GRAPHICAL REPRESENTATION OF STEREOCHEMICAL CONFIGURATION, Organic chemistry
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Pure Appl. Chem.
, Vol. 78, No. 10, pp. 1897–1970, 2006.
doi:10.1351/pac200678101897
© 2006 IUPAC
INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY
CHEMICAL NOMENCLATURE AND STRUCTURE REPRESENTATION DIVISION*
GRAPHICAL REPRESENTATION OF
STEREOCHEMICAL CONFIGURATION
(IUPAC Recommendations 2006)
Prepared for publication by
JONATHAN BRECHER
CambridgeSoft Corporation, 100 CambridgePark Drive, Cambridge, MA 02140, USA
*Developed by the Task Group for Graphical Representation Standards for Chemical Structure Diagrams:
Chairman
:
W. Town (UK);
Members
:
J. Brecher (USA), K. N. Degtyarenko (UK), H. Gottlieb (USA),
R. M. Hartshorn (New Zealand), G. P. Moss (UK), P. Murray-Rust (UK), J. Nyitrai (Hungary), W. Powell (USA),
A. Smith (USA), S. Stein (USA), K. Taylor (USA), A. Williams (USA), A. Yerin (Russia);
Corresponding
Members
:
S. Conway (UK), H. Cooke (USA), P. Giles (USA), M. Griffiths (USA), B. Košata (Czech Republic),
B. Ramsay (USA).
Comments and suggestions for future revisions of these recommendations may be sent to Jonathan Brecher
(jsb@cambridgesoft.com) or to the Secretary of the Division.
Membership of the Division Committee when this report was approved:
President
:
A. D. McNaught (UK);
Vice
President
:
G. P. Moss (UK);
Secretary
:
W. H. Powell (USA);
Titular Members
:
T. Damhus (Denmark),
R. M. Hartshorn (New Zealand), H. D. Kaesz (USA), J. Kahovec (Czech Republic), J. Nyitrai (Hungary),
A. Williams (USA), A. Yerin (Russia);
Associate Members
:
J. Brecher (USA), S. Heller (USA), M. Hess
(Germany), A. J. Lawson (Germany), G. J. Leigh (UK), M. Toussant (USA);
National Representatives
:
R. Hoyos de Rossi (Argentina), L. F. Lindoy (Australia), R. de Barros Faria (Brazil), J. He (China), P. Righi (Italy),
C. S. Chin (Korea), J. Reedijk (Netherlands), O. Achmatowicz (Poland), M. Ragnar (Sweden);
Ex Officio
:
R. Cammack (UK).
Republication or reproduction of this report or its storage and/or dissemination by electronic means is permitted without the
need for formal IUPAC permission on condition that an acknowledgment, with full reference to the source, along with use of the
copyright symbol ©, the name IUPAC, and the year of publication, are prominently visible. Publication of a translation into
another language is subject to the additional condition of prior approval from the relevant IUPAC National Adhering
Organization.
1897
1898
J. BRECHER
Graphical representation of
stereochemical configuration
(IUPAC Recommendations 2006)
Abstract
: Stereochemical configuration is determined by the relationship of atoms
in three-dimensional space, yet remains most commonly represented in two-di-
mensional media such as printed publications or computer screens. Recom-
mendations are provided for the display of three-dimensional stereochemical in-
formation in two-dimensional diagrams in ways that avoid ambiguity and are
likely to be understood correctly by all viewers. Examples are provided for all
types of stereochemical configuration, with explanation of which styles are pre-
ferred and which should be avoided. Principal recommendations include:
• Know your audience: Diagrams that have a wide audience should be drawn
as simply as possible.
• Avoid ambiguous drawing styles.
• Avoid the use of perspective diagrams and class-specific drawing styles
(Fischer projections, Haworth projections, etc.) when structures are to be in-
terpreted by computers.
• Use solid wedges to indicate bonds that project above the plane of the paper
and hashed wedges to indicate bonds that project below the plane of the
paper; in both cases, the bonds must be oriented with the narrow end at the
stereogenic center.
• Avoid connecting stereogenic centers with a stereobond.
Keywords
: graphical representation; configuration; recommendations, stereo-
chemical; IUPAC Chemical Nomenclature and Structure Representation Division;
stereochemistry; chirality; chemical structures; chemical structure diagrams.
