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Cis–trans isomerism
Cis–trans isomerism
Cis–trans isomerism
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cis-but-2-ene
trans-but-2-ene

Cis–trans isomerism, also known as geometric isomerism, describes certain arrangements of atoms within molecules. The prefixes "cis" and "trans" are from Latin: "this side of" and "the other side of", respectively.[1] In the context of chemistry, cis indicates that the functional groups (substituents) are on the same side of some plane, while trans conveys that they are on opposing (transverse) sides. Cis–trans isomers are stereoisomers, that is, pairs of molecules which have the same formula but whose functional groups are in different orientations in three-dimensional space. Cis and trans isomers occur both in organic molecules and in inorganic coordination complexes. Cis and trans descriptors are not used for cases of conformational isomerism where the two geometric forms easily interconvert, such as most open-chain single-bonded structures; instead, the terms "syn" and "anti" are used.

According to IUPAC, "geometric isomerism" is an obsolete synonym of "cis–trans isomerism".[2]

Cis–trans or geometric isomerism is classified as one type of configurational isomerism.[3]

Organic chemistry

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Very often, cis–trans stereoisomers contain double bonds or ring structures. In both cases the rotation of bonds is restricted or prevented.[4] When the substituent groups are oriented in the same direction, the diastereomer is referred to as cis, whereas when the substituents are oriented in opposing directions, the diastereomer is referred to as trans. An example of a small hydrocarbon displaying cis–trans isomerism is but-2-ene. 1,2-Dichlorocyclohexane is another example.

trans-1,2-dichlorocyclohexane cis-1,2-dichlorocyclohexane

Comparison of physical properties

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Cis and trans isomers have distinct physical properties. Their differing shapes influences the dipole moments, boiling, and especially melting points.

cis-2-pentene trans-2-pentene
cis-1,2-dichloroethene trans-1,2-dichloroethene

These differences can be very small, as in the case of the boiling point of straight-chain alkenes, such as pent-2-ene, which is 37 °C in the cis isomer and 36 °C in the trans isomer.[5] The differences between cis and trans isomers can be larger if polar bonds are present, as in the 1,2-dichloroethenes. The cis isomer in this case has a boiling point of 60.3 °C, while the trans isomer has a boiling point of 47.5 °C.[6] In the cis isomer the two polar C–Cl bond dipole moments combine to give an overall molecular dipole, so that there are intermolecular dipole–dipole forces (or Keesom forces), which add to the London dispersion forces and raise the boiling point. In the trans isomer on the other hand, this does not occur because the two C−Cl bond moments cancel and the molecule has a net zero dipole moment (it does however have a non-zero quadrupole moment).

cis-butenedioic acid
(maleic acid)		 trans-butenedioic acid
(fumaric acid)
cis-9-octadecenoic acid
(oleic acid)		 trans-9-octadecenoic acid
(elaidic acid)

The differing properties of the two isomers of butenedioic acid are often very different.

Properties of isomers of cis- and trans-HO2CH=CHCO2H
maleic acid fumaric acid
color white white
melting point, °C 130 286
water solubility, g/L 788 7
Acid dissociation constant, pKa1 1.90 3.03

Polarity is key in determining relative boiling point as strong intermolecular forces raise the boiling point. In the same manner, symmetry is key in determining relative melting point as it allows for better packing in the solid state, even if it does not alter the polarity of the molecule. Another example of this is the relationship between oleic acid and elaidic acid; oleic acid, the cis isomer, has a melting point of 13.4 °C, making it a liquid at room temperature, while the trans isomer, elaidic acid, has the much higher melting point of 43 °C, due to the straighter trans isomer being able to pack more tightly, and is solid at room temperature.

Thus, trans alkenes, which are less polar and more symmetrical, have lower boiling points and higher melting points, and cis alkenes, which are generally more polar and less symmetrical, have higher boiling points and lower melting points.

