Descriptor (chemistry)

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In chemical nomenclature, a descriptor is a notational prefix placed before the systematic substance name, which describes the configuration or the stereochemistry of the molecule. [1] Some of the listed descriptors should not be used in publications, as they no longer accurately correspond with the recommendations of the IUPAC. Stereodescriptors are often used in combination with locants to clearly identify a chemical structure unambiguously.

Contents

The descriptors, usually placed at the beginning of the systematic name, are not taken into account in the alphabetical sorting.

Configuration descriptors

cis, trans

See: cis–trans isomerism

cis (left) and trans (right) configured double bound: maleic acid and fumaric acid Maleinsaure Fumarsaure EZ.svg
cis (left) and trans (right) configured double bound: maleic acid and fumaric acid
cis (left) and trans isomerism (right) in a ring system. Dimethylcyclopentan cis-trans.svg
cis (left) and trans isomerism (right) in a ring system.

The descriptors cis (lat. on this side of) [2] and trans (lat. over, beyond) [3] are used in various contexts for the description of chemical configurations: [4] [5]

In organic structural chemistry, the configuration of a double bond can be described with cis and trans, in case it has a simple substitution pattern with only two residues. The position of two residues relative to one another at different points in a ring system or a larger molecule can also be described with cis and trans if the structure's configuration is rigid and does not allow simple inversion.

In inorganic complex chemistry, the descriptors cis and trans are used to characterize the positional isomers in octahedral complexes with A2B4X configuration or square planar complexes with A2B2X configuration.

The typographic presentation of cis and trans is italicised and in lower case letters.

The cis/trans nomenclature is not unambiguous for more highly substituted double bonds and is nowadays largely replaced by the (E)/(Z) nomenclature. [6]

(E), (Z)

See: E-Z notation

Violet leaf aldehyde, systematic name (E,Z)-nona-2,6-dienal, is a compound having one (E)- and one (Z)-configured double bond Violet leaf aldehyde.svg
Violet leaf aldehyde, systematic name (E,Z)-nona-2,6-dienal, is a compound having one (E)- and one (Z)-configured double bond

The descriptors (E) (from German entgegen, opposite) and (Z) (from German zusammen, together) are used to provide a distinct description of the substitution pattern for alkenes, cumulenes or other double bond systems such as oximes. [7]

For the attribution of (E) or (Z) is based on the relative position of the two substituents of highest priority are on each side of the double bond, while the priority is based on the CIP nomenclature. The (E)/(Z) nomenclature can be applied to any double bond systems (including heteroatoms), but not to substituted ring systems. The descriptors (E) and (Z) are always capitalized, set italic, and surrounded by parentheses that are set as normal just like additional locants or commas.

o-, m-, p-

See: Arene substitution pattern

O-Kresol.svg M-Kresol.svg P-Kresol.svg
o-Cresol m-Cresol p-Cresol

The abbreviation o- (short for ortho, from Greek orthós for upright, straight), [8] m- (meta, Greek (roughly) for between) [9] and p- (para, from Greek pará for adjoining, to the side) [10] describe the three possible positional isomers of two substituents on a benzene ring. These are usually two independent single substituents, but in case of fused ring systems, ortho-fusing is also mentioned unless the substitution pattern is regarded in the name like in [2.2]paracyclophane. In the current systematic nomenclature, o-, m- and p- are often replaced by using locants (1,2-dimethylbenzene instead of o-xylene).

o-, m- and p- (written out ortho-, meta- and para-) are written in lowercase letters and italic.

exo, endo

See: Endo-exo isomerism

2-endo-bromo-7-syn-fluoro-bicyclo(2.2.1)heptane.svg 2-exo-bromo-7-syn-fluoro-bicyclo(2.2.1)heptane.svg
2-endo-bromo-7-syn-fluoro-
bicyclo[2.2.1]heptane
2-exo-bromo-7-syn-fluoro-
bicyclo[2.2.1]heptane
2-endo-bromo-7-anti-fluoro-bicyclo(2.2.1)heptane.svg 2-exo-bromo-7-anti-fluoro-bicyclo(2.2.1)heptane.svg
2-endo-bromo-7-anti-fluoro-
bicyclo[2.2.1]heptane
2-exo-bromo-7-anti-fluoro-
bicyclo[2.2.1]heptane

exo (from Greek = outside) [11] or endo (from Greek endon = inside) [12] denotes the relative configuration of bridged bicyclic compounds. The position of a substituent in the main ring relative to the shortest bridge is decisive for the assignment of exo or endo (according to IUPAC: the bridge with the highest locant digits [13] in the bridged ring system). The substituent to be classified is attributed with the exo descriptor when facing the bridge. It is endo configured when facing away from the bridge. If two different substituents are located on the same C atom, the exo/endo assignment is based on the substituent with higher priority according to the CIP rules.

