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Tetrahedral stereochemistry recommendations

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Introduction

Need some overview of the general problems in depicting three-dimensional structures on a two-dimensional medium such as a computer screen or a piece of paper.

Depictions

When depicting tetrahedral configuration around a stereogenic atom, the following depictions may be considered. Each of these depictions can be freely rotated in the plane of the paper without affecting the configuration being represented.

As per the general recommendations for depiction of stereochemistry, solid wedged bonds are preferred to hashed wedged bonds. If there are no other constraints on the orientation of the structure (as there would be, for example, in steroids), it would be preferred to position the structure so that it has the maximum number of solid wedged bonds.

PREFERRED ACCEPTABLE

Also, as per the general recommendations for angles between acyclic bonds, if any pair of non-identical substituents attached to a single atom is arranged horizontally, the graphically larger substituent should be to the right of the smaller one for aesthetic purposes. In this context, "graphically larger" refers to the size of the substituent within the drawing itself: An "OH" atom label is graphically larger than an "I" atom label because it consists of two characters rather than one, even though the iodine atom might be physically larger than the hydroxy group in terms of van der Waals radius.

Several of these depiction styles have three plain bonds, which in other cases would imply that those bonds are coplanar. In reality, tetrahedral configurations can never have three coplanar bonds. The use of three plain bonds in these cases is simply a matter of convention, and chemists will readily be able to understand the true tetrahedral nature of the center when any of the preferred or acceptable depiction styles is used.

PREFERRED
Two plain bonds, one solid wedged bond, and one hashed wedged bond, with the two plain bonds depicted as adjacent and separated by less than 180° (ideally, 120° as shown here). Since the two plain bonds are depicted as adjacent, the hashed wedged and solid wedged bond will also necessarily be depicted as adjacent, and they should be separated by less than the separation between the plain bonds (ideally, 60° as shown here).

The bisectors of the A-B and C-D angles should preferably be colinear. If they are not colinear, the depiction is still acceptable, but not preferred.

ACCEPTABLE

It may be noted that these depictions are not geometrically accurate in the strictest sense. If a tetrahedral center were positioned so that it was viewed orthogonal to the plane described by substituents A, B, and the central atom, then substituent D would completely obscure substituent C or vice versa. Nonetheless, chemists have long been trained to ignore that subtlety, and this remains among the preferred representations of tetrahedral configuration.

 

WRONG
Two plain bonds, one solid wedged bond, and one hashed wedged bond, with the two plain bonds depicted as adjacent and separated by 180°. Since the two plain bonds are depicted as adjacent, the hashed wedged and solid wedged bond will also necessarily be depicted as adjacent.

This depiction represents a see-saw configuration rather than a tetrahedral one and is not acceptable for representing tetrahedral configurations.

 

WRONG
Two plain bonds, one solid wedged bond, and one hashed wedged bond, with the two plain bonds depicted as adjacent and separated by greater than 180°. Since the two plain bonds are depicted as adjacent, the hashed wedged bond and solid wedged bond will also necessarily be depicted as adjacent, and are positioned within the smaller angle described by the plain bonds.

This depiction represents a square pyramidal configuration rather than a tetrahedral one and is not acceptable for representing tetrahedral configurations.

 

NOT ACCEPTABLE

Two plain bonds, one solid wedged bond, and one hashed wedged bond, with the two plain bonds separated by other than 180° and not depicted as adjacent.

These depictions are formally ambiguous and cannot be interpreted with certainty. They should never be used. Historically, they have been used in several situations that can sometimes be interpreted without certainty, but alternate acceptable representations are possible in all of those cases.

When depicting substituents at bridgehead atoms, some chemists have been tempted to depict the substituent atom using the wedged bond style that is opposite to the one used for the bridging bonds, apparently on the assumption that "if the bridge goes 'up', then the other substituent must go 'down'." In fact, if the ring system is oriented in the plane of the paper and the bridging bonds are oriented upwards, then the substituents are oriented upwards as well. Such structures should be depicted with substituents that use the same bond type as the bridging bonds. The substituents may also be depicted using plain bonds.

