enzymes. For this latter reason, the two enantiomers of most chiral compounds usually have markedly different effects and roles in living organisms. In biochemistry and food science, the two enantiomers of a chiral molecule – such as glucose – are usually identified and treated as very different substances.

Each enantiomer of a chiral compound typically rotates the plane of polarized light that passes through it. The rotation has the same magnitude but opposite senses for the two isomers, and can be a useful way of distinguishing and measuring their concentration in a solution. For this reason, enantiomers were formerly called "optical isomers". However, this term is ambiguous and is discouraged by the IUPAC.

Some enantiomer pairs (such as those of trans-cyclooctene) can be interconverted by internal motions that change bond lengths and angles only slightly. Other pairs (such as CHFClBr) cannot be interconverted without breaking bonds, and therefore are different configurations.

Diastereomers

Stereoisomers that are not enantiomers are called diastereomers. Some diastereomers may contain chiral centers, and some may not.

Cis–trans isomerism

A double bond between two carbon atoms forces the remaining four bonds (if they are single) to lie on the same plane, perpendicular to the plane of the bond as defined by its π orbital. If the two bonds on each carbon connect to different atoms, two distinct conformations are possible that differ from each other by a twist of 180 degrees of one of the carbons about the double bond.

The classical example is dichloroethene ${\displaystyle {\text{C}}_2^{}{\text{H}}_2^{}{\text{Cl}}_2^{}}$, specifically the structural isomer ${\displaystyle \text{Cl}-\text{HC}=\text{CH}-\text{Cl}}$ that has one chlorine bonded to each carbon. It has two conformational isomers, with the two chlorines on the same side or on opposite sides of the double bond's plane. They are traditionally called cis (from Latin meaning "on this side of") and trans ("on the other side of"), respectively, or Z and E in the IUPAC recommended nomenclature. Conversion between these two forms usually requires temporarily breaking bonds (or turning the double bond into a single bond), so the two are considered different configurations of the molecule.

More generally, cis–trans isomerism (formerly called "geometric isomerism") occurs in molecules where the relative orientation of two distinguishable functional groups is restricted by a somewhat rigid framework of other atoms.

For example, in the cyclic alcohol inositol ${\displaystyle {(\text{CHOH})}_6^{}}$ (a six-fold alcohol of cyclohexane), the six-carbon cyclic backbone largely prevents the hydroxyl ${\displaystyle -\text{OH}}$ and the hydrogen ${\displaystyle -\text{H}}$ on each carbon from switching places. Therefore, one has different configurational isomers depending on whether each hydroxyl is on "this side" or "the other side" of the ring's mean plane. Discounting isomers that are equivalent under rotations, there are nine isomers that differ by this criterion, and behave as different stable substances (two of them being enantiomers of each other). The most common one in nature (myo-inositol) has the hydroxyls on carbons 1, 2, 3 and 5 on the same side of that plane, and can therefore be called cis-1,2,3,5–trans-4,6-cyclohexanehexol. And each of these cis–trans isomers can possibly have stable "chair" or "boat" conformations (although the barriers between these are significantly lower than those between different cis–trans isomers).

The two isomeric complexes, cisplatin and transplatin, are examples of square planar MX₂Y₂ molecules with M = Pt.

Cis and trans isomers also occur in inorganic coordination compounds, such as square planar ${\displaystyle {\text{MX}}_2^{}{\text{Y}}_2^{}}$ complexes and octahedral ${\displaystyle {\text{MX}}_4^{}{\text{Y}}_2^{}}$ complexes.

For more complex organic molecules, the cis and trans labels can be ambiguous. In such cases, a more precise labeling scheme is employed based on the Cahn-Ingold-Prelog priority rules.

Isotopes and spin

Isotopomers

Different isotopes of the same element can be considered as different kinds of atoms when enumerating isomers of a molecule or ion. The replacement of one or more atoms by their isotopes can create multiple structural isomers and/or stereoisomers from a single isomer.

For example, replacing two atoms of common hydrogen (${\displaystyle {}^1\text{H}}$) by deuterium (${\displaystyle {}^2\text{H}}$, or ${\displaystyle \text{D}}$) on an ethane molecule yields two distinct structural isomers, depending on whether the substitutions are both on the same carbon (1,1-dideuteroethane, ${\displaystyle {\text{HD}}_2^{}\text{C}-{\text{CH}}_3^{}}$) or one on each carbon (1,2-dideuteroethane, ${\displaystyle {\text{DH}}_2^{}\text{C}-{\text{CDH}}_2^{}}$); as if the substituent was chlorine instead of deuterium. The two molecules do not interconvert easily and have different properties, such as their microwave spectrum.

