GLOSSARY OF STEREOCHEMICAL TERMS

Snoopy Learns Stereochemistry

Samuel L. Jackson and Samuel D. Jackson

The following glossary may help you learn the terminology and jargon of stereochemistry and to what situations the different terms apply.

At the end of this glossary the terms are listed according to this scheme. Terms in (parentheses) represent sloppy usage commonly found in the literature.

You may want to visit the IUPAC nomenclature Web site for more information.


[AB] [C] [D] [E] [GHI] [LM] [OP] [R] [S] [TUZ] [Classification]
α (A) — (1) Originally, trans to the axial substituent at C(10) in diterpenoids and steroids. (2) Now, most commonly refers to an atom or group that is pointing down or away from the reader as the structure is drawn. (3) In cyclic sugars, a diastereomer in which the anomeric OR group is trans to the CH2OR group. (The convention is to draw D-sugars with the CH2OH group pointing up, so an α-OH group will be trans to the CH2OH group. However, the trans definition for α-sugars is retained for L-sugars, even though their CH2OH group may point down.) Contrast to
β. Examples.

achiral (M) — Identical to one's mirror image. An achiral structure has a plane of symmetry (usually), a center of inversion, or an improper axis of symmetry. An achiral structure does not have an enantiomer.

achiral compound (M) — A compound that has at least one energetically accessible achiral ground state or transition state conformation. (Note that this property is dependent on the time scale. A conformation that is not energetically accessible on the time scale of nanoseconds may be accessible on the time scale of minutes.) An achiral compound does not have a configurational enantiomer. Contrast to chiral compound.

anomer (R) — An epimer at a C atom in the ketone/aldehyde oxidation state. Mostly used to refer to cyclic sugars.

anti (A,X) — (1) Describes the relative stereochemistry of two substituents on an acyclic chain in a molecule. If the chain is drawn in horizontal, zigzag fashion and one substituent is pointing out and the other in, they are anti. Examples. (2) The relationship of two substituents, A and D, on two adjacent atoms, B and C, when the A-B-C-D dihedral angle is 180°. (3) Describes a reaction in which two groups add to opposite faces of a π bond. Contrast to syn.

asymmetric center (A) — Same as stereogenic atom.

asymmetric compound (M) — A compound with no improper or proper axis of symmetry except the C1 axis.

atropisomer (R) — A conformational stereoisomer of a reference compound that converts to the reference compound only slowly on the NMR or laboratory time scale.

(axial chirality) (M) — Describes the shape of certain chiral molecules that lack a tetrahedral stereocenter. The substituents on these molecules can be regarded as residing at the four corners of a stretched tetrahedron. The axis along which the tetrahedron has been stretched is the axis of chirality. Examples. Contrast to (planar chirality).

axis of symmetry (M) — An imaginary line through a compound. Rotation of the compound by an integral fraction of a circle around this axis (1/2, 1/3, etc.) brings the compound to superposition on itself. An axis of symmetry is represented by Cn, where n is the integral fraction. Also called proper axis of symmetry. Contrast to improper axis of symmetry and plane of symmetry.


β (A) — (1) Originally, cis to the axial substituent at C(10) in diterpenoids and steroids. (2) Now, most commonly refers to an atom or group that is pointing up or towards the reader as the structure is drawn. (3) In cyclic sugars, a diastereomer in which the anomeric OR group is cis to the CH2OR group. (The convention is to draw D-sugars with the CH2OH group pointing up, so a β-OH group will be cis to the CH2OH group. However, the cis definition for β-sugars is retained for L-sugars, even though their CH2OH group may point down.) Contrast to α. Examples.


[AB] [C] [D] [E] [GHI] [LM] [OP] [R] [S] [TUZ] [Classification]
Cn axis (n is an integer) (M) — Same as
axis of symmetry.

center of inversion (M) — An imaginary point in a compound. Reflection of the compound through this point brings the compound to superposition on itself. An inversion center is represented by i. Same as an S2 improper axis of symmetry.

chiral (M) — Not identical to one's mirror image. A chiral structure lacks a plane of symmetry, a center of inversion, and an improper axis of symmetry. A chiral structure has an enantiomer. Contrast to achiral.

