Glossary

doi:10.1039/9781788013154-FP011

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Chemistry Student Guides

Introduction to Stereochemistry

DOI:

https://doi.org/10.1039/9781839164132

Paperback ISBN:

978-1-78801-315-4

PDF ISBN:

978-1-83916-413-2

EPUB ISBN:

978-1-83916-182-7

Series: Chemistry Student Guides

Product Type: Textbooks

No. of Pages:

182

Published online:

20 May 2020

Published in print:

23 Oct 2020

Book Chapter

Glossary

Doi:

https://doi.org/10.1039/9781788013154-FP011

Published:

20 May 2020
Series: Chemistry Student Guides

Product Type: Textbooks

Page range:

P011 - P016

Terms included in the glossary are indicated in bold at their first occurrence in the main book and also if they occur in the glossary within other entries.

Term	Definition
Absolute stereochemistry	The precise spatial arrangement of substituents around a stereogenic centre.
Achiral	An object that is superimposable on its mirror image is said to be achiral.
anti	On the opposite side to an atom or group on another carbon atom when the chain is drawn zig-zag.
Anomeric effect	A preference for heteroatomic substituents adjacent to a heteroatom that is part of a ring to adopt the axial, rather than the equatorial, position.
Anticlinal	Of a conformation, eclipsed but not periplanar.
Atomic number	The number of protons in the nucleus of a given element.
Atropisomer	A conformer that can be isolated as a separate chemical species and arises from restricted rotation about a single bond.
Axial	Used to describe groups bonded to cyclic structures where the bonds are perpendicular to the plane of the ring.
Bidentate	Of a ligand, attached to the metal atom of a coordination complex by two interactions.
Boat conformation	A conformation of cyclohexanes and their derivatives with a boat shape.
Chair conformation	An important conformation of cyclohexanes and their derivatives with a chair shape.
Chiral	An object (e.g. a molecule) that is non-superimposable on its mirror image is said to be chiral.
CIP rules	Cahn–Ingold–Prelog rules, which can be used in assignment of configurational descriptors.
cis/trans stereoisomerism	Stereoisomerism due to differing configurational arrangements of two groups that can be on the same or opposite sides of a molecule.
Configuration	The spatial arrangement of atoms in a molecule that can only be altered by breaking and making bonds. Configurational isomers can be e.g. enantiomers or diastereoisomers.
Conformation	The spatial arrangement of atoms in a molecule that can be altered by rotation about one or more single bonds and does not require breaking and making bonds. Conformational isomers are known as conformers.
Conformational isomers	Species that are interchangeable via rotation around one or more single bonds (conformations) and that lie at an energy minimum.
Conformers	Species that are interchangeable via rotation around one or more single bonds (conformations) and that lie at an energy minimum.
Coupling constant	A measure, usually in hertz, of the interaction between two NMR-active nuclei.
Decalin	A bicyclic compound comprising two fused cyclohexane rings.
Diastereoisomer	Diastereoisomers are stereoisomers that are non-superimposable, non-mirror images.
Diastereotopic	A relationship between two groups in a molecule where replacement of one of the two groups vs. the other gives rise to a pair of diastereoisomers.
1,3-Diaxial interactions	Of atoms or groups in axial positions of a chair conformation, the interactions such groups have with similar groups four bonds away (e.g. on carbon atoms 1 and 3).
Dihedral angle	The angle between two planes. Also called the torsion angle when referring to two substituents separated by three bonds.