syn, anti

If a bridged bicyclic system carries a substituent at the shortest bridge, the exo or endo descriptor can not be used for its assignment. Such isomers are classified by the syn/anti notation. [13] If the substituent to be assigned points towards the ring with the highest number of segments it is syn configured (from Greek syn = together). [14] Otherwise it is attributed with the anti descriptor (Greek anti = against). [15] If both rings possess an equal number of segments the ring with the most significant substituent according to the CIP rules is chosen.

Isomerie der Aldoxime: links ein fruher als syn-, heute als (E)-konfiguriert zu beschreibendes Aldoxim, rechts das entsprechende (Z)- (veraltet: anti)-Isomer. Aldoximes General Formulae.png
Isomerie der Aldoxime: links ein früher als syn-, heute als (E)-konfiguriert zu beschreibendes Aldoxim, rechts das entsprechende (Z)- (veraltet: anti)-Isomer.

The use of syn and anti to indicate the configuration of double bonds is nowadays obsolete, especially in case of aldoximes and hydrazones derived from aldehydes. Here, the compounds were designated as syn configured when the aldehyde H and the O (of the oxime) or the N (of the hydrazone) were cis aligned. These compounds are now described by the (E)/(Z) nomenclature. Aldoximes and hydrazones classified as syn are therefore by now described as (E) configurated. [14]

When talking of diastereomers, syn and anti are used to describe groups on the same or opposite sites in zigzag prijection, see Diastereomer#Syn / anti

syn and anti are always written small and italic, locants (if used) are placed in front of the word and separated by hyphens.

fac, mer

The terms fac (from Latin facies) [16] and mer (from meridonal) [17] can specify the arrangement of three identical ligands around the central atom in octahedral complexes. Today, this nomenclature is considered obsolete, but is still permissible. [18] [19] The prefix fac describes the situation when the three identical ligands occupy the three vertices of an octahedron triangular surface. In mer configuration the three ligands span a plane in which the central atom is located.

fac and mer are prefixed in small and italic to the complex name.

n, iso, neo, cyclo

The prefixes n (normal), iso (from Greek ísos = equal), [20] neo (Greek néos = young, new) [21] and cyclo (Greek kyklos = circle) [22] are primarily used to describe the arrangement of atoms, usually of carbon atoms in carbon skeleton. n, iso and neo are no longer used in the systematic nomenclature, but still frequently in trivial names and in laboratory jargon.

The prefix n describes a straight-chain carbon skeleton without branches, whereas iso describes a branched skeleton, without specifying any further details. More generally, iso is a compound which is isomeric to the n compound (a compound in which individual atoms or atomic groups are rearranged)

neo is a non-specific term for "new", usually synthetically produced substances or isomers of long-known n compounds or natural substances (for example neomenthol derived from menthol or neoabietic acid from abietic acid). According to IUPAC neo is only recommended in neopentane or the neopentyl residue. [23] [24]

cyclo is a frequently used prefix for all cyclic and heterocyclic compounds. In many proper names of chemical substances cyclo is not used as a prefix but directly part of the name, for example in cyclohexane or cyclooctatetraene.

While n, iso and neo are written in small and italic letters, for cyclo this is only the case in inorganic compounds. [25] In organic compounds, "cyclo" is frequently used as a name component, not separated by a hyphen and also considered in alphabetical sorting.

sec-, tert-

The prefixes sec and tert are used to indicate the substituent environment in a molecule. Thus, not the exact position of the substituent is described but only the substitution pattern of the adjacent atom (usually a carbon atom). In n-butanol, the OH group is attached to a primary carbon atom, in sec-butanol to a secondary carbon and in tert-butanol to a tertiary carbon atom.