(chiral center) (A) — A tetrahedral stereogenic atom.

chiral compound (M) — A compound that does not have an energetically accessible achiral ground state or transition state conformation. (Note that this property is dependent on the time scale. A conformation that is not energetically accessible on the time scale of nanoseconds may be accessible on the time scale of minutes.) A chiral compound has a configurational enantiomer. Contrast to achiral compound.

cis (A,M) — (1) Describes the stereochemical relationship of two groups on different C atoms of an alkene. If the X–C=C–Y dihedral angle is 0°, the groups are cis. (2) Describes a 1,2-disubstituted alkene whose substituents are cis. (3) Describes the stereochemical relationship of two groups on different tetrahedral C atoms of a single ring in a cyclic compound. Considering the atoms of the ring to be coplanar, if the two groups reside on the same face of the plane, the groups are cis. (4) Describes a 1,n-disubstituted cyclic compound with two substituents that are cis to one another. Contrast to trans.

configuration (A) — The spatial arrangement of groups around a stereogenic atom (R or S) or an alkene (E or Z).

configurational diastereomer (R) — A diastereomer of a reference compound that can be converted to it only by breaking covalent bonds, for example by inverting the configurations of some but not all of the stereocenters in a compound.

configurational enantiomer (R) — An enantiomer of a reference compound that can be converted to it only by breaking covalent bonds, for example by inverting the configurations of all of the tetrahedral stereocenters in a compound.

configurational purity (S) — The extent to which the molecules in a sample of a compound have a particular stereocenter in the same configuration.

configurational stereoisomer (R) — A stereoisomer of a reference compound that can be converted to it only by breaking covalent bonds, for example by inverting the configurations of some or all of the stereocenters in a compound. Refers to either configurational enantiomers or configurational diastereomers.

configurationally pure (S) — Describes a sample in which all the molecules in the sample have a particular stereocenter in the same configuration.

conformation (M) — The spatial arrangement of atoms in a molecule that can be adjusted or changed by rotations about sigma bonds or by lone pair inversions.

conformational diastereomer (R) — A diastereomer of a reference structure that can be converted to it by rotations about sigma bonds or by lone pair inversions.

conformational enantiomer (R) — An enantiomer of a reference structure that can be converted to it by rotations about sigma bonds or by lone pair inversions.

conformational stereoisomer (R) — A stereoisomer of a reference structure that can be converted to it by rotations about sigma bonds or by lone pair inversions. Refers to either conformational enantiomers or conformational diastereomers.

conformer (R) — Same as conformational stereoisomer.

constitutional isomer (R) — Same as structural isomer.


[AB] [C] [D] [E] [GHI] [LM] [OP] [R] [S] [TUZ] [Classification]


D (M) — An archaic term designating the absolute stereochemistry of carbohydrates (sugars) and amino acids. A molecule is D when the arrangement of groups around a
stereocenter is the same as the arrangement of groups about the stereocenter of (R)-glyceraldehyde (2,3-dihydroxypropanal). In carbohydrates with multiple stereocenters, the stereocenter furthest from the C in the aldehyde or carboxylic acid oxidation state determines the absolute stereochemistry. Naturally occurring carbohydrates are mostly D. Not to be confused with dextrorotatory! Contrast to L.

dextrorotatory (M,S) — Rotates the plane of plane-polarized light clockwise, in the (+) direction. Contrast to levorotatory.

diastereomer (R) — (1) A stereoisomer of a reference compound or structure that has a shape that is not the mirror image of the reference compound or structure. Diastereomers have different internal dimensions (interatomic distances, dihedral angles) and different energies. (2) In common usage, same as configurational diastereomer.