Another example would be substituting one atom of deuterium for one of the hydrogens in chlorofluoromethane (${\displaystyle {\text{CH}}_2^{}\text{ClF}}$). While the original molecule is not chiral and has a single isomer, the substitution creates a pair of chiral enantiomers of ${\displaystyle \text{CHDClF}}$, which could be distinguished (at least in theory) by their optical activity.

When two isomers would be identical if all isotopes of each element were replaced by a single isotope, they are described as isotopomers or isotopic isomers. In the above two examples if all ${\displaystyle \text{D}}$ were replaced by ${\displaystyle \text{H}}$, the two dideuteroethanes would both become ethane and the two deuterochlorofluoromethanes would both become ${\displaystyle {\text{CH}}_2^{}\text{ClF}}$.

The concept of isotopomers is different from isotopologs or isotopic homologs, which differ in their isotopic composition. For example, ${\displaystyle {\text{C}}_2^{}{\text{H}}_5^{}\text{D}}$ and ${\displaystyle {\text{C}}_2^{}{\text{H}}_4^{}{\text{D}}_2^{}}$ are isotopologues and not isotopomers, and are therefore not isomers of each other.

Spin isomers

Another type of isomerism based on nuclear properties is spin isomerism, where molecules differ only in the relative spin magnetic quantum numbers m_s of the constituent atomic nuclei. This phenomenon is significant for molecular hydrogen, which can be partially separated into two long-lived states described as spin isomers or nuclear spin isomers: parahydrogen, with the spins of the two nuclei pointing in opposite directions, and orthohydrogen, where the spins point in the same direction.

Applications

Isomers having distinct biological properties are common; for example, the placement of methyl groups. In substituted xanthines, theobromine, found in chocolate, is a vasodilator with some effects in common with caffeine; but, if one of the two methyl groups is moved to a different position on the two-ring core, the isomer is theophylline, which has a variety of effects, including bronchodilation and anti-inflammatory action. Another example of this occurs in the phenethylamine-based stimulant drugs. Phentermine is a non-chiral compound with a weaker effect than that of amphetamine. It is used as an appetite-reducing medication and has mild or no stimulant properties. However, an alternate atomic arrangement gives dextromethamphetamine, which is a stronger stimulant than amphetamine.

In medicinal chemistry and biochemistry, enantiomers are a special concern because they may possess distinct biological activity. Many preparative procedures afford a mixture of equal amounts of both enantiomeric forms. In some cases, the enantiomers are separated by chromatography using chiral stationary phases. They may also be separated through the formation of diastereomeric salts. In other cases, enantioselective synthesis have been developed.

As an inorganic example, cisplatin (see structure above) is an important drug used in cancer chemotherapy, whereas the trans isomer (transplatin) has no useful pharmacological activity.

History

Isomerism was first observed in 1827, when Friedrich Wöhler prepared silver cyanate and discovered that, although its elemental composition of ${\displaystyle \text{AgCNO}}$ was identical to silver fulminate (prepared by Justus von Liebig the previous year), its properties were distinct. This finding challenged the prevailing chemical understanding of the time, which held that chemical compounds could be distinct only when their elemental compositions differ. (We now know that the bonding structures of fulminate and cyanate can be approximately described as ${\displaystyle {\text{O}}^{-}{\text{N}}^{+}}$≡${\displaystyle {\text{C}}^{-}}$ and ${\displaystyle \text{O}=\text{C}={\text{N}}^{-}}$, respectively.)

Additional examples were found in succeeding years, such as Wöhler's 1828 discovery that urea has the same atomic composition (${\displaystyle {\text{CH}}_4^{}{\text{N}}_2^{}\text{O}}$) as the chemically distinct ammonium cyanate. (Their structures are now known to be ${\displaystyle {({\text{H}}_2^{}\text{N}-)}_2^{}\text{C}=\text{O}}$ and ${\displaystyle [{\text{NH}}_4^{+}][\text{O}=\text{C}={\text{N}}^{-}]}$, respectively.) In 1830 Jöns Jacob Berzelius introduced the term isomerism to describe the phenomenon.

In 1848, Louis Pasteur observed that tartaric acid crystals came into two kinds of shapes that were mirror images of each other. Separating the crystals by hand, he obtained two version of tartaric acid, each of which would crystallize in only one of the two shapes, and rotated the plane of polarized light to the same degree but in opposite directions. In 1860, Pasteur explicitly hypothesized that the molecules of isomers might have the same composition but different arrangements of their atoms.