Eclipsed	Having substituents at the closest spatial distance from substituents on an adjacent centre, so the dihedral angle is zero.
Enantiomer	A pair of enantiomers is a pair of stereoisomers that are non-superimposable mirror images of one another.
Enantiotopic	A relationship between two groups in a molecule where replacement of one group vs. the other group gives rise to a pair of enantiomers.
Equatorial	Used to describe groups bonded to cyclic structures where the bonds lie approximately in the plane of the ring.
E/Z stereochemistry	Stereoisomerism due to differing configurational arrangements of groups in alkenes, defined using the Cahn–Ingold–Prelog (CIP) rules.
Facial (fac)	Of an octahedral MA₃B₃ coordination complex, when the three A ligands (and B ligands) lie on a face of the octahedron.
Fiducial point	A reference point added to a diagram to aid visualisation.
Flip method	A way of manipulating structural drawings to aid assignment of configuration, in which an assignment is flipped according to a protocol.
Functionality (functional group)	Groups of atoms within a molecule that have characteristic properties.
Furanose	A carbohydrate containing a five-membered ring with four carbon atoms and one oxygen atom.
Gauche	Of a conformation, staggered but not periplanar. See also synclinal.
Geminal	Of two groups, on the same carbon atom.
Geometric isomers	Isomers that differ in the spatial arrangement of atoms or groups with respect to a bond where rotation is restricted.
Half-chair	A conformation of cyclohexane and derivatives with part of a chair shape and five carbon atoms in the same plane.
Hashed	By convention, a bond drawn hashed is projecting away from the viewer.
Homotopic	A relationship between two groups in a molecule where replacement of one group vs. the other gives the same compound.
Hybridisation	A combination of orbitals on the same atom.
Inversion	Of a pyramidal sp³ hybridised centre with a lone pair, a switch in configuration passing through a planar sp² hybridised transition state.
Isomers	Molecules that have the same molecular formula but have different line or stereochemical formulae and so have different properties.
Karplus relationship	A mathematical model of how coupling constants vary with dihedral angle.
Magnetic equivalence	Where nuclei are indistinguishable by NMR spectroscopy.
Meridional (mer)	Of an octahedral MA₃B₃ coordination complex, when the three A ligands (and B ligands) lie in a plane with each other and the central metal atom.
meso compound	A compound that contains two or more stereogenic atoms but that is superimposable on its mirror image and therefore achiral.
Monodentate	Of a ligand, attached to the metal atom of a coordination complex by one interaction.
Newman projection	A way of drawing a molecule to represent the relative positions of bonds on two adjacent atoms. The viewer imagines looking along the bond between the two atoms in question.
Octahedral	Of a coordination complex with six ligands, when all the ligands are approximately equidistant from each other and as far apart as possible.
Optical activity	The way in which non-racemic chiral molecules rotate a plane of polarised light.
Optical rotation	The rotation of a plane of polarised light by a non-racemic, chiral sample, usually measured in a polarimeter.
Orthogonal	Perpendicular.
Periplanar	Of a conformation, in the same plane as. May be syn or anti.
Pi bond (π bond)	Bond formed through lateral overlap of lobes of p orbitals on adjacent atoms.
Pseudoaxial	As axial, but used when discussing rings or cyclic transition states that are not in true chair conformations.
Pseudochirality	Apparent chirality that arises from two otherwise identical substituents having opposite configurations.