diastereoselective (X) — A reaction in which more of one diastereomer is obtained than another.

diastereospecific (X) — A reaction in which the mechanism requires that only one diastereomer be obtained.

diastereotopic (A) — Refers to the relationship between two atoms of the same element or two groups of the same composition in a compound. Diastereotopic atoms or groups have the same atom-to-atom connections, and their environments do not exchange by free rotation about σ bonds or lone pair inversion, and they cannot be related by an axis of symmetry. Diastereotopic atoms or groups have different reactivities and spectroscopic properties. Examples: The two H atoms on C(3) of 2-butanol; the two H atoms on C(1) on propene. Contrast to enantiotopic and homotopic.

dissymmetric compound (M) — Same as chiral.


[AB] [C] [D] [E] [GHI] [LM] [OP] [R] [S] [TUZ] [Classification]
E (M) — Designates the
configuration of an alkene. The four substituents of the alkene are assigned priorities. The alkene has the E configuration when the higher priority substituent on one C is trans to the higher priority substituent on the other C. Contrast to Z. Examples.

ee (S) — Same as enantiomeric excess.

enantioenriched (S) — Same as enantiomerically enriched.

enantiomer (R) — (1) A stereoisomer of a reference compound or structure that is the nonsuperimposable mirror image of the reference compound or structure. Enantiomers have identical internal dimensions (interatomic distances, dihedral angles) and identical energies, but they rotate plane-polarized light in equal but opposite directions, and they interact with other chiral objects in different ways. Structures that have enantiomers are always chiral. (2) In common usage, same as configurational enantiomer.

enantiomeric excess (ee) (S) — The excess of one enantiomer over racemic material in a sample of a chiral compound. Defined as (er – 1) / (er + 1), and expressed as a percentage. A racemic sample has an ee of 0%; an enantiomerically pure sample has an ee of 100%. The ee of a sample of a compound can be measured by dividing the specific rotation of the sample by the specific rotation of an enantiomerically pure sample of the same compound.

enantiomeric ratio (er) (S) — The ratio of the amounts of the two enantiomers in a particular sample of a chiral compound.

enantiomerically enriched (S) — A sample of a chiral compound that consists of more of one enantiomer than the other. The extent to which a sample is enantiomerically enriched is quantified by the enantiomeric ratio or the enantiomeric excess.

enantiomerically pure (S) — A sample of a chiral compound that consists of a single enantiomer.

enantiopure (S) — Same as enantiomerically pure.

enantioselective (X) — A reaction in which more of one enantiomer is obtained than the other.

enantiotopic (A) — Refers to the relationship between two atoms of the same element or two groups of the same composition in a compound. Enantiotopic atoms or groups have the same atom-to-atom connections, and their environments do not exchange by free rotation about σ bonds or lone pair inversion, but they can be related by an improper axis of symmetry in at least one conformation. Enantiotopic atoms or groups have identical reactivities and spectroscopic properties unless they are placed in a chiral environment (such as a chiral solvent). Example: The two H atoms on C(3) of 2-butanone. Contrast to diastereotopic and homotopic.

epimer (R) — A diastereomer that differs from a reference molecule in the configuration of exactly one stereocenter.

epimerize (A,M,S) — To become an epimer. May happen to:

  1. a compound or a sample of compound that changes into its epimer in the course of a reaction (M,S), or
  2. a specific stereocenter in a compound that inverts its configuration in the course of a reaction (A).
Contrast to racemize.

er (S) — Same as enantiomeric ratio.

erythro (M) — An archaic term describing the relative configuration of two stereocenters in an acyclic compound. If the compound is drawn in a Fischer projection and the major substituents at the two stereocenters are pointed to the same side, the compound is the erythro diastereomer. The modern way of describing the stereochemistry is anti. Contrast to threo. Examples.