PREFERRED ACCEPTABLE WRONG

When depicting substituents at fusion atoms, one acceptable orientation of the substituent is vertically upwards/downwards from the atom, even if that places the substituent within the ring system (this is particularly common for steroids). Wedged bonds placed in this orientation may conflict with an opposite wedge on another of the fusion bonds. In such a case, that other fusion bond should be depicted using a plain bond.

NOT ACCEPTABLE PREFERRED

When depicting substituents to rings drawn in perspective, some chemists have been tempted to use solid wedged bond and hashed wedged bonds to indicate the substituents' positions relative to the ring without regard to their positioning in the diagram. The use of solid wedged bonds and hashed wedged bonds should always take into consideration the actual orientation of each substituent as drawn.

NOT ACCEPTABLE ACCEPTABLE

 

WRONG
Two plain bonds, one solid wedged bond, and one hashed wedged bond, with the two plain bonds separated by 180° and not depicted as adjacent.

These depictions represent square planar configurations rather than tetrahedral ones and are not acceptable for representing tetrahedral configurations.

 

PREFERRED
Three plain bonds and one wedged bond, with each pair of plain bonds separated by less than 180° (ideally, 120° as shown here). The wedged bond can be positioned in any orientation but will usually bisect one of the other angles as shown here. Additionally, the substituent D at the end of the wedged bond should generally be among the graphically smallest of the four.

Since in this style the drawing implies that the central atom is coplanar with substituents A, B, and C, it is technically incorrect in the strictest sense. In preference it should only be used for cases where the central atom is in a fused or bridged ring system.

PREFERRED PREFERRED

When at least two of the central atom's substituents are acyclic, the first recommendation above, with two plain bonds, one solid wedged bond, and one hashed wedged bond, is preferred.

PREFERRED ACCEPTABLE

 

ACCEPTABLE (*)

Three plain bonds and one wedged bond, with one pair of plain bonds separated by 180° or more and the wedged bond positioned within that largest space between plain bonds.

This depiction style should be used with caution. It is a preferred style when substituents A, B, and C are all part of the same ring system. In depiction of ring systems, the constraints of the ring system determine the positioning of the three plain bonds and those constraints take precedence over other matters.

PREFERRED PREFERRED

This depiction is an acceptable style when two of the plain bonds are within a ring. There would likely be a more preferred way of representing a tetrahedral stereocenter of this type, but this depiction is unambiguous.

ACCEPTABLE

This depiction is also an acceptable style when the wedged bond is itself within a ring system. This style is used primarily when the ring system is shown in perspective, with the wedged bond helping to indicate that perspective.

ACCEPTABLE

This depiction style must not be used when all four substituents are acyclic, since structures of this sort are ambiguous and cannot be interpreted reliably.

NOT ACCEPTABLE

 

WRONG

Three plain bonds and one wedged bond, with one adjacent pair of plain bonds separated by 180° or more and the wedged bond not positioned within that largest space between plain bonds.

These depictions represent see-saw or square pyramidal configurations rather than tetrahedral ones and are not acceptable for representing tetrahedral configurations.

 

NOT ACCEPTABLE

Three bonds of the same wedged type (solid wedged or hashed wedged) and one bond of another type (the opposite wedge type, or plain), with each pair of identically wedged bonds separated by less than 180° (ideally, 120° as shown here). The fourth bond can be positioned in any orientation but will usually bisect one of the other angles as shown here.

Although these depictions are formally unambiguous, they should be avoided due to the overabundance of wedged bonds.

NOT ACCEPTABLE

Three bonds of the same wedged type (solid wedged or hashed wedged) and one bond of another type (the opposite wedge type, or plain), with one adjacent pair of identically wedged bonds separated by 180° or more and the fourth bond positioned within that largest space between the identically wedged bond bonds.

These depictions are formally ambiguous and cannot be interpreted with certainty. They should never be used.