In the case of geometric isomers that are a consequence of double bonds, and, in particular, when both substituents are the same, some general trends usually hold. These trends can be attributed to the fact that the dipoles of the substituents in a cis isomer will add up to give an overall molecular dipole. In a trans isomer, the dipoles of the substituents will cancel out [7] due to being on opposite sides of the molecule. Trans isomers also tend to have lower densities than their cis counterparts.[citation needed]

As a general trend, trans alkenes tend to have higher melting points and lower solubility in inert solvents, as trans alkenes, in general, are more symmetrical than cis alkenes.[8]

Vicinal coupling constants (3JHH), measured by NMR spectroscopy, are larger for trans (range: 12–18 Hz; typical: 15 Hz) than for cis (range: 0–12 Hz; typical: 8 Hz) isomers.[9]

Stability

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Usually for acyclic systems trans isomers are more stable than cis isomers. This difference is attributed to the unfavorable steric interaction of the substituents in the cis isomer. Therefore, trans isomers have a less-exothermic heat of combustion, indicating higher thermochemical stability.[8] In the Benson heat of formation group additivity dataset, cis isomers suffer a 1.10 kcal/mol stability penalty. Exceptions to this rule exist, such as 1,2-difluoroethylene, 1,2-difluorodiazene (FN=NF), and several other halogen- and oxygen-substituted ethylenes. In these cases, the cis isomer is more stable than the trans isomer.[10] This phenomenon is called the cis effect.[11]

E–Z notation

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Main article: E–Z notation
Bromine has a higher CIP priority than chlorine, so this alkene is the Z isomer

In principle, cis–trans notation should not be used for alkenes with two or more different substituents. Instead the E–Z notation is used based on the priority of the substituents using the Cahn–Ingold–Prelog (CIP) priority rules for absolute configuration. The IUPAC standard designations E and Z are unambiguous in all cases, and therefore are especially useful for tri- and tetrasubstituted alkenes to avoid any confusion about which groups are being identified as cis or trans to each other.

Z (from the German zusammen) means "together". E (from the German entgegen) means "opposed" in the sense of "opposite". That is, Z has the higher-priority groups cis to each other and E has the higher-priority groups trans to each other. Whether a molecular configuration is designated E or Z is determined by the CIP rules; higher atomic numbers are given higher priority. For each of the two atoms in the double bond, it is necessary to determine the priority of each substituent. If both the higher-priority substituents are on the same side, the arrangement is Z; if on opposite sides, the arrangement is E.

Because the cis–trans and E–Z systems compare different groups on the alkene, it is not strictly true that Z corresponds to cis and E corresponds to trans. For example, trans-2-chlorobut-2-ene (the two methyl groups, C1 and C4, on the but-2-ene backbone are trans to each other) is (Z)-2-chlorobut-2-ene (the chlorine and C4 are together because C1 and C4 are opposite).

Undefined alkene stereochemistry

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Wavy single bonds are the standard way to represent unknown or unspecified stereochemistry or a mixture of isomers (as with tetrahedral stereocenters). A crossed double-bond has been used sometimes; it is no longer considered an acceptable style for general use by IUPAC but may still be required by computer software.[12]

Alkene stereochemistry

Inorganic chemistry

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Cis–trans isomerism can also occur in inorganic compounds.

Diazenes

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Diazenes (and the related diphosphenes) can also exhibit cis–trans isomerism. As with organic compounds, the cis isomer is generally the more reactive of the two, being the only isomer that can reduce alkenes and alkynes to alkanes, but for a different reason: the trans isomer cannot line its hydrogens up suitably to reduce the alkene, but the cis isomer, being shaped differently, can.

trans-diazene cis-diazene

Coordination complexes

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Coordination complexes with octahedral or square planar geometries can also exhibit cis-trans isomerism.

The two isomeric complexes, cisplatin and transplatin

For example, there are two isomers of square planar Pt(NH3)2Cl2, as explained by Alfred Werner in 1893. The cis isomer, whose full name is cis-diamminedichloroplatinum(II), was shown in 1969 by Barnett Rosenberg to have antitumor activity, and is now a chemotherapy drug known by the short name cisplatin. In contrast, the trans isomer (transplatin) has no useful anticancer activity. Each isomer can be synthesized using the trans effect to control which isomer is produced.

cis-[Co(NH3)4 Cl2]+ and trans-[Co(NH3)4 Cl2]+

For octahedral complexes of formula MX4Y2, two isomers also exist. (Here M is a metal atom, and X and Y are two different types of ligands.) In the cis isomer, the two Y ligands are adjacent to each other at 90°, as is true for the two chlorine atoms shown in green in cis-[Co(NH3)4Cl2]+, at left. In the trans isomer shown at right, the two Cl atoms are on opposite sides of the central Co atom.

