B and C

Continued from terms starting with A

Contents

Baeyer Strain; Basal; Berry Pseudorotation; (Beta); Bisecting Conformation, Eclipsing Conformation; Boat; Bond Opposition Strain; Bowsprit, Flagpole; Bredt's Rule; C.I.P. System; Cahn-Ingold-Prelog System; Centre of Chirality; Chair, Boat, Twist; Chair-Chair Interconversion; Chemical Species; Chiral; Chirality ; Chirality Axis; Chirality Centre; Chirality Element; Chirality Plane; Chirality Sense; Chiroptic/Chiroptical; Chirotopic; CIP Priority; cis, trans; cisoid Conformation; cis-trans Isomers; Clinal; Compensation; Configuration; Conformation; Conformational Analysis; Conformer; Conglomerate; Constitution; Constitutional Isomerism; Crown Conformation

Basal See apical, basal, equatorial.

Berry Pseudorotation See pseudorotation.

(Beta) See (alpha), (beta)

Bisecting Conformation, Eclipsing Conformation

For a structure containing the grouping R₃C-C(Y)=X (with identical or different groups R) the conformation in which the torsion angle is such that X is antiperiplanar to one of the groups R, and, in a Newman projection, the double bond C=X bisects one of the R-C-R angles. In this conformation the bond C-Y eclipses one of the C-R bonds. The other conformation, in which X is synperiplanar to one of the groups R, is called an eclipsing conformation.

Boat See chair, boat, twist; and half-chair, half-boat.

Bond Opposition Strain See eclipsing strain.

Bowsprit, Flagpole

In the boat form of cyclohexane and related structures there are two ring atoms lying out of the plane of the other four; exocyclic bonds to these two atoms pointing in a direction roughly parallel to that plane are called bowsprit, the other two are called flagpole.

Bredt's Rule

See entry in 'Glossary of Terms Used in Physical Organic Chemistry', Pure Appl. Chem. 66, 1077-1184 (1994).

C.I.P. System

Short for Cahn-Ingold-Prelog system (see CIP Priority).

Cahn-Ingold-Prelog System See CIP Priority.

Centre of Chirality See chiral centre.

Chair, Boat, Twist

If carbon atoms 1, 2, 4 and 5 of cyclohexane occupy coplanar positions and when carbon atoms 3 and 6 are on opposite sides of the plane the conformation (of symmetry group D_3d) is called a chair form.

The same term is applied to similar conformations of analogous saturated six-membered ring structures containing hetero-atoms and/or bearing substituent groups, but these conformations may be distorted from the exact D_3d symmetry. For cyclohexane and most such analogues, the chair form is the most stable conformation. If the cyclohexane conformation has no centre of symmetry but possesses two planes of symmetry, one of them bisecting the bonds between atoms 1 and 2 and between 4 and 5 and the other plane passing through atoms 3 and 6 (which lie out of the plane and on the same side of the plane containing 1, 2, 4 and 5), that conformation (of symmetry group C_2v) is called a boat form and it is generally not a stable form. Again, this term is also applied to structural analogues.

The conformation of D₂ symmetry passed through in the interconversion of two boat forms of cyclohexane is called the twist form (also known as skew boat, skew form and stretched form). See also half-chair.

In a five-membered ring a conformation in which two adjacent atoms are maximally displaced, in opposite directions, relative to the plane containing the other three carbon atoms has been called a half-chair but is better called a twist conformation (see also envelope conformation).

In carbohydrate chemistry the term twist refers to a five-membered ring and the D₂ symmetry six-membered ring is referred to as skew.

Chair-Chair Interconversion See ring reversal.

Chemical Species

A set of chemically identical atomic or molecular structural units in a solid array or of chemically identical molecular entities that can explore the same set of molecular energy levels on the time scale of the experiment.

For example, two conformational isomers may interconvert sufficiently slowly to be detected by their separate n.m.r. spectra and hence to be considered to be separate chemical species on a time scale governed by the radiofrequency of the spectrometer used. On the other hand, in a slow chemical reaction the same mixture of conformers may behave as a single chemical species, i.e. there is a virtually complete equilibrium population of the total set of molecular energy levels belonging to the two conformers.

Except where the context requires otherwise, the term is taken to refer to a set of molecular entities containing isotopes in their natural abundance.

['Glossary of Terms Used in Physical Organic Chemistry', Pure Appl. Chem. 66, 1077-1184 (1994)].

Chiral

Having the property of chirality.

As applied to a molecule the term has been used differently by different workers. Some apply it exclusively to the whole molecule, whereas others apply it to parts of a molecule. For example, according to the latter view, a meso-compound is considered to be composed of two chiral parts of opposite chirality sense; this usage is to be discouraged. See enantiomorph.

In its application to an assembly of molecules, some restrict the term to an assembly in which all of the molecules have the same chirality sense, which is better called enantiopure. Others extend it to a racemic assembly, which is better just called a racemate. Use of the term to describe molecular assemblies should be avoided.

Chirality

The geometric property of a rigid object (or spatial arrangement of points or atoms) of being non-superposable on its mirror image; such an object has no symmetry elements of the second kind (a mirror plane, = S₁, a centre of inversion, i = S₂, a rotation-reflection axis, S_2n). If the object is superposable on its mirror image the object is described as being achiral. See also handedness.

Chirality Axis

An axis about which a set of ligands is held so that it results in a spatial arrangement which is not superposable on its mirror image. For example with an allene abC=C=Ccd the chiral axis is defined by the C=C=C bonds; and with an ortho-substituted biphenyl the atoms C-1, C-1', C-4 and C-4' lie on the chiral axis.