ACCEPTABLE

Two bonds of the same wedged type (solid wedged or hashed wedged) and one bond of another type (the opposite wedge type, or plain), with each adjacent pair separated by 90°, and with alternating bond types.

This depiction style is not preferred, but it is still acceptable.

 

ACCEPTABLE

Two bonds of the same wedged type (solid wedged or hashed wedged) and one bond of another type (the opposite wedge type, or plain), with each adjacent pair separated by other than 90°, and with alternating bond types.

Although these depictions are formally unambiguous, they can be extremely confusing to the reader due to their infrequent use in the published literature. They should be avoided.

 

WRONG
Two solid wedged bonds and two hashed wedged bonds, with each adjacent pair of bonds separated by less than 180°, and with similar bond types depicted as adjacent.

This depiction represents a square planar configuration rather than a tetrahedral one and is not acceptable for representing tetrahedral configurations.

 

WRONG
Two solid wedged bonds and two hashed wedged bonds, with one pair of identically-wedged bonds separated by 180° or more and with the other pair positioned within the smaller angle described by the first pair.

These depictions represent square pyramidal configurations rather than tetrahedral ones and are not acceptable for representing tetrahedral configurations.

 

NOT ACCEPTABLE

Two wedged bonds of the same type (either solid wedged or hashed wedged) and two plain bonds, with each adjacent pair of bonds separated by 180° or less, and with similar bond types depicted as adjacent.

These depictions are formally ambiguous and cannot be interpreted with certainty. They should never be used.

 

WRONG
Two wedged bonds of the same type (either solid wedged or hashed wedged) and two plain bonds, with the pair of plain bonds separated by more than 180°, and with the wedged bonds positioned within the smaller angle described by the first pair.

These depictions represent square pyramidal configurations rather than tetrahedral ones and are not acceptable for representing tetrahedral configurations.

 

WRONG

Four wedged bonds of the same type (either solid wedged or hashed wedged) positioned at any angles.

These depictions represent square pyramidal configurations rather than tetrahedral ones and are not acceptable for representing tetrahedral configurations.

NOT ACCEPTABLE
One plain bond and two wedged bonds of the same type (either solid wedged or hashed wedged), each pair separated by less than 180°, and a fourth bond of the opposite wedged type positioned between the two similar wedged bonds.

Although these depictions are formally unambiguous, they should be avoided due to the overabundance of wedged bonds.

NOT ACCEPTABLE

One plain bond and two wedged bonds of the same type (either solid wedged or hashed wedged) and a fourth bond of the opposite wedged type positioned between the two similar wedged bonds, with any adjacent pair of bonds separated by 180° or more.

Although these depictions may represent square planar, square pyramidal, or see-saw configurations, they should be avoided regardless due to the overabundance of wedged bonds. These configurations will be formally ambiguous in some combinations of bond angles.

NOT ACCEPTABLE
One plain bond and two wedged bonds of the same type (either solid wedged or hashed wedged), each adjacent pair separated by less than 180°, and a fourth bond of the opposite wedged type not positioned between the two similar wedged bonds.

Although these depictions are formally unambiguous, they should be avoided due to the overabundance of wedged bonds.

NOT ACCEPTABLE

One plain bond and two wedged bonds of the same type (either solid wedged or hashed wedged) and a fourth bond of the opposite wedged type not positioned between the two similar wedged bonds, with any adjacent pair of bonds separated by 180° or more.

Although these depictions may represent square planar, square pyramidal, or see-saw configurations, they should be avoided regardless due to the overabundance of wedged bonds. These configurations will be formally ambiguous in some combinations of bond angles.

 

The drawing of a stereocenter containing a hydrogen atom will generally appear less encumbered if that substituent is omitted. Tetrahedral atoms with one hydrogen substituent can usually omit the hydrogen (this is a change from earlier recommendations), but it is always acceptable to depict the hydrogen explicitly. Structures depicted with explicit hydrogens are less ambiguous than those with implicit hydrogens; however, the rigorous display of all explicit hydrogens also adds to the overall congestion of a diagram and can quickly render a depiction illegible even for moderately sized structures.