[AB] [C] [D] [E] [GHI] [LM] [OP] [R] [S] [TUZ] [Classification]
gauche (A) — The relationship of two substituents, A and D, on two adjacent atoms, B and C, when the A-B-C-D dihedral angle is 60°.

geometric isomer (M) — Same as diastereomer, but used only to refer to alkenes.

heterochiral (R) — Describes the relationship between two enantiomeric chiral molecules. Contrast with homochiral.

homochiral (R) — Describes the relationship between two identical chiral molecules. Contrast with heterochiral.

(homochiral) (S) — Same as enantiomerically pure.

homomer (R) — A compound or structure that is identical to a reference compound or structure.

homotopic (A) — Refers to the relationship between two atoms of the same element or two groups of the same composition in a compound. Homotopic atoms or groups have the same atom-to-atom connections, and either their environments exchange by free rotation about σ bonds or lone pair inversion, or they can be related by an axis of symmetry in at least one conformation. Homotopic atoms or groups have identical reactivities and spectroscopic properties. Example: Any two H atoms in cyclohexane. Contrast to diastereotopic and enantiotopic.

improper axis of symmetry (M) — An imaginary line through a compound. Rotation of the compound by an integral fraction of a circle around this axis (1/2, 1/4, etc.) followed by reflection through a plane perpendicular to this axis brings the compound to superposition on itself. An improper axis of symmetry is represented by Sn, where n is the integral fraction (must be even or 1). The plane of symmetry is an S1 axis, and the center of inversion is an S2 axis. Contrast to proper axis of symmetry.

inversion center (M) — Same as center of inversion.

isomer (R) — A compound that has the same formula as a reference compound but whose structure (and hence, properties) is not superimposable. Isomers may be either structural isomers or stereoisomers.


[AB] [C] [D] [E] [GHI] [LM] [OP] [R] [S] [TUZ] [Classification]
L (M) — An archaic term designating the absolute stereochemistry of carbohydrates (sugars) and amino acids. A molecule is L when the arrangement of groups around a
stereocenter is the same as the arrangement of groups about the stereocenter of (S)-glyceraldehyde (2,3-dihydroxypropanal). In carbohydrates with multiple stereocenters, the stereocenter furthest from the C in the aldehyde or carboxylic acid oxidation state determines the absolute stereochemistry. The amino acids coded by DNA are exclusively L. (But cysteine has the absolute R stereochemistry, whereas all the other amino acids are S.) Not to be confused with levorotatory! Contrast to D.

levorotatory (M,S) — Rotates the plane of plane-polarized light counterclockwise, in the (–) direction. Contrast to dextrorotatory.

like (abbrev. lk) (A) — Same as syn, definition 1. Contrast to unlike.

lone pair inversion (A) — The "umbrella effect" that enables N to rapidly switch (invert) its configuration.

meso (M) — An achiral compound that has chiral configurational diastereomers. Such a compound usually has tetrahedral stereocenters.

mirror plane (M) — Same as plane of symmetry.


[AB] [C] [D] [E] [GHI] [LM] [OP] [R] [S] [TUZ] [Classification]
optical activity (S) — The ability to rotate the plane of plane-polarized light. A sample of an
enantiomerically enriched chiral compound is usually optically active. Crystals of achiral compounds may also be optically active.

(optical isomer) (R) — Same as enantiomer.

optical rotation (S) — The number of degrees, α, by which the plane of plane-polarized light is rotated.

(optically pure) (S) — Same as enantiomerically pure.