A related type of isomerism in octahedral MX3Y3 complexes is facial–meridional (or fac–mer) isomerism, in which different numbers of ligands are cis or trans to each other. Metal carbonyl compounds can be characterized as fac or mer using infrared spectroscopy.

See also

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References

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Revisions and contributorsEdit on WikipediaRead on Wikipedia

Cis–trans isomerism

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Cis–trans isomerism, also referred to as geometric isomerism, is a form of in which molecules exhibit different spatial arrangements of atoms or groups around a site of restricted , such as a carbon-carbon in alkenes or bonds in cyclic compounds and coordination complexes, resulting in distinct cis (substituents on the same side) and trans (substituents on opposite sides) configurations that are not superimposable. This phenomenon occurs when each atom involved in the restricted bond has two different substituents, preventing free and leading to stable, separable isomers with identical molecular formulas and connectivity but differing three-dimensional structures. The cis and trans isomers typically display significant differences in physical properties, including melting points, boiling points, , and moments, due to variations in and intermolecular forces; for example, trans isomers often have higher melting points and greater stability in non-polar environments compared to cis isomers. In , cis–trans isomerism is most prominently observed in alkenes like 2-butene, where the restricts rotation, and in cycloalkanes such as 1,2-dimethylcyclopropane, where enforces the geometric distinction. Beyond simple hydrocarbons, this isomerism extends to coordination compounds, particularly in square planar (e.g., (II) complexes) and octahedral (e.g., (III) complexes) geometries, where arrangements around the central metal ion yield cis and trans forms with distinct colors, reactivities, and biological activities. In biochemical contexts, cis–trans isomerism plays crucial roles in molecular recognition and function, such as in the of during vision, where the cis to trans switch triggers neural signals, and in peptide bonds involving , where cis configurations influence and enzymatic activity. These isomers can interconvert under specific conditions, like , light, or , which has applications in for designing switches and in for developing drugs with targeted stereospecific effects. Modern notation often employs the E/Z system based on Cahn-Ingold-Prelog priority rules for unambiguous designation, especially in complex molecules where cis/trans descriptors may be ambiguous.

Fundamentals

Definition and principles

Cis–trans isomerism, also known as geometric isomerism, refers to a type of in which molecules have the same molecular formula and connectivity of atoms but differ in the spatial arrangement of substituents due to restricted around certain bonds. This form of isomerism typically arises in compounds featuring carbon-carbon , where each carbon of the double bond bears two different substituents, or in cyclic structures, where the rigidity prevents free , leading to distinct cis and trans configurations. In the cis isomer, the substituents of interest are located on the same side of the bond or plane, whereas in the trans isomer, they are on opposite sides. The underlying principle is the restricted rotation caused by the pi bond in a carbon-carbon double bond (C=C), which overlaps sideways between the p orbitals of the adjacent carbons, creating a barrier to that requires breaking the pi bond to overcome. Similarly, in cyclic compounds, the ring structure imposes geometric constraints that limit positions, mimicking the effect of restricted . These cis and trans isomers are configurational stereoisomers, meaning interconversion between them necessitates breaking and reforming bonds, unlike conformational isomers that can interconvert by around single bonds. A classic example is 2-butene (C₄H₈), where the between the second and third carbon atoms allows for cis and trans forms. In cis-2-butene, the two methyl groups (–CH₃) are on the same side of the , resulting in a structure where the molecule is more compact; in trans-2-butene, the methyl groups are on opposite sides, leading to a more extended arrangement. These can be represented as: For cis-2-butene:
CH₃–CH=CH–CH₃ (methyl groups same side) For trans-2-butene:
CH₃–CH=CH–CH₃ (methyl groups opposite sides) This isomerism was first systematically described in 1874 by Jacobus Henricus van 't Hoff in his work La Chimie dans l'Espace, where he introduced the concepts of spatial arrangements around double bonds and rings as part of the foundational development of stereochemistry.