The terms sec and tert are considered obsolete and should only be used for unsubstituted sec-butoxy, sec-butyl [26] [27] or tert-butyl groups. [28] [27] There are various spellings such as "sec-butyl", "s-butyl", "sBu" or "bus" which are also considered obsolete. [29] [30]

spiro

Spiro[4.5]decane Spiro-4.5-decane V.1.svg
Spiro[4.5]decane

The prefix "spiro" followed by a Von-Baeyer descriptor describes in the nomenclature of organic compounds ring systems linked by only one common atom, the spiro atom. If several spiro atoms are present in the molecule, the prefix "spiro" is provided with a prefix ("dispiro", "trispiro", etc.) corresponding to the number of spiro atoms. Typically "spiro" is set as normal. [31]

catena

The term catena is used in the inorganic nomenclature [32] to describe linear, chain-like polymers from identical polyatomic units. [33] One example is are catenatriphosphazenes. [34] [35] Related compounds in organic chemistry are the catenanes.

sn

The notation sn stands for stereospecific numbering, and indicates a particular way of numbering the carbon atoms in a molecule based on glycerol.

Stereodescriptors of absolute configurations

(R), (S)

See: Cahn–Ingold–Prelog priority rules

Configuration assignment of the stereo center "X", the substituents are decreasingly prioritized from "A" - "D" according to the CIP rules. R S configuration.png
Configuration assignment of the stereo center "X", the substituents are decreasingly prioritized from "A" → "D" according to the CIP rules.

The stereochemical descriptors (R) (from Latin rectus = right) and (S) (from lat. sinister = left) [36] are used to describe the absolute configuration of a stereocenter (usually a chiral carbon atom). [37] For this purpose, all substituents at the stereocentre are prioritized according to the CIP rules and the substituent with the lowest priority ("D") is pointed backwards (away from the viewing direction). The stereocenter is (S) configured if the remaining substituents describe a circle descending in priority ("A" → "B" → "C") to the left. The (R) configuration is assigned to the stereocenter if the direction of rotation is directed to the right.

If one molecule contains several stereocenters, a locant must be placed before the descriptor (for example, in (1R, 2S)-2-amino-1-phenylpropan-1-ol, the systematic designation of norephedrine). If all stereocenters are configured the same, the naming of the locants can be omitted in favor of an "all-R" or "(all-S)" spelling.

Typographically, (R) and (S) are placed in uppercase and italic; the frequently preceding locants, the enclosing round brackets and the commas, on the other hand, as normal.

(r), (s)

Example molecules having pseudoasymmetric atoms
(1R,2s,3S)-1,2,3-trichlorocyclopentane.svg
All-cis 1,2,3-trichlorocyclopentane

The descriptors (r) and (s) are used to describe the absolute configuration of pseudoasymmetric centers. [38] Pseudoasymmetry occurs when four different substituents are attached to one carbon atom, two of which differ only by their absolute stereochemical configuration. Examples of such are meso compounds such the tropane alkaloids; the parent compound is tropine, whose systematic name is (1R, 3r, 5S)-8-methyl-8-azabicyclo[3.2.1]octane-3-ol. In this structure, the C3 atom—the carbon to which the hydroxyl group is attached—is pseudo-asymmetric; therefore, the stereochemical descriptor in the systematic name is written in lower-case italics rather than upper-case italics as for regular chiral atoms.

D-, L-

See: Fischer projection

The stereoscriptors D- (from Latin dexter, right) and L- (Latin laevus, left) are used to describe the configuration of α-amino acids and sugars. [39] First, the three-dimensional molecule must be transformed in a defined notation as a two-dimensional image ("Fischer projection"). [40] For this, the C atom with the highest priority according to the normal nomenclature rules is arranged on top and the further carbon chain is arranged vertically underneath. The chiral C-atom most remote from the group with the highest priority is used for the assignment of D- or L-. If the residue located on this carbon atom (usually an OH group) points to the left, the molecule originates from the L-series. If the residue points to the right, the descriptor D- is used. [41]

The descriptors D- and L- are written as small capitals and separated by a hyphen from the rest of the name. [42]

d-, l-

Sometimes the small capital D- and L- stereodescriptors mentioned above are mistakenly confused with the obsolete italic d- and l- stereodescriptors, which are equivalent with dextrorotatory and levorotatory optical rotation, i.e. (+)- and (−)- stereodescriptors, respectively.