(planar chirality) (M) — Describes the shape of certain chiral molecules that lack a tetrahedral stereocenter. These molecules generally contain a flat group, which by itself has only a single plane of symmetry, but whose π orbitals are coordinated on one face to a metal. Examples. Contrast to (axial chirality).

plane of symmetry (M) — A plane through an achiral object that relates its identical halves. A plane of symmetry is represented by σ. Same as an S1 improper axis of symmetry.

point group (M) — A description of the symmetry of a molecule according to the number and location of axes of symmetry, improper axes of symmetry, and planes of symmetry.

priority — A convention used to assign stereochemistry. Group A bound to a stereocenter has higher priority than group B bound to the same stereocenter when the first atom in group A has a higher atomic number than the first atom in group B. If the first atoms have the same atomic number, the second atoms are compared, etc.

prochiral (M) — Refers to an achiral compound with a single plane of symmetry. A chemical manipulation that breaks that plane of symmetry will make it chiral.

proper axis of asymmetry (M) — Same as axis of symmetry.

prostereogenic (A) — Refers to a nonstereogenic atom on which replacement of one substituent with a different one or addition of a new substituent will render the atom stereogenic.


[AB] [C] [D] [E] [GHI] [LM] [OP] [R] [S] [TUZ] [Classification]
R (A) — Designates the
configuration of a tetrahedral stereocenter. The four groups about the stereocenter are assigned priorities, and the lowest priority group is pointed away from the reader. The stereocenter has the R configuration if the three remaining groups are arranged clockwise from highest to lowest priority. Contrast to S.

r (A) — Same as R, but refers to a stereocenter in an achiral molecule that has the property that switching two groups attached to this stereocenter generates a configurational diastereomer that is also achiral. Contrast to s.

racemic (S) — A sample of a chiral compound that consists of a 1:1 mixture of enantiomers.

(racemic) (A) — Refers to a stereocenter in a compound that is a 1:1 mixture of configurations in a sample of that compound.

racemize (A,S)-- To become racemic. May happen to:

  1. a sample whose enantiomeric excess decreases in the course of a reaction (S), or
  2. a stereocenter whose configurational purity decreases in the course of a reaction (A).
Contrast to epimerize.

resolution (S) — The process of separating the enantiomers of a racemic mixture.


[AB] [C] [D] [E] [GHI] [LM] [OP] [R] [S] [TUZ] [Classification]
S (A) — Designates the
configuration of a tetrahedral stereocenter. The four groups about the stereocenter are assigned priorities, and the lowest priority group is pointed away from the reader. The stereocenter has the S configuration if the three remaining groups are arranged counterclockwise from highest to lowest priority. Contrast to R.

s (A) — Same as S, but refers to a stereocenter in an achiral molecule that has the property that switching two groups attached to this stereocenter generates a configurational diastereomer that is also achiral. Contrast to r.

σ plane (M) — Same as plane of symmetry.

Sn axis (n is an integer) (M) — Same as improper axis of symmetry.

scalemic (S) — Same as enantiomerically enriched.

skeletal isomer (R) — Same as structural isomer.

specific rotation ([α]) (M) — Defined as α / l × c, where α is the measured optical rotation, l is the path length (in cm), and c is the concentration (in g/mL; if the compound is a pure liquid, c = 1). The specific rotation [α] is measured at a particular temperature, written as a superscript in °C (e.g., [α]25), and wavelength (usually the sodium D line, 589 nm), written as a subscript (e.g., [α]D). It is an immutable physical characteristic of a particular compound, like a melting point.

stereocenter (A) — Same as stereogenic atom.

stereogenic (A) — Describes an atom within a molecule that has the property that switching two groups attached to the atom generates a new stereoisomer of the molecule. Stereogenic atoms may be trigonal, tetrahedral, or have higher coordination numbers.

stereoisomer (R) — An isomer of a reference compound or structure that has the same atom-to-atom connections as the reference compound or structure, but has a shape that is nonsuperimposable with it. Contrast to structural isomer. Stereoisomers may be configurational or conformational stereoisomers, and they may be diastereomers or enantiomers.

stereoselective (X) — Same as diastereoselective.

stereospecific (X) — Same as diastereospecific.

structural isomer (R) — An isomer of a reference compound whose atom-to-atom connections are different from the reference compound. Same as skeletal isomer and constitutional isomer. Contrast to stereoisomer.

syn (A,X) — (1) Describes the relative stereochemistry of two substituents on an acyclic chain in a molecule. If the chain is drawn in horizontal, zigzag fashion and both substituents are pointing out or in, they are syn. Examples. (2) The relationship of two substituents, A and D, on two adjacent atoms, B and C, when the A-B-C-D dihedral angle is 0°. (3) Describes a reaction in which two groups add to the same face of a π bond. Contrast to anti.


