Absolute Configuration; ac; Achiral ; Achirotopic ; (Alpha), (Beta); Ambo; Angle Strain; Anisometric ; Anomeric Effect; Anomers; Anti; Anticlinal ; Antiperiplanar ; Antipodes; ap ; Apical, Basal, Equatorial; Asymmetric ; Asymmetric Carbon Atom; Asymmetric Centre ; Asymmetric Destruction ; Asymmetric Induction; Asymmetric Synthesis; Asymmetric Transformation; Atropisomers; Axial, Equatorial; Axial Chirality; Axis of Chirality ; Axis of Helicity
The spatial arrangement of the atoms of a chiral molecular entity (or group) and its stereochemical description e.g. R or S. See also relative configuration and (alpha), (beta) (3).
ac See torsion angle.
Achiral See chirality.
Achirotopic See chirotopic.
These stereodescriptors are used in a number of different ways.
1. Relative stereodescriptors used in carbohydrate nomenclature to describe the configuration at the anomeric carbon by relating it to the anomeric reference atom. For simple cases the anomeric reference atom is the same as the configurational reference atom. Thus in -D-glucopyranose the reference atom is C-5 and the OH at C-1 is on the same side as the OH at C-5 in the Fischer projection. See 'Tentative rules for Carbohydrate Nomenclature. Part 1', Eur. J. Biochem., 21, 455-477 (1971).
2. Relative stereodescriptors used by Chemical Abstracts Service to describe the configuration of a cyclic molecule (including suitable polycyclic systems) with several stereogenic centres whereby the side of the reference plane is the side on which the substituent with CIP priority lies at the lowest numbered stereogenic centre. The other side is .
3. Absolute stereodescriptors originally devised for steroid nomenclature. However in this sense it is only meaningful if there is an agreed absolute configuration and orientation of the structure so as to define the plane and which way up the molecule is represented. Substituents above the plane of the steroid are described as and shown as a solid line ( or ), those below the plane are described as and shown by a broken line ( |||||||| or ----- ). The extension of this system to tetrapyrroles has been documented and it has been widely used elsewhere. See 'Nomenclature of Steroids', Pure Appl. Chem. 61, 1783-1822 (1989); 'Nomenclature of Tetrapyrroles', Pure Appl. Chem. 59, 779-832 (1987).
A prefix used to indicate that a molecule with two (or more) chiral elements is present as a mixture of the two racemic diastereoisomers in unspecified proportions. For example, the dipeptide formed from L-alanine and DL-leucine is L-alanyl-ambo-leucine. (See 'Nomenclature and Symbolism for Amino Acids and Peptides', Pure Appl. Chem. 56, 595-624 (1984); 'Nomenclature of Tocopherols and Related Compounds', Pure Appl. Chem. 54, 1507-1510 (1982).)
Strain due to a departure in bond angle from "normal" values. The term is often used in the context of non-aromatic cyclic compounds in which the internal angles differ from the regular tetrahedral angle of 109o 28'; in this sense angle strain is also known as Baeyer strain.
Anisometric See isometric.
Originally the thermodynamic preference for polar groups bonded to C-1 (the anomeric carbon of a glycopyranosyl derivative) to take up an axial position.
This effect is now considered to be a special case of a general preference (the generalised anomeric effect) for synclinal (gauche) conformations about the bond C-Y in the system X-C-Y-C where X and Y are heteroatoms having nonbonding electron pairs, commonly at least one of which is nitrogen, oxygen or fluorine. For example in chloro(methoxy)methane the anomeric effect stabilises the synclinal conformation.
In alkyl glycopyranosides the anomeric effect operates at two sites (i) along the endocyclic C-1 oxygen bond (endo-anomeric effect) and (ii) along the exocyclic C-1 oxygen bond (exo-anomeric effect).
The opposite preference is claimed for some systems e.g. glycopyranosyltrialkylammonium salts, and has been referred to as the reverse anomeric effect.
Diastereoisomers of glycosides, hemiacetals or related cyclic forms of sugars, or related molecules differing in configuration only at C-1 of an aldose, C-2 of a 2-ketose, etc.
1. See torsion angle.
2. See endo, exo, syn, anti.
3. See also 'Glossary of Terms Used in Physical Organic Chemistry', Pure Appl. Chem. 66, 1077-1184 (1994) for use as a term to describe antarafacial addition or elimination reactions.
4. It was formerly used to describe the stereochemistry of oximes and related systems (See E,Z).
Anticlinal See torsion angle.