Related Research Articles

<span class="mw-page-title-main">Cahn–Ingold–Prelog priority rules</span> Naming convention for stereoisomers of molecules

In organic chemistry, the Cahn–Ingold–Prelog (CIP) sequence rules are a standard process to completely and unequivocally name a stereoisomer of a molecule. The purpose of the CIP system is to assign an R or S descriptor to each stereocenter and an E or Z descriptor to each double bond so that the configuration of the entire molecule can be specified uniquely by including the descriptors in its systematic name. A molecule may contain any number of stereocenters and any number of double bonds, and each usually gives rise to two possible isomers. A molecule with an integer n describing the number of stereocenters will usually have 2n stereoisomers, and 2n−1 diastereomers each having an associated pair of enantiomers. The CIP sequence rules contribute to the precise naming of every stereoisomer of every organic molecule with all atoms of ligancy of fewer than 4.

<i>Cis</i>–<i>trans</i> isomerism Pairs of molecules with same chemical formula showing different spatial orientations

Cistrans 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. 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. Cistrans 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.

<span class="mw-page-title-main">Stereoisomerism</span> When molecules have the same atoms and bond structure but differ in 3D orientation

In stereochemistry, stereoisomerism, or spatial isomerism, is a form of isomerism in which molecules have the same molecular formula and sequence of bonded atoms (constitution), but differ in the three-dimensional orientations of their atoms in space. This contrasts with structural isomers, which share the same molecular formula, but the bond connections or their order differs. By definition, molecules that are stereoisomers of each other represent the same structural isomer.

<span class="mw-page-title-main">Cycloalkane</span> Saturated alicyclic hydrocarbon

In organic chemistry, the cycloalkanes are the monocyclic saturated hydrocarbons. In other words, a cycloalkane consists only of hydrogen and carbon atoms arranged in a structure containing a single ring, and all of the carbon-carbon bonds are single. The larger cycloalkanes, with more than 20 carbon atoms are typically called cycloparaffins. All cycloalkanes are isomers of alkenes.

In organic chemistry, an alkyl group is an alkane missing one hydrogen. The term alkyl is intentionally unspecific to include many possible substitutions. An acyclic alkyl has the general formula of −CnH2n+1. A cycloalkyl group is derived from a cycloalkane by removal of a hydrogen atom from a ring and has the general formula −CnH2n−1. Typically an alkyl is a part of a larger molecule. In structural formulae, the symbol R is used to designate a generic (unspecified) alkyl group. The smallest alkyl group is methyl, with the formula −CH3.

In chemical nomenclature, the IUPAC nomenclature of organic chemistry is a method of naming organic chemical compounds as recommended by the International Union of Pure and Applied Chemistry (IUPAC). It is published in the Nomenclature of Organic Chemistry. Ideally, every possible organic compound should have a name from which an unambiguous structural formula can be created. There is also an IUPAC nomenclature of inorganic chemistry.

<span class="mw-page-title-main">Diastereomer</span> Molecules which are non-mirror image, non-identical stereoisomers

In stereochemistry, diastereomers are a type of stereoisomer. Diastereomers are defined as non-mirror image, non-identical stereoisomers. Hence, they occur when two or more stereoisomers of a compound have different configurations at one or more of the equivalent (related) stereocenters and are not mirror images of each other. When two diastereoisomers differ from each other at only one stereocenter, they are epimers. Each stereocenter gives rise to two different configurations and thus typically increases the number of stereoisomers by a factor of two.

<span class="mw-page-title-main">Chirality (chemistry)</span> Geometric property of some molecules and ions

In chemistry, a molecule or ion is called chiral if it cannot be superposed on its mirror image by any combination of rotations, translations, and some conformational changes. This geometric property is called chirality. The terms are derived from Ancient Greek χείρ (cheir) 'hand'; which is the canonical example of an object with this property.

In the nomenclature of organic chemistry, a locant is a term to indicate the position of a functional group or substituent within a molecule.

<span class="mw-page-title-main">Axial chirality</span> Type of symmetry in molecules

In chemistry, axial chirality is a special case of chirality in which a molecule contains two pairs of chemical groups in a non-planar arrangement about an axis of chirality so that the molecule is not superposable on its mirror image. The axis of chirality is usually determined by a chemical bond that is constrained against free rotation either by steric hindrance of the groups, as in substituted biaryl compounds such as BINAP, or by torsional stiffness of the bonds, as in the C=C double bonds in allenes such as glutinic acid. Axial chirality is most commonly observed in substituted biaryl compounds wherein the rotation about the aryl–aryl bond is restricted so it results in chiral atropisomers, as in various ortho-substituted biphenyls, and in binaphthyls such as BINAP.