Pseudoequatorial	As equatorial, but used when discussing rings or cyclic transition states that are not in true chair conformations.
Pyranose	A carbohydrate containing a six-membered ring with five carbon atoms and one oxygen atom.
Racemic mixture (racemate)	A racemic mixture or racemate is a 1 : 1 mixture of enantiomers.
Relative stereochemistry	The spatial arrangement of a substituent (e.g. at one stereogenic centre) relative to a substituent at another atom e.g. on the same side (*syn) or the opposite side (anti*).
Resonance	A way of representing a structure as the sum of localised contributory structures.
Sawhorse projection	A way of drawing a molecule to represent the relative positions of bonds on two adjacent atoms. The bond between the two key atoms is drawn as a diagonal from lower left to upper right. One of the bonds to each of the two key atoms is then drawn as vertical, these two pointing towards each other. Remaining bonds are drawn at 120°.
Sigma bond (σ bond)	Bond formed through overlap of orbitals lying along the axis of the bond.
Square planar	Of a four-coordinate complex, when the metal and four ligands all lie in the same plane with the ligands approximately equidistant.
Square pyramidal	Of a five-coordinate complex, when four of the ligands all lie in the same plane with the ligands equidistant and a fifth ligand lies out of the plane to form a pyramid with a square base.
Staggered	Having substituents at the maximum spatial distance from substituents on an adjacent centre.
Stereogenic axis (axis of chirality)	An axis about which a set of groups is held so that it results in a spatial arrangement that is not superimposable on its mirror image.
Stereogenic centre (stereocentre)	For atoms with tetrahedral geometry, an atom that has four different substituents attached to it.
Stereochemistry	A topic in chemistry concerned with the spatial arrangement of atoms in a molecule and how the spatial arrangement affects structure and reactivity.
Stereoisomers	Isomers that have the same connectivity between atoms, including the same bond multiplicities, and so differ only in the spatial arrangement of their atoms.
Substituent	An atom or group other than a hydrogen atom that is bonded to an atom of interest.
Superimposable	Of two objects (e.g. molecules), identical, so that an image of one object maps exactly onto an image of the other.
Swap method	A way of manipulating structural drawings to aid assignment of configuration, in which substituents are swapped according to a protocol.
syn	On the same side as an atom or group on another carbon atom when the chain is drawn zig-zag.
Synclinal	Of a conformation, staggered but not periplanar. See also gauche.
Theoretical modelling	A way to use a theory to make predictions about a system.
Torsional strain	The increase in energy resulting from the unfavourable interaction of electrons in two separate bonds.
Tridentate	Of a ligand, attached to the metal atom of a coordination complex by three interactions.
Trigonal bipyramidal	Of a coordination complex, when the metal and three of the five ligands all lie in the same plane with the ligands equidistant and the fourth and fifth ligand lie out of the plane on opposite sides to form two fused pyramids with a common triangular base.
Twist-boat	A conformation of cyclohexane and derivatives that resembles a twisted boat conformation.
VSEPR	Valence Shell Electron Pair Repulsion theory.
Vicinal angle	Used in NMR spectroscopy with the same meaning as dihedral angle.
Wedged	By convention, a bond drawn as a bold wedge is projecting towards the viewer.
Zig-zag	By convention, the main chain of a molecule is drawn in the plane of the page so that the chain extends continually across the page, creating a zig-zag pattern.

