How To Know Whether To Use A Dashed Or Wedged Bond When Drawing Bond Line Structures With R And S

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Conventions for representing stereoconfiguration

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Introduction

Stereochemistry, is the aspect of chemistry concerned with the unlike spatial arrangement of atoms in molecules and compounds and the issue that those differences have on their concrete properties and reactivity. The significance of stereochemistry fifty-fifty in everyday life is famously demonstrated by the two isomers of carvone, where the (S)-(+)-grade of carvone provides the odor of caraway while the (R)-(-)-form instead smells similar spearmint.

	(Southward)-(+)-carvone caraway	(R)-(-)-carvone spearmint

Chemical structures are inherently three dimensional, simply they are commonly depicted on two-dimensional media such as printed paper or electronic reckoner displays. Any delineation of a iii-dimensional object on a two-dimensional surface is going to require some level of baloney.

Chemical data has traditionally been communicated using two-dimensional media such equally the printed page and more recently the figurer screen. The problems associated with the communication of iii-dimensional data in two-dimensional media are far from unique to chemistry. The introduction of perspective, for example, was 1 of the hallmarks of early on Renaissance artwork. Although the utilize of perspective is commonplace today in pictorial images, information technology is less ordinarily used in conjunction with symbolic information: mapmakers use contour lines to indicate elevation or varying shades of bluish to indicate ocean depth.

In chemistry, the need to show the truthful iii-dimensional molecular architecture in two-dimensional media has given rise to a variety of structure drawing conventions. Ane convention depends on perspective to convey spatial relationships, merely equally a pictorial image would. The use of perspective in structure cartoon is discussed here, only in its own section. By far the near mutual way to represent spatial configurations in chemic structures is through the insertion of special bond types -- bold, hashed, dashed, and/or wedged -- into an otherwise planar depiction of a chemical structure. Each special bond blazon would bespeak the spatial system of ii atoms in relation to each other, commonly specifying that one or the other atom was closer to or further from the viewer relative to the plane of the diagram. The proper utilize of hashed wedged and solid wedged bonds occupies the majority of these recommendations.

Historically, the varying conventions for depiction of configuration accept acquired confusion among chemists. Whatsoever one diagram may or may not have had a unmarried interpretation either past the pharmacist who viewed the information or, every bit is now becoming more important, past the computer into which the data was stored. This publication contains a self-consistent series of recommendations for the unambiguous depiction of molecules in two dimensions using standards that are for the most part understandable past both human and machine.

Overview

Throughout this publication are numerous examples of chemical structures fatigued in styles that are labeled every bit "preferred", "acceptable", "not acceptable", or occasionally "wrong". Since the depiction of chemic structures 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 chemic structure diagram is most commonly used just equally a means of identification, a style to answer the unsaid question, "What is the chemic structure of X?". The styles labeled as "preferred" bear witness how the configuration of a structure should best exist indicated in such cases, where there are no other overriding concerns. These depiction styles are mostly applicable across many classes of chemic structures.

Sometimes, however, overriding concerns are nowadays. Steroids, for example, must be drawn in a specific fixed orientation. A complex construction might need to be distorted in order to avoid overlap in other parts of the diagram. Bridged band systems can be particularly interesting, since the topology of the ring system itself can force its bonds into orientations that are not otherwise seen in acyclic systems. Solid wedged and hashed wedged bonds should not be placed betwixt ii atoms that are both disproportionate except when literally unavoidable; that restriction solitary accounts for many of the infrequent cases in this publication. The diagrams labeled as "acceptable" indicate additional depiction styles that could exist considered if the preferred fashion is inappropriate for some well-considered reason.

Many of the structural depictions included in this document are provided as counterexamples, offering clarification of how structures should not be shown. Those depictions are labeled equally "not acceptable", indicating that they should be strongly avoided in normal usage. Where possible, they accept been accompanied by further description of why they are non acceptable, and why the alternative depictions are preferred or more acceptable.

Finally, a small number of examples are labeled as simply "wrong". Those show representations that should be avoided in all cases, generally considering they depict something that is either self-contradictory or because they accurately represent a substance other than the 1 intended.

Some structural depictions are described as being formally right, formally incorrect, or formally 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 iv wedged bonds continued to a central atom. Such a depiction would imply that all iv substituents are on the aforementioned 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 arrangement. The formal definiteness of a structural depiction is related to the acceptability of the delineation, but the two are not exactly the same. Some depictions may be formally incorrect but however preferred considering of long-standing convention. Other depictions may be formally correct just not acceptable. Discussions of formal correctness are included principally in cases where the correctness and the acceptability are different.

