Introduction

Synopsis.
Introduction
Graphic Representation of Three-Dimensional Structures
References

This is a glossary of the more important, and most widely-used, stereochemical terms. It extends the list of those defined in the IUPAC Nomenclature of Organic Chemistry, Section E: Stereochemistry (Recommendations 1974) [1] and includes some terms from the Glossary of Terms used in Physical Organic Chemistry (Recommendations 1994).[4]. Additional terms have been added from inorganic and macromolecular chemistry. Some misleading terms are included together with guidance on correct usage or acceptable alternatives.

Many of the symbols used in stereochemical nomenclature are mentioned but details of their assignment or their incorporation into chemical names are left to the appropriate recommendations. Terminology related to techniques used in the determination of stereochemistry are largely excluded as well as terms used to describe reaction mechanisms.

Introduction

When the IUPAC Commission on Nomenclature of Organic Chemistry prepared section E: Stereochemistry (Recommendations 1974) [1] the document was primarily intended to describe the naming of stereochemical features as part of the overall nomenclature of organic compounds.[2] In the absence of any IUPAC recommendations on stereochemical terminology Section E included appropriate aspects of the vocabulary of the subject. In 1983 the Commission on Physical Organic Chemistry published a Glossary of terms used in that field [4]. In view of the previous publication of section E stereochemical terms were excluded from this Glossary. However it became apparent that a separate glossary of stereochemical terms would facilitate the work of both commissions and accordingly a joint working party was established with additional representation from the Commission on Nomenclature of Inorganic Chemistry and the Commission on Macromolecular Nomenclature.

The working party considered a very long list of possible terms for inclusion but decided to initially concentrate on those terms which were essential for the work of the commissions and any others which were very widely used, or misused. In the latter case, as well as condemnation of inappropriate terms, guidance on the correct usage, or acceptable alternatives were to be provided. The preparation of a more comprehensive Glossary of Stereochemical Terms was left to a possible second edition, or possibly in a combined glossary with other physical organic chemistry terms.

Many of the symbols used in stereochemical nomenclature are mentioned in this document but it is not intended to provide details of their assignment or how they are incorporated into chemical names. Interested readers are referred in the text to the original published papers and some details are given in the appropriate IUPAC recommendations on organic [2], inorganic [5], and macromolecular [6] chemical nomenclature.

Terminology which relates to techniques used in the determination of stereochemistry [7] is also largely excluded. Some stereochemical terms used to describe reaction mechanisms are already included in the Glossary of Physical Organic Chemistry [4].

Graphic Representation of Three-Dimensional Structures [8]

Structural diagrams which depict stereochemistry must be prepared with extra care to ensure there is no ambiguity. In general plain lines depict bonds approximately in the plane of the drawing; bonds to atoms above the plane are shown with a bold wedge (starting from an atom in the plane of the drawing at the narrow end of the wedge); and bonds to atoms below the plane are shown with short parallel lines . As an alternative a bold bond may be used instead of a bold wedge. A broken line has been used instead of parallel lines but this is better reserved for a partial bond, delocalisation, or a hydrogen bond. The use of a wedge of parallel lines is not recommended as it is ambiguous. It is used commonly in two directly opposite ways. Different workers define the narrow end as being in the plane of the drawing or furthest from the viewer. If stereochemistry is unknown this can be indicated explicitly by a wavy line . The use of dots or open circles at a centre to show stereochemistry is strongly deprecated. Other specific conventions mentioned in the Glossary include Fischer projection, Newman projection, sawhorse projection and wedge projection.

Strict rules for drawing stereochemistry are not possible. In general it is most clear if all rings of an ortho- fused ring system (or saturated derivatives) are kept in the plane of the drawing and bridgehead substituents are shown above or below the plane (1). With an acyclic structure (2) or other substituents on a ring (3) [including bridges (4)] bonds are shown as above or below the plane. Hydrogen atoms attached at stereochemically designated positions should not be omitted (3).

The stereochemistry due to substituents attached to a ring should not be shown at a re-entrant angle [marked with an asterisk on (5); although this is suitable for a carbonyl or N-methyl]. Any bond between two stereochemically designated positions should be left plain (6).

With tetrahedral stereochemistry the following are recommended:

A wavy line can be used to indicate either that the stereochemistry is unknown (7), but only one form is present, or, if explained in the text, that both isomers are present and will be defined when required. If it is intended not to show any stereochemistry it is best to only use plain lines for all bonds. Note that the square planar molecule (8) may also be drawn as (9) or (10).

Double bonds should be shown [(11), (12) and (13)] as far as possible with accurate angles (ca. 120°) if stereochemistry is implied. To show the absence of stereochemical information a linear representation should be used [(14), (15) and (16)].

In a perspective drawing it is preferable to indicate which edge of a ring is considered in front by bold or wedge lines [(17), (18) and (19)]; and "breaking" the bond at the back when a bond passes in front [(17) and (18)]. In this type of stereochemical representation bonds to substituents should usually be left plain.

References

1. IUPAC, Commission on Nomenclature of Organic Chemistry, Section E: Stereochemistry (Recommendations 1974), Pure Appl. Chem. 45, 11-30 (1976), see also [2], [3].

2. IUPAC, Commission on Nomenclature of Organic Chemistry, Nomenclature of Organic Chemistry, Sections A, B, C, D, E, F and H, 1979, Pergamon Press, pp. 473-490; see also IUPAC, Commission on the Nomenclature of Organic Chemistry, A Guide to IUPAC Nomenclature of Organic Chemistry, 1993, Blackwell Scientific Publications, pp. 149-154.

3. International Union of Biochemistry and Molecular Biology, Biochemical Nomenclature and Related Documents, 2nd edition, 1992, Portland Press, pp.1-18.

4. IUPAC, Commission on Physical Organic Chemistry, Glossary of Terms Used in Physical Organic Chemistry, (Recommendations 1994) Pure Appl. Chem., 66, 1077-1184 (1994).

5. IUPAC, Commission on Nomenclature of Inorganic Chemistry, Nomenclature of Inorganic Chemistry (Recommendations 1990), 3rd edition, 1990, Blackwell Scientific Publications, pp. 159-189.

6. IUPAC, Commission on Macromolecular Nomenclature, Compendium of Macromolecular Nomenclature, 1991, Blackwell Scientific Publications, pp. 25-46.

7. IUPAC, Analytical Chemistry Division, Compendium of Analytical Nomenclature, 2nd edition, 1987, Blackwell Scientific Publications; IUPAC, Compendium of Chemical Terminology (IUPAC Recommendations), 1987, Blackwell Scientific Publications.

8. K.L. Loening, in Chemical Structures edited W.A. Warr, 1988, Springer Verlag, pp. 413-423.

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