Chirality Centre

An atom holding a set of ligands in a spatial arrangement which is not superposable on its mirror image. A chirality centre is thus a generalised extension of the concept of the asymmetric carbon atom to central atoms of any element, for example N⁺abcd, Pabc as well as Cabcd.

Chirality Element

General name for a chirality axis, chirality centre or chirality plane. Also referred to as an element of chirality.

Chirality Plane

A planar unit connected to an adjacent part of the structure by a bond which results in restricted torsion so that the plane cannot lie in a symmetry plane. For example with (E)-cyclooctene the chiral plane includes the double bond carbon atoms and all four atoms attached to the double bond; with a monosubstituted paracyclophane the chiral plane includes the monosubstituted benzene ring with its three hydrogen atoms and the three other atoms linked to the ring (i.e. from the substituent and the two chains linking the two benzene rings).

Chirality Sense

The property that distinguishes enantiomorphs. The specification of two enantiomorphic forms by reference to an oriented space e.g. of a screw, a right threaded one or a left threaded one. The expression 'opposite chirality' is short for 'opposite chirality sense'.

Chiroptic/Chiroptical

A term referring to the optical techniques (using refraction, absorption or emission of anisotropic radiation) for investigating chiral substances [e.g. measurements of optical rotation at a fixed wavelength, optical rotatory dispersion (ORD), circular dichroism (CD), and circular polarisation of luminescence (CPL)].

Chirotopic

The description of an atom (or point, group, face, etc. in a molecular model) that resides within a chiral environment. One that resides within an achiral environment has been called achirotopic.

CIP Priority

In the CIP rules the conventional order of ligands established for the purpose of unambiguous designation of stereoisomers. It is deduced by application of sequence rules, the authoritative statement of which appears in R.S. Cahn, C.K. Ingold and V. Prelog, Angew. Chem. 78, 413-447 (1966), Angew. Chem. Internat. Ed. Eng. 5, 385-415, 511 (1966) ; and V. Prelog and G. Helmchen, Angew. Chem. 94, 614-631 (1982), Angew. Chem. Internat. Ed. Eng. 21, 567-583 (1982).

cis, trans

Descriptors which show the relationship between two ligands attached to separate atoms that are connected by a double bond or are contained in a ring. The two ligands are said to be located cis to each other if they lie on the same side of a plane. If they are on opposite sides, their relative position is described as trans. The appropriate reference plane of a double bond is perpendicular to that of the relevant -bonds and passes through the double bond. For a ring (the ring being in a conformation, real or assumed, without re-entrant angles at the two substituted atoms) it is the mean plane of the ring(s). For alkenes the terms cis and trans may be ambiguous and have therefore largely been replaced by the E, Z convention for the nomenclature of organic compounds. If there are more than two entities attached to the ring the use of cis and trans requires the definition of a reference substituent (See IUPAC, Nomenclature of Organic Chemistry, Sections A, B, C, D, E, F and H, Pergamon Press, 1979, p. 478, Rule E-2.3.3, E-2.3.4; IUPAC, A Guide to IUPAC Nomenclature of Organic Chemistry, Blackwell Scientific Publications, 1993, pp. 149-151, Rule R-7.1.1).

cisoid Conformation (usage strongly discouraged)

See s-cis, s-trans. The terms cisoid and transoid are also used to describe the stereochemistry of fused ring systems (See IUPAC, Nomenclature of Organic Chemistry, Sections A, B, C, D, E, F and H, Pergamon Press, 1979, p. 478, Rule E-3.2).

cis-trans Isomers

Stereoisomeric olefins or cycloalkanes (or hetero-analogues) which differ in the positions of atoms (or groups) relative to a reference plane: in the cis-isomer the atoms are on the same side, in the trans-isomer they are on opposite sides.

Clinal See torsion angle.

Compensation

1. For internal compensation, see meso-compound.

2. See external compensation.

Configuration

In the context of stereochemistry, the term is restricted to the arrangements of atoms of a molecular entity in space that distinguishes stereoisomers, the isomerism between which is not due to conformation differences. See also absolute configuration; relative configuration.

Conformation

The spatial arrangement of the atoms affording distinction between stereoisomers which can be interconverted by rotations about formally single bonds. Some authorities extend the term to include inversion at trigonal pyramidal centres and other polytopal rearrangements. See also conformer; bisecting conformation, eclipsing conformation; chair, boat, twist; crown conformation; envelope conformation; half-chair; staggered conformation; tub conformation.

Conformational Analysis

The assessment of the relative energies (or thermodynamic stabilities), reactivities, and physical properties of alternative conformations of a molecular entity, usually by the application of qualitative or semi-quantitative rules or by semi-empirical calculations.

Conformer

One of a set of stereoisomers, each of which is characterised by a conformation corresponding to a distinct potential energy minimum. See also rotamer.

Conglomerate See racemic conglomerate.

Constitution

The description of the identity and connectivity (and corresponding bond multiplicities) of the atoms in a molecular entity (omitting any distinction arising from their spatial arrangement).

Constitutional Isomerism

Isomerism between structures differing in constitution and described by different line formulae e.g. CH₃OCH₃ and CH₃CH₂OH.

Crown Conformation

A conformation of a saturated cyclic molecular entity, containing an even number (>= 8) of atoms in the ring, in which these atoms lie alternately in each of two parallel planes and are symmetrically equivalent (D_4d for cyclooctane, D_5d for cyclodecane etc). It is analogous to the chair conformation of cyclohexane. See also tub conformation.

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