Several of the depiction styles include descriptions with specific angular measurements. For the sake of readability, athwart measurements are listed with verbal numerical values, such as 180�. Unless otherwise specified, all such measurements should be considered to be estimate, and specifying a range within roughly 10� of the listed value. The aforementioned applies to textual descriptions of angles, so the term "linear" should be interpreted as "forming an bending between 170� and 190�". In other words, two bonds that look near linear should exist treated as exactly linear, even that is non exactly true for their actual geometric relationship.

Similarly, whatever mention of bonds being "adjacent" refers to their appearance in the two-dimensional representation. Any bond in a physical (three-dimensional) tetrahedron is physically next to every other bond, but in a two-dimensional representation it is depicted as next to only two others, and "reverse" to the third.

The recommendations in this publication are intended for apply in structural diagrams drawn in the "standard" ii-dimensional format where unmarried bonds are represented with 1 line segment connecting a pair of atoms, double bonds are represented with ii parallel line segments connecting a pair of atoms, atoms are labeled with atomic symbols (or not shown at all in the example of carbon atoms), and so on. At that place are other valid ways to represent structures including Newman projections, ball-and-stick models, and many others. These recommendations should non be overgeneralized as applying to annihilation beyond the "standard" 2-dimensional chemic construction diagrams.

This publication extends and supersedes the section titled "Graphic Representation of Three-Dimensional Structures" in the before publication on the Basic Terminology of Stereochemistry [Moss, Chiliad. P. Basic Terminology of Stereochemistry. IUPAC Recommendations 1996. Pure and Practical Chemistry 1996, 68, 2193-2222.]. Only issues related to the depiction of stereochemistry are discussed here; a time to come publication is planned that volition make recommendations regarding non-stereochemical aspects of chemical structure depiction.

Evidently bonds

All single bonds attached to nonstereogenic atoms should normally be drawn as plain bonds, that is, as uncomplicated thin lines that are not assuming or dashed or hashed or wavy or adorned in any other way. The utilise of stereobonds (, , , , , etc.) at nonstereogenic atoms should be avoided.

It is always acceptable to use stereobonds when emphasizing three-dimensional configuration, whether the associated atoms are stereogenic or not. For example, solid wedged bonds and hashed wedged bonds might be used when designating the pro-R and pro-S substituents on a prochiral tetrahedral heart, or when depicting syn, gauche, or anti conformations of a torsion bending. This does not contradict the previous paragraph, as prochiral centers and torsional angles are in fact non normally emphasized every bit such. The utilise of solid wedged bonds and hashed wedged bonds in nonstereogenic environments is outside the telescopic of these recommendations.

Manifestly bonds should be used for nonstereogenic atoms even though the atom�s substituents are not physically coplanar.

When attached to stereogenic atoms, plain bonds indicate the set of bonds that is to be considered as being in the plane of the paper. Other solid wedged or hashed wedged bonds are considered to extend above or below this plane. As a general dominion, structures should be drawn to maximize the number of plain bonds, although there are exceptions (particularly for inorganic complexes with coordination numbers greater than four).

As discussed above, it is always acceptable to use solid and hashed wedged bonds when emphasizing the perspective of three-dimensional configuration, even if an alternate representation is possible that uses fewer stereobonds. Over again, all the same, such exceptions should be considered only when necessary to accommodate some other aspect of the diagram and are not preferred in the general case.

Adequate

Simple rings and fused band systems should be fatigued using plain bonds within the rings. If configuration is to be indicated with hashed wedged and solid wedged bonds, those bonds should be restricted to acyclic substituents. This is true even though in nigh cases the ring atoms will not all be coplanar; the implied coplanarity should be considered on a per-atom basis only, just every bit with acyclic compounds. Depiction of a solid wedged or hashed wedged bond within a band is acceptable just in cases where no reasonable alternative is bachelor (every bit in a spiro fusion, meet ST-i.3, or ) or where all acyclic neighbors are themselves stereogenic (ST-0.5).

Hashes, dashes, and wedges

Structural diagrams that draw configuration must exist prepared with extra intendance to ensure that there is no ambiguity. As discussed above, obviously lines depict bonds approximately in the airplane of the drawing. Bonds to atoms above the airplane should exist shown with a solid wedge (starting from an cantlet in the aeroplane of the drawing at the narrow end of the wedge). A bold bond has sometimes been used instead of a bold wedge just is non recommended.