CONTENTS
ST-0. INTRODUCTION
0.1 Overview
0.2 Plain bonds
0.3 Hashes, dashes, and wedges
0.4 Wavy bonds
0.5 Stereobonds between stereocenters
0.6 Asterisks
0.7 CIP stereodescriptors
0.8 Mixtures of diastereoisomers
ST-1. TETRAHEDRAL CONFIGURATIONS
1.1 Tetrahedral configurations depicted with four explicit bonds
1.2 Tetrahedral configurations depicted with three explicit bonds
1.3 Stereogenic centers in rings
1.4 Tetrahedral centers at re-entrant atoms
1.5 Tetrahedral stereocenters including higher-order bonds
1.6 Systems with an even number of consecutive double bonds
© 2006 IUPAC,
Pure and Applied Chemistry
78, 1897–1970
Graphical representation of stereochemical configuration
1899
1.7 Hindered biaryls
1.8 Fischer projections
1.9 Haworth projections
1.10 Mills depictions
1.11 H-Dot/H-Dash/H-Circle
ST-2. CONFIGURATIONS AT NON-TETRAHEDRAL ATOMS
2.1 Linear
2.2 Angular
2.3 T-shaped
2.4 Trigonal planar
2.5 Trigonal pyramidal
2.6 Square planar
2.7 Square pyramidal
2.8 See-saw
2.9 Trigonal bipyramidal
2.10 Square pyramidal
2.11 Octahedral
2.12 Trigonal prismatic
2.13 Higher coordination numbers
ST-3. USE OF PERSPECTIVE TO INDICATE CONFIGURATION
3.1 Restrictions on perspective drawings
3.2 Configuration in perspective drawings
3.3 Use of bold bonds to emphasize perspective
ST-4. DOUBLE-BOND CONFIGURATIONS
4.1 Positioning of substituents on double bonds
4.2 Other systems with an odd number of consecutive double bonds
4.3 Double bonds in rings
4.4 Double bonds of unspecified configuration
4.5 Double bonds with implicit bonds to substituents
ST-5. OTHER CONFIGURATIONS
5.1 Planar chirality
5.2 Helicenes
5.3 Möbius bands
5.4 Molecular propellers
ST-6. ENANTIOMERS: MIXTURES AND UNKNOWN ABSOLUTE CONFIGURATIONS
6.1 Representation goals
6.2 Absence of indicators indicates configuration as drawn
6.3 Mixtures should be represented with additional explanatory text
6.4 Racemic mixtures and other mixtures in known proportions
6.5 Avoid use of “racemate” and “relative” as structural labels
ST-0. INTRODUCTION
Stereochemistry is the aspect of chemistry concerned with the spatial arrangement of atoms in molec-
ular entities and the effect that differences in the spatial arrangement of atoms have on physical prop-
erties and chemical reactivity. The significance of stereochemistry even in everyday life is famously
demonstrated by the two enantiomers of carvone, where the (
S
)-form provides the odor of caraway
while the (
R
)-form instead smells like spearmint.
© 2006 IUPAC,
Pure and Applied Chemistry
78, 1897–1970
1900
J. BRECHER
Molecular entities are inherently three-dimensional, but they are commonly depicted on two-di-
mensional media such as paper or computer displays. Any depiction of a three-dimensional object on a
two-dimensional surface is going to require some level of distortion, and the problems associated with
the communication of three-dimensional information in two-dimensional media are far from unique to
chemistry. The introduction of perspective, for example, was one of the hallmarks of early Renaissance
artwork. Although the use of perspective is commonplace today in pictorial images, it is less commonly
used in conjunction with symbolic information: mapmakers use contour lines to indicate elevation or
varying shades of blue to indicate ocean depth.
In chemistry, the need to imply the true three-dimensional molecular architecture in two-dimen-
sional media has given rise to a variety of structure drawing conventions. One convention depends on
perspective to convey spatial relationships, just as a pictorial image would. The use of perspective in
structure drawing is discussed in its own section. By far the most common way to represent spatial con-
figuration is through the insertion of special bond types—bold, hashed, dashed, and/or wedged—into
an otherwise planar depiction. Each special bond type would indicate the spatial arrangement of two
atoms in relation to each other, usually specifying that one or the other atom was closer to or further
from the viewer relative to the plane of the diagram. The proper use of hashed wedged and solid wedged
bonds occupies the majority of these recommendations.
Issues of configuration are “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”
[1]. That is, this document is concerned with arrangements of atoms that cannot be interconverted
through the unhindered rotation about single bonds. Historically, the varying conventions for depiction
of configuration have caused confusion among chemists. Any one diagram may or may not have had a
single interpretation either by the chemist who viewed the information or, as is now becoming more im-
portant, by the computer program into which the information was stored. This publication provides a
self-consistent series of recommendations for the unambiguous depiction of molecules in two dimen-
sions using standards that are, for the most part, understandable by both human and machine.