Hydrogens should be omitted from tetrahedral atoms only when the resulting structure is unambiguous. In this context, it means that a substituent at the end of the wedged bond should have a maximum of two non-hydrogen substituents including the wedged bond itself. It is also acceptable to omit the hydrogen in cases where the substituent has more than two non-hydrogen substituents as long as the substituent itself is achiral. Care should be taken in that case, however, that the substituent cannot possibly be interpreted as being asymmetric, and should generally be limited to common small substituents such as unsubstituted rings, tert-butyl groups, and so on.

PREFERRED

Hydrogens must not be omitted when the other substituent is itself asymmetric, since stereobonds must be avoided between two stereocenters when any alternative is available.

PREFERRED NOT ACCEPTABLE

A trigonal pyramidal atom may be considered as similar to a tetrahedral atom having three explicit bonds, where the position of the fourth "bond" in the case of a trigonal pyramidal atom is occupied by a lone pair rather than an implicit hydrogen atom. Depictions of trigonal pyramidal atoms are discussed more fully as part of the non-tetrahedral stereochemistry recommendations.

When depicting tetrahedral configuration around a stereogenic atom with three explicitly drawn bonds, the following configurations may be considered:

PREFERRED

Two plain bonds and one wedged bond, with the pair of plain bonds separated by less than 180° (ideally, 120° as shown here) and the wedged bond opposing the A-B angle. Additionally, the substituent C at the end of the wedged bond should generally be among the graphically smallest of the three.

The wedged bond should preferably be colinear with the bisector of the A-B angle. If it is not colinear, the depiction is still acceptable, but not preferred.

ACCEPTABLE

The implied hydrogen or lone pair in this depiction is assumed to be behind the C substituent, thus: 

 

ACCEPTABLE

Two plain bonds and one wedged bond, with the pair of plain bonds separated by less than 180° and the wedged bond positioned within the smaller space between plain bonds.

The implied hydrogen or lone pair in this depiction is assumed to be opposite the A-B angle relative to the C substituent. This leads to the observation that the absolute stereochemistry of a tetrahedral configuration depicted with two plain bonds and one wedged bond is unchanged regardless of where the wedged bond is positioned, thus: 

This depiction style should be used with caution. It is the preferred style when substituent C is a bridgehead bond of a bridged ring system. In depiction of ring systems, the constraints of the ring system determine the positioning of the three bonds and those constraints take precedence over other matters.

PREFERRED

This depiction is also an acceptable style when at least two of the three bonds are within a ring system. This style is used primarily when the ring system is shown in perspective, with the wedged bond helping to indicate that perspective.  As discussed in the secton on perspective diagrams, it is preferred to use exclusively plain bonds in perspective diagrams, but the use of solid wedged bonds within a perspective ring remains acceptable.

ACCEPTABLE ACCEPTABLE

When substituents A and B are both within the same non-perspective ring, and the A-B angle is re-entrant (pointing "inward" relative to the ring), this depiction style is not acceptable and should be avoided. In such cases, it will never be clear to the user whether the wedged bond was intended to be interpreted in its normal sense or whether it was intended to be interpreted relative to the plane of the ring as depicted -- and the two senses would result in opposite stereochemical configurations.

NOT ACCEPTABLE ACCEPTABLE ACCEPTABLE

 

WRONG

Two plain bonds and one wedged bond, with the pair of plain bonds separated by 180°.

These depictions represent T-shaped configurations rather than tetrahedral ones and are not acceptable for representing tetrahedral configurations.

ACCEPTABLE

Two plain bonds and one wedged bond, with the wedged bond separated from one of its adjacent plain bonds by 180° or more.

These depictions are acceptable but not preferred. They are most commonly used when the two plain bonds are within a ring displayed in perspective. As discussed in the secton on perspective diagrams, it is preferred to use exclusively plain bonds in perspective diagrams, but the use of solid wedged and hashed wedged bonds within a perspective diagram remains acceptable.