In organic chemistry, syn- and anti-addition are different ways in which substituent molecules can be added to an alkene or alkyne. The concepts of syn and anti addition are used to characterize the different reactions of organic chemistry by reflecting the stereochemistry of the products in a reaction.

Arene substitution patterns are part of organic chemistry IUPAC nomenclature and pinpoint the position of substituents other than hydrogen in relation to each other on an aromatic hydrocarbon.

<span class="mw-page-title-main">Prochirality</span> Ability of an achiral molecule to be made chiral in one step

In stereochemistry, prochiral molecules are those that can be converted from achiral to chiral in a single step. An achiral species which can be converted to a chiral in two steps is called proprochiral.

In organic chemistry, endoexo isomerism is a special type of stereoisomerism found in organic compounds with a substituent on a bridged ring system. The prefix endo is reserved for the isomer with the substituent located closest, or "syn", to the longest bridge. The prefix exo is reserved for the isomer with the substituent located farthest, or "anti", to the longest bridge. Here "longest" and "shortest" refer to the number of atoms that comprise the bridge. This type of molecular geometry is found in norbornane systems such as dicyclopentadiene.

<span class="mw-page-title-main">Hapticity</span> Number of contiguous atoms in a ligand that bond to the central atom in a coordination complex

In coordination chemistry, hapticity is the coordination of a ligand to a metal center via an uninterrupted and contiguous series of atoms. The hapticity of a ligand is described with the Greek letter η ('eta'). For example, η2 describes a ligand that coordinates through 2 contiguous atoms. In general the η-notation only applies when multiple atoms are coordinated. In addition, if the ligand coordinates through multiple atoms that are not contiguous then this is considered denticity, and the κ-notation is used once again. When naming complexes care should be taken not to confuse η with μ ('mu'), which relates to bridging ligands.

<span class="mw-page-title-main">Absolute configuration</span> Stereochemistry term

Absolute configuration refers to the spatial arrangement of atoms within a chiral molecular entity and its resultant stereochemical description. Absolute configuration is typically relevant in organic molecules where carbon is bonded to four different substituents. This type of construction creates two possible enantiomers. Absolute configuration uses a set of rules to describe the relative positions of each bond around the chiral center atom. The most common labeling method uses the descriptors R or S and is based on the Cahn–Ingold–Prelog priority rules. R and S refer to rectus and sinister, Latin for right and left, respectively.

In chemical nomenclature, nor- is a prefix to name a structural analog that can be derived from a parent compound by the removal of one carbon atom along with the accompanying hydrogen atoms. The nor-compound can be derived by removal of a CH
3
, CH
2
, or CH group, or of a C atom. The "nor-" prefix also includes the elimination of a methylene bridge in a cyclic parent compound, followed by ring contraction.. The terms desmethyl- or demethyl- are synonyms of "nor-".

<i>E</i>–<i>Z</i> notation Notation in organic chemistry for double bonds

EZ configuration, or the EZ convention, is the IUPAC preferred method of describing the absolute stereochemistry of double bonds in organic chemistry. It is an extension of cistrans isomer notation that can be used to describe double bonds having two, three or four substituents. E and Z notation are only used when a compound doesn't have two identical substituents.

<span class="mw-page-title-main">Denticity</span> Number of atoms in a ligand that bond to the central atom of a coordination complex

In coordination chemistry, denticity refers to the number of donor groups in a given ligand that bind to the central metal atom in a coordination complex. In many cases, only one atom in the ligand binds to the metal, so the denticity equals one, and the ligand is said to be monodentate. Ligands with more than one bonded atom are called polydentate or multidentate. The denticity of a ligand is described with the Greek letter κ ('kappa'). For example, κ6-EDTA describes an EDTA ligand that coordinates through 6 non-contiguous atoms.

In chemistry, a ring is an ambiguous term referring either to a simple cycle of atoms and bonds in a molecule or to a connected set of atoms and bonds in which every atom and bond is a member of a cycle. A ring system that is a simple cycle is called a monocycle or simple ring, and one that is not a simple cycle is called a polycycle or polycyclic ring system. A simple ring contains the same number of sigma bonds as atoms, and a polycyclic ring system contains more sigma bonds than atoms.

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