Relation to stereoisomerism

Stereoisomerism refers to a form of isomerism in which molecules possess the same molecular formula and connectivity of atoms but differ in the spatial arrangement of their atoms. According to IUPAC definitions, stereoisomers are isomers that have identical constitutions but differ in the arrangement of their atoms in space. This contrasts with constitutional isomerism, where isomers differ in the connectivity or bonding sequence of atoms, such as in the case of ethanol (CH₃CH₂OH) and dimethyl ether (CH₃OCH₃). Stereoisomers are broadly classified into two main categories: enantiomers and diastereomers. Enantiomers are pairs of stereoisomers that are non-superimposable mirror images of each other, often exhibiting optical activity. Diastereomers, on the other hand, are stereoisomers that are not mirror images and thus possess different physical and chemical properties. Cis-trans isomers fall under the category of diastereomers because they arise from restricted rotation around double bonds or in ring structures, leading to distinct spatial configurations that are not mirror images. It is important to distinguish stereoisomerism, including cis-trans isomerism, from conformational isomerism. Conformational isomers differ only in the rotation about single bonds and can interconvert readily at without breaking bonds, whereas cis-trans isomers require bond breakage or high energy to interconvert due to their configurational nature. Cis-trans isomerism represents a specific subset of geometric isomerism, a type of characterized by differences in the spatial orientation of substituents due to restricted rotation; geometric isomerism can also encompass cases of , such as in or biphenyls, though the focus here is on cis-trans configurations. Unlike enantiomers, which are chiral and rotate plane-polarized light, cis-trans isomers are typically achiral and do not exhibit optical activity unless they incorporate additional chiral centers. For example, both cis- and trans-1,4-dichlorocyclohexane possess a plane of , rendering them achiral. This achirality stems from the symmetric arrangement possible in their configurations, distinguishing them further from other stereoisomeric forms.

Organic Chemistry

Alkenes

Cis–trans isomerism in alkenes occurs due to the restricted around the carbon-carbon , which is composed of one and one . The arises from the sideways overlap of p orbitals on adjacent carbon atoms, creating above and below the plane of the that resists and maintains the of the substituents. This restricted leads to two possible geometric s when the conditions for isomerism are met: the cis isomer, where similar substituents are on the same side of the , and the trans isomer, where they are on opposite sides. For cis–trans isomerism to be possible in an alkene, each carbon atom of the double bond must be bonded to two different substituents; if either carbon has two identical substituents, the molecule lacks distinct geometric forms. A representative example is 2-butene (molecular formula C₄H₈), in which the double bond is between the second and third carbon atoms, with methyl groups (-CH₃) and hydrogen atoms as substituents. In cis-2-butene, the two methyl groups are positioned on the same side of the double bond, resulting in greater proximity between them, whereas in trans-2-butene, the methyl groups are on opposite sides, increasing their separation. Another key example is butenedioic acid (molecular formula C₄H₄O₄), where maleic acid represents the cis isomer and fumaric acid the trans isomer; in maleic acid, the two carboxylic acid groups (-COOH) are on the same side of the C=C bond, while in fumaric acid, they are trans to each other. One common method to synthesize exhibiting cis–trans is the partial of alkynes, where the addition of can be controlled to produce either isomer depending on the catalyst used. For instance, Lindlar's catalyst—a on poisoned with lead and —facilitates syn addition of to yield the cis selectively. In general, trans alkenes are more stable than their cis counterparts owing to reduced steric hindrance between substituents, which minimizes repulsive interactions in the trans configuration.