ACCEPTABLE ACCEPTABLE

If these depictions are used, the implied hydrogen is assumed to be positioned in the largest free angle:

 

ACCEPTABLE

One plain bond, one solid wedged bond, and one hashed wedged bond, with the plain bond separated from one of its adjacent wedged bonds by 180° or more.

These depictions are acceptable, but not preferred because they can typically be drawn with fewer wedged bonds. If these depictions are used, the implied hydrogen is assumed to be positioned in the largest free angle:

 

WRONG

One plain bond, one solid wedged bond, and one hashed wedged bond, with the plain bond separated from both of its adjacent wedged bonds by 180° or less.

These depictions represent trigonal planar configurations rather than tetrahedral ones and are not acceptable for representing tetrahedral configurations.

NOT ACCEPTABLE

One plain bond and two wedged bonds of the same type (either solid wedged or hashed wedged) positioned at any angles.

These depictions are acceptable, but not preferred because they can typically be drawn with fewer wedged bonds. If these depictions are used, the implied hydrogen is assumed to be opposite the A-B angle relative to the C substituent:

WRONG

Two wedged bonds of the same type (either solid wedged or hashed wedged) and one wedged bond of the opposite type, with all pairs of adjacent bonds separated by 180° or less.

These depictions represent trigonal planar configurations rather than tetrahedral ones and are not acceptable for representing tetrahedral configurations.
 

NOT ACCEPTABLE

Two wedged bonds of the same type (either solid wedged or hashed wedged) separated by 180° or more and one wedged bond of the opposite type positioned within the smaller angle described by the first two bonds.

Although these depictions are formally unambiguous, they should be avoided due to the overabundance of wedged bonds.

NOT ACCEPTABLE

One solid wedged bond and one hashed wedged bond separated by 180° or more and one wedged bond of either type positioned within the smaller angle described by the first two bonds.

These depictions are formally ambiguous and cannot be interpreted with certainty. They should never be used.

NOT ACCEPTABLE

Three wedged bonds of the same type (either solid wedged or hashed wedged), with all pairs of adjacent bonds separated by 180° or less.

Although these depictions are formally unambiguous, they should be avoided due to the overabundance of wedged bonds.

NOT ACCEPTABLE

Three wedged bonds of the same type (either solid wedged or hashed wedged), with one pair of adjacent bonds separated by 180° or more.

These depictions are formally ambiguous and cannot be interpreted with certainty. They should never be used.
 


Stereogenic atoms in rings

Because of the importance of rings in organic chemistry, it is generally best to keep the ring system(s) as uncomplicated as possible while also preserving the clarity of any individual stereogenic atoms within those rings.

Asymmetric ring atoms with a single non-hydrogen exocyclic substituent should usually be drawn with a wedged bond to that substituent and with the hydrogen implicit. The wedged bond should be positioned so that it is parallel with the bisector of the angle between the two other ring bonds on that atom. However, also see below for a discussion of avoiding stereobonds between stereocenters.

PREFERRED

Asymmetric ring atoms with two simple exocyclic substituents should be drawn with a wedged bond to one substituent and a hashed bond to the other. The two exocyclic bonds should be positioned so that the bisector of the angle between them is colinear with the bisector of the angle between the ring bonds, and the angle between the exocyclic bonds should ideally be close to 60°.

PREFERRED

If one of the exocyclic substituents is complex, it is best to connect it to the ring with a plain bond. The plain bond in that case should itself bisect the angle between the ring bonds, and the remaining substituent, regardless of stereochemical nature (solid wedged or hashed wedged bond), should be positioned to maximize legibility. Typically, that final substituent would be positioned outside the ring and near the bisector of the angle between one of the ring bonds and the larger exocyclic substituent.

PREFERRED

Asymmetric ring fusion atoms should be drawn with hashed wedged or solid wedged bonds to the exocyclic substituent at the fusion atom whenever possible. If necessary, an implicit hydrogen should be made explicit in order to provide an exocyclic substituent to bear the hashed wedged or solid wedged bond. When one of the fusion bonds is oriented vertically and the exocyclic substituent is graphically small (such as a hydrogen or a methyl group, or even such physically larger substituents as a phenyl group represented with a graphically small "Ph" atom label), the exocyclic substituent is also preferentially oriented vertically and opposite to the vertical fusion bond. This orientation is preferred even if it results in the substituent being placed within the ring system, and is particularly common in the depiction of steroids and other natural products.