Antiperiplanar See torsion angle.
Antipodes (usage strongly discouraged)
Obsolete synonym for enantiomers.
ap See torsion angle.
Apical, Basal, Equatorial
In trigonal bipyramidal structures (e.g. a five-coordinate trigonal bipyramid with phosphorus as central atom) the term apical refers to the two positions that are collinear with the central atom or to the bonds linking these positions to the central atom. The three equivalent bonds (or positions) in a plane passing through the central atom and perpendicular to the direction of the apical bonds are described as equatorial (See axial, equatorial for alternative use). The term apical is also used for the bond pointing from the atom at or near the centre of the base to the apex of a pyramidal structure. The positions at or near the base of the pyramid, or the bonds linking those positions to the central atom of the base are described as basal. The apical bonds have also been called axial.
Lacking all symmetry elements (other than the trivial one of a one-fold axis of symmetry), i.e. belonging to the symmetry point group C1. The term has been used loosely (and incorrectly) to describe the absence of an rotation-reflection axis (alternating axis) in a molecule, i.e. as meaning chiral, and this usage persists in the traditional terms asymmetric carbon atom, asymmetric synthesis, asymmetric induction, etc.
Asymmetric Carbon Atom
The traditional name (van't Hoff) for a carbon atom that is attached to four different entities (atoms or groups) e.g. Cabcd. See also chirality centre.
Asymmetric Centre See chirality centre.
Asymmetric Destruction See kinetic resolution.
The traditional term describing the preferential formation in a chemical reaction of one enantiomer or diastereoisomer over the other as a result of the influence of a chiral feature present in the substrate, reagent, catalyst or environment.
A traditional term used for stereoselective synthesis of chiral compounds.
The conversion of a racemate into a pure enantiomer or into a mixture in which one enantiomer is present in excess, or of a diastereoisomeric mixture into a single diastereoisomer or into a mixture in which one diastereoisomer predominates. This is sometimes called deracemisation.
If the two enantiomers of a chiral substrate A are freely interconvertible and if an equal amount or excess of a non-racemising second enantiomerically pure chemical species, say (R)-B, is added to a solution of racemic A, then the resulting equilibrium mixture of adducts A*B will, in general, contain unequal amounts of the diastereoisomers (R)-A*(R)-B and (S)-A*(R)-B. The result of this equilibration is called asymmetric transformation of the first kind.
If, in such a system, the two diastereoisomeric adducts differ considerably in solubility so that only one of them, say (R)-A*(R)-B, crystallises from the solution, then the equilibration of diastereoisomers in solution and concurrent crystallisation will continue so that all (or most) of the substrate A can be isolated as the crystalline diastereoisomer (R)-A*(R)-B. Such a "crystallisation-induced asymmetric transformation" is called an asymmetric transformation of the second kind. See also stereoconvergence
A subclass of conformers which can be isolated as separate chemical species and which arise from restricted rotation about a single bond (see rotational barrier) e.g. ortho-substituted biphenyl, 1,1,2,2-tetra-tert-butylethane
In the chair form of cyclohexane ring bonds to ring atoms (and molecular entities attached to such bonds) are termed axial or equatorial according to whether the bonds make a relatively large or small angle, respectively, with the plane containing or passing closest to a majority of the ring atoms. Thus the axial bonds are approximately parallel to the C3 axis and the equatorial bonds approximately parallel to two of the ring bonds. These terms are also used for the chair form of other saturated six-membered rings. The corresponding bonds occurring at the allylic positions in mono-unsaturated six-membered rings are termed pseudo-axial (or quasi-axial) and pseudo-equatorial (or quasi-equatorial). The terms axial and equatorial have similarly been used in relation to the puckered conformation of cyclobutane, crown conformer of cyclooctane, etc. and the terms pseudo-axial and pseudo-equatorial in the context of the non-planar structures of cyclopentane and cycloheptane. (See apical, basal, equatorial for an alternative use of axial and equatorial with bipyramidal structures)
Term used to refer to stereoisomerism resulting from the non-planar arrangement of four groups in pairs about a chirality axis. It is exemplified by allenes abC=C=Ccd (or abC=C=Cab) and by the atropisomerism of ortho-substituted biphenyls.
The configuration in molecular entities possessing axial chirality is specified by the stereodescriptors Ra and Sa (or by P or M).
Axis of Chirality See chirality axis.
Axis of Helicity See helicity.
Return to home page for Basic Terminology of Stereochemistry.