Cyclic compounds

Cis–trans isomerism occurs in cyclic organic compounds, particularly disubstituted cycloalkanes, where the ring restricts and fixes the relative positions of substituents. In such molecules, the cis configuration places both substituents on the same side of the average plane of the ring, while the trans configuration positions them on opposite sides. This is a consequence of the cyclic framework's inability to undergo bond like acyclic alkanes, leading to distinct, non-superimposable . For example, 1,2-dimethylcyclohexane exhibits this behavior, with the cis isomer having both methyl groups adjacent (up-up or down-down relative to the ring) and the trans isomer having them opposite (up-down). The feasibility and stability of cis and trans isomers depend on due to variations in strain and flexibility. In small rings like , the nearly planar structure allows both cis and trans 1,2-disubstituted isomers, but the trans form is highly strained because the substituents on opposite faces distort the equilateral geometry. thus supports cis isomers more readily, with trans variants requiring significant angle and torsional strain. In contrast, for rings with seven or more members, both configurations are more accessible. A representative example is 1,2-dichlorocyclohexane, where the ring adopts a conformation that highlights the stereochemical differences. In the cis isomer, the two atoms occupy one axial and one equatorial position, enabling rapid ring flipping between two identical conformers. The trans isomer, however, prefers the diequatorial arrangement for minimal steric hindrance, with the alternative diaxial form being higher in energy due to 1,3-diaxial interactions. These axial/equatorial distinctions arise from the puckered ring geometry and underscore how cis–trans influences conformational preferences. In natural products such as , cis–trans isomerism is critical at ring fusion points, where trans junctions predominate for stability. For instance, in and other steroid hormones, the B/C and C/D ring fusions are typically trans, enhancing the molecule's planar rigidity and facilitating receptor binding, while the A/B fusion can be either cis or trans depending on the specific compound. Fundamentally, this isomerism in cyclic compounds stems from the substituents' fixed orientations relative to the ring plane, distinguishing it as a form of geometric without involving double bonds.

Physical properties

Cis–trans isomers of organic compounds exhibit distinct physical properties arising from differences in molecular polarity, shape, and intermolecular interactions. Cis isomers typically possess higher dipole moments due to the alignment of substituents on the same side of the or ring, leading to greater overall polarity compared to trans isomers, where substituents are on opposite sides. This polarity influences several measurable properties, including and points, , , and spectroscopic signatures. Boiling points are generally higher for cis isomers because their increased polarity enhances dipole-dipole interactions, requiring more to separate molecules in the liquid phase. For example, in 2-butene, the cis isomer has a of 3.7 °C, while the trans isomer boils at 0.9 °C. Similarly, melting points can differ markedly; (cis-butenedioic acid) melts at 130 °C, whereas its trans counterpart, , has a much higher melting point of 287 °C, attributed to the trans isomer's more symmetrical structure facilitating stronger crystal lattice packing. Solubility patterns reflect the polarity trend, with cis isomers showing greater solubility in polar solvents like due to better solvation of their dipole moments. , for instance, exhibits higher solubility (up to 392.6 g/100 g at 100 °C) than , which is sparingly soluble under similar conditions. In , cis and trans isomers display characteristic differences. (IR) spectra of cis isomers often show stronger absorption for the C=C stretching vibration (around 1650–1680 cm⁻¹) because the change in dipole moment during vibration is larger than in trans isomers, where reduces intensity. (NMR) spectra reveal variations in chemical shifts and coupling constants; for instance, vicinal protons in trans isomers typically exhibit larger ³J_HH coupling constants (12–18 Hz) compared to cis (6–12 Hz), aiding isomer identification. Density is usually higher for cis isomers owing to their more compact molecular shape, which allows closer packing. In 2-butene, the cis form has a liquid of 0.621 g/cm³ at 20 °C, exceeding the trans value of 0.604 g/cm³.

Stability

In cis–trans isomerism, trans isomers are generally more stable than their cis counterparts due to reduced steric repulsion between substituents on the same side of the or in cyclic structures. This energetic preference typically ranges from 1 to 5 kcal/mol, as determined by conformational in systems like disubstituted cyclohexanes, where A-values quantify the energy cost of axial positions leading to steric interactions in cis configurations. The primary factor influencing this stability is steric hindrance, which is more pronounced in cis isomers where substituents are closer together, increasing nonbonding interactions. For example, in cis-1,2-dimethylcyclopropane, the methyl groups on the same face of the strained ring exacerbate crowding, making the cis form less stable than the trans by several kcal/mol, as evidenced by data. Electronic effects can also play a role in conjugated systems, where trans configurations often allow better orbital overlap for π-delocalization, further favoring their stability over cis forms with potential misalignment. A quantitative illustration comes from the heats of hydrogenation of 2-butene isomers: the cis isomer releases 28.6 kcal/mol upon hydrogenation to , while the trans releases only 27.6 kcal/mol, indicating the trans is more stable by approximately 1 kcal/mol due to lower ground-state energy from minimized steric strain. Exceptions occur in small rings or with polar substituents, where cis isomers can be stabilized. In cycloalkenes with fewer than 11 members, cis isomers are more stable than trans due to the severe imposed by a trans , which distorts the geometry. Similarly, polar groups like hydroxyls in cis-1,2-cyclopentanediol can enable intramolecular , offsetting steric costs and enhancing cis stability relative to trans in such compact systems. This stability difference significantly impacts reaction selectivity, as seen in , where catalysts preferentially form trans products under thermodynamic control, influencing the stereochemical outcome of polymerizations and cross-metathesis reactions.