ST-0.1 Overview
Throughout this publication are numerous examples of chemical structure diagrams drawn in styles that
are labeled as “preferred”, “acceptable”, “not acceptable”, or occasionally “wrong”. Since the depiction
of chemical structure diagrams is something of an art form and will likely remain so, it is worthwhile
to clarify the meaning of those terms as they are used here.
A chemical structure diagram is most commonly used simply as a means of identification, a way
to answer the implied question, “What is the chemical structure of X?”. The styles labeled as “pre-
ferred” show how the configuration of a structure should best be indicated in such cases, where there
are no other overriding concerns. These depiction styles are generally applicable across many classes
of compounds.
Sometimes, however, overriding concerns are present. Steroids, for example, should normally be
drawn in a specific fixed orientation [2]. A complex structure might need to be distorted in order to
avoid overlap in other parts of the diagram. Bridged ring systems can be particularly interesting, since
the topology of the ring system itself can force its bonds into orientations that are not seen in acyclic
© 2006 IUPAC,
Pure and Applied Chemistry
78, 1897–1970
Graphical representation of stereochemical configuration
1901
systems. Solid wedged bonds and hashed wedged bonds should not be placed between
two stereogenic centers except when literally unavoidable; that restriction alone accounts for many of
the exceptional cases in this publication. The diagrams labeled as “acceptable” indicate additional de-
piction styles that could be considered if the usually preferred style is problematic in a particular case.
Many of the structural depictions included in this document are provided as counterexamples, to
increase awareness of how structures should
not
be shown. Those depictions are labeled as “not ac-
ceptable”, indicating that they should be strongly avoided in normal usage. Where possible, they have
been accompanied by further description of why they are not acceptable, and why the alternative de-
pictions are preferred or more acceptable. Depictions labeled as “not acceptable” are not acceptable
under any circumstances. They are not simply undesirable alternatives to be avoided when depicting the
specific compounds better shown in nearby diagrams labeled as “preferred” or “acceptable”, but are
“not acceptable” for representing any molecular entities.
Finally, a small number of examples are labeled as simply “wrong”. Those show representations
that should be avoided in all cases, generally because they depict something that is either self-contra-
dictory or because they accurately represent a molecular entity other than the one intended.
Some structural depictions are described as being formally correct, formally incorrect, or for-
mally ambiguous, referring to whether a depiction might possibly represent the intended configuration
from a strictly logical or formal analysis. For example, it is formally incorrect to depict a tetrahedral
configuration using four solid wedged bonds connected to a central atom. Such a depiction would imply
that all four substituents are on the same side of the central atom (all “nearer” the viewer relative to the
plane of the diagram), whereas the geometrical definition of a tetrahedron precludes such an arrange-
ment. The formal correctness of a structural depiction is related to the acceptability of the depiction, but
the two are not exactly the same. Some depictions may be formally incorrect but still preferred because
of long-standing convention. Other depictions may be formally correct but not acceptable. Discussions
of formal correctness are included principally in cases where correctness and acceptability differ.
Several of the depiction styles include descriptions with specific angular measurements. For the
sake of readability, angular measurements are listed with exact numerical values, such as 180°. Unless
otherwise specified, all such measurements should be considered to be approximate, and as specifying
a range within roughly 10° of the listed value. The same applies to textual descriptions of angles, so the
term “linear” should be interpreted as “forming an angle between 170° and 190°”. In other words, two
bonds that look nearly collinear should be treated as exactly collinear, even if that is not exactly true of
their actual geometric relationship.
Similarly, any mention of bonds being “adjacent” refers to their appearance in the two-dimen-
sional representation. Any bond in a physical (three-dimensional) tetrahedron is physically adjacent to
every other bond, but in a two-dimensional representation it is depicted as adjacent to only two others,
and “opposite” to the third. Any pair of bonds described as “separated by” an angle refers only to ad-
jacent bonds, without a third bond drawn within the span of that angle in the two-dimensional depic-
tion.
The recommendations in this publication are intended for use in structural diagrams drawn in the
“standard” two-dimensional format where single bonds are represented with one line segment connect-
ing a pair of atoms, double bonds are represented with two parallel line segments connecting a pair of
atoms, atoms are labeled with atomic symbols (except in the case of most carbon atoms), and so on.
© 2006 IUPAC,
Pure and Applied Chemistry
78, 1897–1970
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