[AB] [C] [D] [E] [GHI] [LM] [OP] [R] [S] [TUZ] [Classification]
threo (M) — An archaic term describing the relative configuration of two stereocenters in an acyclic compound. If the compound is drawn in a Fischer projection and the major substituents at the two stereocenters are pointed to opposite sides, the compound is the threo diastereomer. The modern way of describing the stereochemistry is
syn. Contrast to erythro. Examples.

trans (A,M) — (1) Describes the stereochemical relationship of two groups on different C atoms of an alkene. If the X–C=C–Y dihedral angle is 180°, the groups are trans. (2) Describes a 1,2-disubstituted alkene whose substituents are trans. (3) Describes the stereochemical relationship of two groups on different tetrahedral C atoms of a single ring in a cyclic compound. Considering the atoms of the ring to be coplanar, if the two groups reside on opposite faces of the plane, the groups are trans. (4) Describes a 1,n-disubstituted cyclic compound with two substituents that are trans to one another. Contrast to cis.

unlike (abbrev. ul) (A) — Same as anti, definition 1. Contrast to like.

Z (M) — Designates the configuration of an alkene. The four substituents of the alkene are assigned priorities. The alkene has the Z configuration when the higher priority substituent on one C is cis to the higher priority substituent on the other C. Contrast to E. Examples.


[AB] [C] [D] [E] [GHI] [LM] [OP] [R] [S] [TUZ] [Classification]

Classification of stereochemical terms.

Terms referring to:
Atoms or groups within a molecule (A) Single molecules (M) Relationship between two compounds or structures (R) Macroscopic sample of a compound (S) Reaction (X)
α
anti
asymmetric center
β
(chiral center)*
cis
configuration
diastereotopic
enantiotopic
epimerize
homotopic
like
lone pair inversion
prostereogenic
R
r
(racemic)*
racemize
S
s
stereocenter
stereogenic
syn
trans
unlike
achiral
achiral compound
asymmetric compound
(axial chirality)*
axis of symmetry
Cn axis
center of inversion
chiral
chiral compound
cis
conformation
D
dextrorotatory
E
epimerize
erythro
improper axis of symmetry
inversion center
L
levorotatory
meso
mirror plane
(planar chirality)*
plane of symmetry
prochiral
proper axis of symmetry
σ plane
Sn axis
specific rotation
threo
trans
Z
anomer
atropisomer
configurational diastereomer
configurational enantiomer
configurational stereoisomer
conformational diastereomer
conformational enantiomer
conformational stereoisomer
conformer
constitutional isomer
diastereomer
enantiomer
epimer
heterochiral
homochiral
homomer
isomer
(optical isomer)*
skeletal isomer
stereoisomer
structural isomer
configurational purity
configurationally pure
dextrorotatory
ee
enantioenriched
enantiomeric excess
enantiomeric ratio
enantiomerically enriched
enantiomerically pure
enantiopure
epimerize
er
(homochiral)*
levorotatory
optical activity
optical rotation
(optically pure)*
racemic
racemize
resolution
scalemic
anti
diastereoselective
diastereospecific
enantioselective
stereoselective
stereospecific
syn

*Terms in (parentheses) are improper and should be avoided.


Additional vocabulary help

You might want to look at some definitions of stereoisomers.

Or you might want to look at some examples of the different kinds of stereoisomers.

Or you might want to look at a flow chart showing how to determine the isomeric relationship between two structures.

Or you might want to look at definitions and examples of point groups.


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This page was last updated March 16, 2010.