Nomenclature

Cis–trans designation

The cis–trans designation is a traditional for geometric isomers in organic compounds where rotation around a bond is restricted, such as in alkenes and cyclic structures. Under this system, the prefix "cis-" (from Latin cis, meaning "on this side") is used when the two similar substituents are located on the same side of the reference plane—typically the plane defined by the carbon-carbon in alkenes or the average plane of the ring in cyclic compounds—while "trans-" (from Latin trans, meaning "across" or "on the other side") applies when the substituents are on opposite sides of that plane. This descriptive approach relies on visual and is straightforward for symmetric disubstituted cases, where each carbon atom involved in the restricted bond bears one and one substituent group. This nomenclature was introduced in the 19th century as a simple method to distinguish configurations in early studies of geometric isomerism, particularly for symmetric molecules, and remains useful for educational and basic descriptive purposes in disubstituted systems. It applies to alkenes like 2-pentene, where cis-2-pentene features the methyl group and the ethyl chain on the same side of the double bond, contrasting with the trans isomer where they are on opposite sides. In cyclic compounds, such as cyclobutane derivatives, the designation is used relative to the ring plane; for instance, trans-1,3-dimethylcyclobutane has the two methyl groups positioned on opposite faces of the four-membered ring, leading to a more extended conformation compared to the cis isomer. A classic example is stilbene (1,2-diphenylethene), where cis-stilbene has the two phenyl groups on the same side of the central , resulting in a bent structure with closer phenyl-phenyl proximity, while trans-stilbene has them on opposite sides, yielding a more linear and stable arrangement. In line-angle notation, cis-stilbene is represented with both phenyl rings attached to the same side of the C=C bond (like two flags on the same post), whereas trans-stilbene shows them on opposing sides (flags on opposite posts). This isomerism highlights the convention's utility in symmetric diarylalkenes. The cis–trans system has limitations, as it is only reliable for 1,2-disubstituted alkenes or cycles with identical substituents on each relevant carbon, failing in trisubstituted or tetrasubstituted alkenes where substituent priorities differ and "same side" becomes ambiguous without additional rules. For example, in 1-bromo-1-chloro-2-methylpropene, assigning cis or trans is unclear because the substituents on one carbon ( and ) are not equivalent to those on the other (methyl and ). Such cases require more rigorous priority-based methods for unambiguous naming.

E–Z notation

The , recommended by the International Union of Pure and Applied Chemistry (IUPAC) for specifying the of double bonds in alkenes, relies on the Cahn–Ingold–Prelog (CIP) priority rules to assign configurations unambiguously. These rules, developed to describe molecular systematically, evaluate the substituents attached to each carbon atom of the by comparing their atomic numbers starting from the atom directly bonded to the double-bonded carbon. To determine priorities, the with the higher at the first point of difference is ranked higher; if atomic numbers are tied, the comparison proceeds to the next set of attached atoms, treating branches as duplicated or phantom atoms to resolve ties, and continuing outward until a difference is found. For instance, in a carbon–carbon , a (atomic number 35) outranks a (atomic number 17), which in turn outranks a (starting with carbon, atomic number 6). This hierarchical ranking ensures a clear high-priority and low-priority group on each side of the double bond. Once priorities are assigned, the configuration is labeled Z (from the German zusammen, meaning "together") if the two high-priority substituents are on the same side of the double bond, and E (from entgegen, meaning "opposite") if they are on opposite sides; the double bond is visualized in a plane with substituents above or below it for assignment. For example, in but-2-ene (CH₃–CH=CH–CH₃), the methyl groups have higher priority than the hydrogens on each carbon, so the with methyls on opposite sides is (E)-but-2-ene, equivalent to the traditional trans form, while methyls on the same side yield (Z)-but-2-ene, the cis form. Another case is 1-bromo-2-chloroethene (BrHC=CHCl), where has higher priority than on one carbon and higher than on the other; the Z places Br and Cl on the same side. The E–Z system offers a precise alternative to cis–trans nomenclature, particularly for alkenes where the two substituents on at least one carbon of the double bond differ, rendering relative descriptors ambiguous. It was introduced within the CIP framework in the 1960s to address such complexities and formally adopted by IUPAC in the late 1970s as the standard for stereodescriptors in organic nomenclature, ensuring consistency across diverse molecular structures.