PREFERRED

Asymmetric spiro fusions are treated similarly to a ring with two exocyclic substituents. The two bonds associated with one of the rings in the spiro fusion should be drawn as plain bonds, while the two bonds associated with the other ring should be drawn with one solid wedged bond and one hashed wedged bond.

PREFERRED

In asymmetric spiro fusions involving rings of different sizes, the solid wedged and hashed wedged bonds are usually associated with the smaller ring.

PREFERRED ACCEPTABLE

Asymmetric spiro fusions involving rings of the same size are often depicted with one ring distorted toward the spiro axis. In such cases, the solid wedged and hashed wedged bonds should be associated with the distorted ring.

PREFERRED NOT ACCEPTABLE

Asymmetric spiro fusions that are themselves adjacent to other stereogenic atoms should be represented using one of the other preferred or acceptable depiction styles for tetrahedral configurations, so that wedged bonds are not depicted with stereogenic atoms on both ends.

PREFERRED

Atoms participating in both regular and spiro fusions should similarly be drawn with one solid wedged and one hashed wedged bond. Those two bonds should be the ones that do not participate in a regular ring fusion. The two bonds that do participate in a regular ring fusion should remain plain.

PREFERRED

Atoms participating in both regular and spiro fusions that are themselves adjacent to other stereogenic atoms should be represented using one of the other preferred or acceptable depiction styles for tetrahedral configurations, so that wedged bonds are not depicted with stereogenic atoms on both ends.

PREFERRED

Tetrahedral centers at re-entrant atoms

Although small ring systems are generally drawn as convex polygons, larger rings containing 9 or more atoms are preferentially drawn as non-convex polygons, with two or more atoms "pointing inward" relative to the rest of the ring. As discussed above, it is not acceptable to depict tetrahedral stereochemistry at re-entrant atoms when any other option is available.

NOT ACCEPTABLE ACCEPTABLE ACCEPTABLE

In some cases there are few appealing alternatives to having stereogenic atoms at some re-entrant positions. A classic example is the core ring of the antibiotic Erythromycin A, shown below. Traditionally, that ring has been depicted with 120° angles at each atom of its 14-membered ring, which results in two stereogenic centers at re-entrant atoms. In such a case, the substituents at the re-entrant atoms should be oriented inwards to the ring as well. It would be preferable to depict the ring in a way that did not require any stereogenic centers at re-entrant atoms.

NOT ACCEPTABLE ACCEPTABLE PREFERRED PREFERRED

In some cases there are few appealing alternatives to having stereogenic atoms at some re-entrant positions. A classic example is the core ring of the antibiotic Erythromycin A, shown below. Traditionally, that ring has been depicted with 120° angles at each atom of its 14-membered ring, which results in two stereogenic centers at re-entrant atoms. In such a case, the substituents at the re-entrant atoms should be oriented inwards to the ring as well. It would be preferable to depict the ring in a way that did not require any stereogenic centers at re-entrant atoms.

ACCEPTABLE NOT ACCEPTABLE

 

ACCEPTABLE ACCEPTABLE

The examples above also demonstrate that solid wedged bonds must be converted to hashed wedged bonds and vice versa when a re-entrant atom is converted to a more-standard convex environment.

Tetrahedral stereocenters connected to a double bond

Tetrahedral stereochemistry requires a tetrahedral arrangement of ligands around a central point. It does not require that all of those ligands be connected to a central atom using single bonds. It is perfectly reasonable to have one or more ligands connected to the central atom using higher-order bonds. This is most commonly seen with chiral sulfoximides, phosphates, and related compounds, each of which is commonly drawn with one or more double bonds. Stereocenters of this type should be indicated by the appropriate placement of bold and/or hashed wedged bonds connecting the central atom to the singly-bonded ligands. Although wedged and hashed double bonds have appeared in the literature, they are rarely required for chemical clarity, and their use is infrequent enough to be confusing to the casual viewer.