Term	Definition
Absolute stereochemistry	The precise spatial arrangement of substituents around a stereogenic centre.
Achiral	An object that is superimposable on its mirror image is said to be achiral.
anti	On the opposite side to an atom or group on another carbon atom when the chain is drawn zig-zag.
Anomeric effect	A preference for heteroatomic substituents adjacent to a heteroatom that is part of a ring to adopt the axial, rather than the equatorial, position.
Anticlinal	Of a conformation, eclipsed but not periplanar.
Atomic number	The number of protons in the nucleus of a given element.
Atropisomer	A conformer that can be isolated as a separate chemical species and arises from restricted rotation about a single bond.
Axial	Used to describe groups bonded to cyclic structures where the bonds are perpendicular to the plane of the ring.
Bidentate	Of a ligand, attached to the metal atom of a coordination complex by two interactions.
Boat conformation	A conformation of cyclohexanes and their derivatives with a boat shape.
Chair conformation	An important conformation of cyclohexanes and their derivatives with a chair shape.
Chiral	An object (e.g. a molecule) that is non-superimposable on its mirror image is said to be chiral.
CIP rules	Cahn–Ingold–Prelog rules, which can be used in assignment of configurational descriptors.
cis/trans stereoisomerism	Stereoisomerism due to differing configurational arrangements of two groups that can be on the same or opposite sides of a molecule.
Configuration	The spatial arrangement of atoms in a molecule that can only be altered by breaking and making bonds. Configurational isomers can be e.g. enantiomers or diastereoisomers.
Conformation	The spatial arrangement of atoms in a molecule that can be altered by rotation about one or more single bonds and does not require breaking and making bonds. Conformational isomers are known as conformers.
Conformational isomers	Species that are interchangeable via rotation around one or more single bonds (conformations) and that lie at an energy minimum.
Conformers	Species that are interchangeable via rotation around one or more single bonds (conformations) and that lie at an energy minimum.
Coupling constant	A measure, usually in hertz, of the interaction between two NMR-active nuclei.
Decalin	A bicyclic compound comprising two fused cyclohexane rings.
Diastereoisomer	Diastereoisomers are stereoisomers that are non-superimposable, non-mirror images.
Diastereotopic	A relationship between two groups in a molecule where replacement of one of the two groups vs. the other gives rise to a pair of diastereoisomers.
1,3-Diaxial interactions	Of atoms or groups in axial positions of a chair conformation, the interactions such groups have with similar groups four bonds away (e.g. on carbon atoms 1 and 3).
Dihedral angle	The angle between two planes. Also called the torsion angle when referring to two substituents separated by three bonds.
Eclipsed	Having substituents at the closest spatial distance from substituents on an adjacent centre, so the dihedral angle is zero.
Enantiomer	A pair of enantiomers is a pair of stereoisomers that are non-superimposable mirror images of one another.
Enantiotopic	A relationship between two groups in a molecule where replacement of one group vs. the other group gives rise to a pair of enantiomers.
Equatorial	Used to describe groups bonded to cyclic structures where the bonds lie approximately in the plane of the ring.
E/Z stereochemistry	Stereoisomerism due to differing configurational arrangements of groups in alkenes, defined using the Cahn–Ingold–Prelog (CIP) rules.
Facial (fac)	Of an octahedral MA₃B₃ coordination complex, when the three A ligands (and B ligands) lie on a face of the octahedron.
Fiducial point	A reference point added to a diagram to aid visualisation.
Flip method	A way of manipulating structural drawings to aid assignment of configuration, in which an assignment is flipped according to a protocol.
Functionality (functional group)	Groups of atoms within a molecule that have characteristic properties.
Furanose	A carbohydrate containing a five-membered ring with four carbon atoms and one oxygen atom.
Gauche	Of a conformation, staggered but not periplanar. See also synclinal.
Geminal	Of two groups, on the same carbon atom.
Geometric isomers	Isomers that differ in the spatial arrangement of atoms or groups with respect to a bond where rotation is restricted.
Half-chair	A conformation of cyclohexane and derivatives with part of a chair shape and five carbon atoms in the same plane.
Hashed	By convention, a bond drawn hashed is projecting away from the viewer.
Homotopic	A relationship between two groups in a molecule where replacement of one group vs. the other gives the same compound.
Hybridisation	A combination of orbitals on the same atom.
Inversion	Of a pyramidal sp³ hybridised centre with a lone pair, a switch in configuration passing through a planar sp² hybridised transition state.
Isomers	Molecules that have the same molecular formula but have different line or stereochemical formulae and so have different properties.
Karplus relationship	A mathematical model of how coupling constants vary with dihedral angle.
Magnetic equivalence	Where nuclei are indistinguishable by NMR spectroscopy.