Ambiguous cases

Cis–trans notation encounters ambiguity in alkenes where the substituents on each carbon of the double bond are not identical, particularly in trisubstituted or tetrasubstituted cases, as there is no clear definition of "same side" for all groups. For instance, in 2-pentene, one carbon of the double bond bears a methyl group and a hydrogen, while the other bears an ethyl group and a hydrogen; labeling the isomer where the methyl and ethyl are on the same side as "cis" is arbitrary, since it could alternatively refer to the hydrogens being cis. Similarly, in tetrasubstituted alkenes where the substituents on each carbon differ, such as 1,2-dichloro-1,2-difluoroethene ((Cl)(F)C=C(Cl)(F)), cis–trans descriptors fail because no pairs of identical substituents exist to define relative positions unambiguously, and priorities must be considered. In contrast, symmetric disubstituted alkenes such as 3-hexene allow straightforward cis–trans assignment, where the ethyl groups can be clearly on the same or opposite sides, corresponding to (Z)-3-hexene and (E)-3-hexene, respectively. To resolve these issues, the IUPAC recommends using exclusively for alkenes in formal nomenclature, as it relies on to unambiguously assign configurations regardless of substituent identity. Cis–trans descriptors are retained only for educational purposes in simple, symmetric disubstituted cases like 2-butene, but their use in publications is discouraged to avoid confusion. In cyclic compounds, cis–trans notation remains applicable for simple disubstituted rings where substituents are on the same or opposite faces, without priority conflicts, such as in 1,2-dimethylcyclohexane. However, for fused ring systems with stereogenic double bonds or complex substituent arrangements, is preferred to handle potential priority ambiguities. In chemical databases, undefined or ambiguous stereochemistry is often marked as "undesignated" or "unspecified" to prevent erroneous assignments and ensure accurate representation of molecular structures.

Inorganic Chemistry

Diazenes

Diazenes, compounds featuring an N=N bond, exhibit cis–trans isomerism analogous to that in alkenes, arising from restricted around the partial double bond due to its sp²-hybridized atoms. This leads to two geometric isomers: the trans (E) form, where substituents are on opposite sides of the N=N bond, and the cis (Z) form, where they are on the same side, resulting in a more . A prototypical example is (C₆H₅–N=N–C₆H₅), where the trans isomer adopts a planar configuration with the phenyl rings trans to each other, while the cis isomer twists out of plane with a CNNC of approximately 180° reduced to near 0° across the bond. The trans isomer of azobenzene is thermodynamically more stable than the cis form by about 12 kcal/mol, rendering the trans configuration predominant under equilibrium conditions at room temperature. The trans-azobenzene displays a red-orange color due to its extended conjugation, whereas the cis isomer is pale yellow and less conjugated owing to its bent structure. The energy barrier to thermal rotation around the N=N bond is high, approximately 20–30 kcal/mol, preventing facile interconversion in the ground state and stabilizing the isomers. Isomerization in diazenes like is highly efficient under photochemical conditions: irradiation with ultraviolet light (around 320–350 nm) excites the trans isomer to its S₁ state, facilitating rapid conversion to the cis form via torsional motion or inversion with a low barrier of ~23 kcal/mol in the excited state. The reverse cis-to-trans process occurs thermally with an of about 25.8 kcal/mol or upon visible light absorption, restoring the stable trans geometry. This reversible photo-thermal switching is represented as: trans-azobenzene→hν (UV)cis-azobenzene→Δtrans-azobenzene\text{trans-azobenzene} \xrightarrow{h\nu \ (UV)} \text{cis-azobenzene} \xrightarrow{\Delta} \text{trans-azobenzene}
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