PREFERRED PREFERRED ACCEPTABLE

Cumulenes with an even number of double bonds

Cumulenes with an even number of double bonds can be considered as systems with a chiral axis or possessing axial chirality. Four substituents of an even cumulenic system form a distorted tetrahedral arrangement and can be viewed as similar to an atomic center, except with double bonds inserted in the middle and connecting two pairs of substituents. These systems can be interpreted by "squeezing out" the double bonds in the viewer's mind, and considering the four isolated substituents, but this sort of "squeezing out" should be used only to understand this configuration as a distorted tetrahedron and cannot be used to determine absolute Cahn-Ingold-Prelog (CIP) stereodescriptors.

These stereogenic units should be drawn using rules similar to those for regular atomic centers discussed above with a difference that stereobonds may not be used on both ends of the cumulenic system.

PREFERRED PREFERRED PREFERRED PREFERRED PREFERRED

 

NOT ACCEPTABLE NOT ACCEPTABLE NOT ACCEPTABLE

It is unambiguous to depict a cumulenic system with three plain bonds and one hashed or wedged bond, so that depiction style is acceptable. It is, however, fairly unusual to have a plain bond on the same end of a cumulenic system as a solid wedged bond or a hashed wedged bond. This depiction style should be limited to cases when one of the atoms adjacent to the cumulenic system is itself asymmetric, in which case it is desirable to avoid drawing a stereobond between the cumulenic system and a second stereocenter.

ACCEPTABLE ACCEPTABLE

Hindered biaryls

Hindered biaryls (such as 2,2'-disubstituted 1,1'-binaphthyl) represent yet another case of axial chirality. The additional substituents in this system constrain the aromatic rings so that they can no longer rotate freely, and such systems are described as having "hindered rotation". As with cumulenic systems with an even number of double bonds, the stereogenic unit in hindered biaryls can be viewed as a distorted tetrahedron. It can be interpreted by "squeezing out" the rotatable bonds joining the two ring systems in the viewer's mind, and considering the four isolated substituents. As with cumulenic systems, this "squeezing out" should be used only to understand this configuration as a distorted tetrahedron and cannot be used to determine absolute Cahn-Ingold-Prelog (CIP) stereodescriptors.

All biaryls with at least three substituents in the ortho positions have hindered rotation, as the ortho-substituents inhibit coplanarity at least to some extent .

Hindered biaryls should always be drawn with hashed and wedged bonds within the aryl rings and directly connected to the single bonds about which they rotate. Additional bonds within the aryl systems may also optionally be drawn with solid wedged or hashed wedged bonds. Preferably, one ring system of each pair should be drawn exclusively with plain bonds, and the other should be drawn with two solid wedged bonds, one directly connected to the rotating bond and one opposite. In even-membered systems, the bond between the solid wedged bonds should be depicted as bold and unwedged if it does not itself participate in a ring fusion.

PREFERRED ACCEPTABLE ACCEPTABLE ACCEPTABLE ACCEPTABLE ACCEPTABLE

 

PREFERRED ACCEPTABLE ACCEPTABLE ACCEPTABLE ACCEPTABLE

The configuration of the biaryl system should not solely be represented by solid wedged and hashed wedged bonds to other ring substituents that are distant from the rotatable bond.

NOT ACCEPTABLE NOT ACCEPTABLE

Fischer projections

Fischer projections are characterized by one or more asymmetric centers surrounded by four plain bonds arranged in a plus-shaped pattern, with multiple adjacent asymmetric centers aligned vertically. They were originally proposed for the depiction of carbohydrates, and they remain acceptable for the depiction of carbohydrates and their derivatives.