Meridional (mer)	Of an octahedral MA₃B₃ coordination complex, when the three A ligands (and B ligands) lie in a plane with each other and the central metal atom.
meso compound	A compound that contains two or more stereogenic atoms but that is superimposable on its mirror image and therefore achiral.
Monodentate	Of a ligand, attached to the metal atom of a coordination complex by one interaction.
Newman projection	A way of drawing a molecule to represent the relative positions of bonds on two adjacent atoms. The viewer imagines looking along the bond between the two atoms in question.
Octahedral	Of a coordination complex with six ligands, when all the ligands are approximately equidistant from each other and as far apart as possible.
Optical activity	The way in which non-racemic chiral molecules rotate a plane of polarised light.
Optical rotation	The rotation of a plane of polarised light by a non-racemic, chiral sample, usually measured in a polarimeter.
Orthogonal	Perpendicular.
Periplanar	Of a conformation, in the same plane as. May be syn or anti.
Pi bond (π bond)	Bond formed through lateral overlap of lobes of p orbitals on adjacent atoms.
Pseudoaxial	As axial, but used when discussing rings or cyclic transition states that are not in true chair conformations.
Pseudochirality	Apparent chirality that arises from two otherwise identical substituents having opposite configurations.
Pseudoequatorial	As equatorial, but used when discussing rings or cyclic transition states that are not in true chair conformations.
Pyranose	A carbohydrate containing a six-membered ring with five carbon atoms and one oxygen atom.
Racemic mixture (racemate)	A racemic mixture or racemate is a 1 : 1 mixture of enantiomers.
Relative stereochemistry	The spatial arrangement of a substituent (e.g. at one stereogenic centre) relative to a substituent at another atom e.g. on the same side (*syn) or the opposite side (anti*).
Resonance	A way of representing a structure as the sum of localised contributory structures.
Sawhorse projection	A way of drawing a molecule to represent the relative positions of bonds on two adjacent atoms. The bond between the two key atoms is drawn as a diagonal from lower left to upper right. One of the bonds to each of the two key atoms is then drawn as vertical, these two pointing towards each other. Remaining bonds are drawn at 120°.
Sigma bond (σ bond)	Bond formed through overlap of orbitals lying along the axis of the bond.
Square planar	Of a four-coordinate complex, when the metal and four ligands all lie in the same plane with the ligands approximately equidistant.
Square pyramidal	Of a five-coordinate complex, when four of the ligands all lie in the same plane with the ligands equidistant and a fifth ligand lies out of the plane to form a pyramid with a square base.
Staggered	Having substituents at the maximum spatial distance from substituents on an adjacent centre.
Stereogenic axis (axis of chirality)	An axis about which a set of groups is held so that it results in a spatial arrangement that is not superimposable on its mirror image.
Stereogenic centre (stereocentre)	For atoms with tetrahedral geometry, an atom that has four different substituents attached to it.
Stereochemistry	A topic in chemistry concerned with the spatial arrangement of atoms in a molecule and how the spatial arrangement affects structure and reactivity.
Stereoisomers	Isomers that have the same connectivity between atoms, including the same bond multiplicities, and so differ only in the spatial arrangement of their atoms.
Substituent	An atom or group other than a hydrogen atom that is bonded to an atom of interest.
Superimposable	Of two objects (e.g. molecules), identical, so that an image of one object maps exactly onto an image of the other.
Swap method	A way of manipulating structural drawings to aid assignment of configuration, in which substituents are swapped according to a protocol.
syn	On the same side as an atom or group on another carbon atom when the chain is drawn zig-zag.
Synclinal	Of a conformation, staggered but not periplanar. See also gauche.
Theoretical modelling	A way to use a theory to make predictions about a system.
Torsional strain	The increase in energy resulting from the unfavourable interaction of electrons in two separate bonds.
Tridentate	Of a ligand, attached to the metal atom of a coordination complex by three interactions.
Trigonal bipyramidal	Of a coordination complex, when the metal and three of the five ligands all lie in the same plane with the ligands equidistant and the fourth and fifth ligand lie out of the plane on opposite sides to form two fused pyramids with a common triangular base.
Twist-boat	A conformation of cyclohexane and derivatives that resembles a twisted boat conformation.
VSEPR	Valence Shell Electron Pair Repulsion theory.
Vicinal angle	Used in NMR spectroscopy with the same meaning as dihedral angle.
Wedged	By convention, a bond drawn as a bold wedge is projecting towards the viewer.
Zig-zag	By convention, the main chain of a molecule is drawn in the plane of the page so that the chain extends continually across the page, creating a zig-zag pattern.

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