ACCEPTABLE ACCEPTABLE

The use of Fischer projections in non-carbohydrates is problematic. Any drawings of this type are necessarily ambiguous since it is unclear if the author of the drawing intended to make a Fischer projection or simply happened to draw a diagram in that orientation. Structures depicted in the style of Fischer projections are likely to be recognized as such when they contain at least two acyclic stereogenic centers oriented vertically, although such interpretation is not guaranteed. Structures containing a single stereogenic center pose even greater problems since it is often convenient to separate the four ligands by equal angles whether or not a single stereoisomer is intended.

Accordingly, although Fischer projections of carbohydrates are acceptable, similar depictions of non-carbohydrates should be used only when the viewer of the diagram is certain to understand that the diagram was intended to represent a Fischer projection. Fischer projections should be avoided where ambiguity is possible, including when used in computer applications.

In an earlier document ["Stereochemical Definitions and Notations Relating to Polymers (Recommendations 1980)", Pure Appl. Chem. 53, 733-752 (1981).], a related depiction style was discussed in which asymmetric centers were aligned horizontally instead of vertically. That style is no longer preferred, and should not be used outside the context of polymers in any case.

PREFERRED ACCEPTABLE NOT ACCEPTABLE

It is also worth noting that Fischer projections are the only representations of stereochemistry that are not invariant with respect to rotation in the plane of the paper. A Fischer projection rotated 90° represents the enantiomer of the original unrotated structure; in all other cases, a rotated diagram is identical to a non-rotated one.

These comments do not apply to the assorted variants of Fischer projections that have one or more wedged or hashed bonds on each stereocenter. Those can readily be interpreted according to the same rules used for interpreting wedged and hashed bonds in other (non-Fischer) cases.

ACCEPTABLE PREFERRED

Haworth projections

Haworth projections, like Fischer projections, are used primarily in depicting carbohydrates and related compounds such as inositols. These diagrams are characterized by a ring system viewed "in perspective", with wedged and/or bold bonds. There are several subtypes of Haworth projections, including variations with and without hydrogens and variations with and without the bottom-most ring bond drawn as bold. The wedges may also be omitted entirely.

ACCEPTABLE ACCEPTABLE ACCEPTABLE

It is also acceptable to depict the acyclic carbon atoms in a Fischer projection when the main carbohydrate ring is depicted in a Haworth projection.

ACCEPTABLE ACCEPTABLE ACCEPTABLE

Diagrams of this type can be ambiguous in many ways. Even when wedges are present, only two of the four or five asymmetric ring atoms are situated at the narrow ends of wedges. In six-membered rings, one of the stereogenic atoms isn't attached to a wedge at all, either at the wide or the narrow end. When wedges are omitted, matters only get worse.

Any drawings of this type are necessarily ambiguous since it is unclear if the author of the drawing intended to make a Haworth projection or simply happened to draw a diagram in that orientation. Accordingly, these depictions should be used only when the viewer of the diagram is certain to understand that the diagram was intended to represent a Haworth projection. Haworth projections should be avoided where ambiguity is possible, including when used in computer applications.

An alternative to Haworth projections would be to draw the ring system according to standard conventions for depicting structures within a plane. In the context of carbohydrate chemistry, this "from above" drawing style is also known as the Mills depiction [Mills, J. A., Advances in Carbohydrate Chemistry 10, 1-53 (1956)].

PREFERRED PREFERRED

H-Dot/H-Dash/H-Circle

The use of the H-Dot, H-Dash, and H-Circle symbols remains strongly deprecated. These symbols have been used to indicate the position of a hydrogen atom at a ring fusion, with the dot form representing a hydrogen above the plane of the ring and the dash or circle form representing a similar hydrogen below the plane of the ring:

PREFERRED NOT ACCEPTABLE

 

PREFERRED NOT ACCEPTABLE NOT ACCEPTABLE

Unfortunately, the dashes and especially the dots and circles are often very subtle and can be easily overlooked. When clarity is important, they should be avoided.

Even when used, H-Dots, H-Dashes, and H-Circles are meaningful only when positioned on unsaturated ring-fusion carbon atoms containing a single exocyclic hydrogen substituent. They should never be used in any other circumstances.

WRONG