Unfortunately, bonds below the plane of the drawing have historically been represented in many different ways. Each of those representations has involved a bond fatigued with pocket-sized line segments either parallel () or perpendicular (, ) to the main axis of the bond. The two schools of thought that adopt the use of a hashed wedge bond assign information technology two direct opposite interpretations -- ane schoolhouse says that the cantlet at the narrow finish should be considered in the plane of the newspaper, while the other says that the cantlet at the wide end should be and so considered. Additionally, a dashed line is ofttimes used also to correspond a partial bail, delocalization, or a hydrogen bond. The biggest problem is that there is no style to intuit an author'southward desired meaning from a chemical structure cartoon solitary. For these reasons, chemical structure diagrams should be created so as to avoid these sorts of bonds when doing and then volition non otherwise compromise the clarity of the drawing, and solid wedged bonds should be used instead:

Although a solid wedged bond can frequently be used instead of a hashed wedged bond past drawing the structure slightly differently (as above), that situation is far from universal. There are many cases where the utilise of a hashed bond produces a more artful structure. 1 mutual situation happens with ring systems, where it is ofttimes preferable to depict an explicit hydrogen with a hashed bail rather than put a solid wedge on a ring bond. Another common situation arises when showing a series of enantiomers or diastereoisomers where the contrast between the solid and hashed types directly emphasizes the chemical differences.

In cases where such below-the-plane bonds are required, there is no option that will please everyone. Before recommendations proposed the employ of an unwedged hashed bond , but today such bonds are in fact encountered in the literature to the lowest degree frequently of all options. This document at present recommends the use of a hashed wedged bond interpreted in a sense similar to the solid wedged bond (starting from an atom in the aeroplane of the cartoon at the narrow end of the wedge). This recommendation is fabricated primarily because the hashed wedge is easier to clarify visually than the unwedged type, particularly when it is used in a sense similar to the wedged bold bond. Strictly speaking, unwedged assuming and hashed lines testify that BOTH atoms are higher up or beneath the plane of the drawing (as is used in Haworth drawings of carbohydrates). If these bonds are used to convey chirality, they require actress effort to determine which atoms are truly asymmetric and which are not. The wedged hashed bond contains more than -- and more than useful -- information than the unwedged version. While the use of an unwedged hashed bond is often unambiguous, such a bond is not e'er unambiguous, and in the rare cases that cannot avoid having a hashed bail between stereocenters (see beneath), the unwedged version will never be unambiguous. Additionally, the consistent use of a wedged bond is simpler: in each instance, the sharp end of the bond shows the stereogenic center, and there is no need to analyze both ends to effigy out what was intended. After conscientious consideration, it appears that the merely responsible recommendation is that just the hashed wedged bond be used when representing beneath-the-plane bonds..

Admittedly, potent cases tin be made in favor of other systems. A system based entirely on a perspective-based analysis is possibly the most popular of these other systems. In a perspective-based analysis, more-distant objects are always perceived as smaller than objects that are nearer. Appropriately, a wedged bond is interpreted as extending in a higher place the plane of the newspaper from the narrow finish to the wide cease, and extending behind the plane of the paper when considered from the wide end to the narrow end. Lin et al. have shown that a arrangement of this blazon can be internally self-consistent and can exist used to represent almost types of tetrahedral configurations (Shu-Kun Lin, Luc Patiny, Andrey Yerin, Janusz L. Wisniewski and Bernard Testa. Ane-Wedge Convention for Stereochemical Representations. Enantiomer 2000 , 5, 571-583. http://www.unibas.ch/mdpi/molecules/wedge/wedge2.pdf). Unfortunately, it cannot be used in all cases. Since this system always specifies the configuration of atoms at both ends of every wedged bail, it cannot be used to depict, for example, a tetrahedral center of known configuration continued to four other centers of unknown configuration. Additionally, the One-Wedge system as described past Lin et al. eliminates the use of a hashed wedge bail entirely, thereby discarding a very popular cartoon manner widely used for many years. This simplification has some appeal in terms of simplicity of usage, just the benefits of a hashed bond -- in particular, the ease with which a hashed bond can be distinguished from a bold bond at a quick glance -- are too cracking to eliminate.

Others have recommended a perspective-based analysis that preserves the utilize of a hashed bail. The scheme described before, where a hashed wedged bail would exist interpreted every bit "downwardly" from the broad finish to the narrow end, is a perspective-based approach. Unfortunately, this organization not merely suffers from the same weaknesses as the One-Wedge approach above, only additionally results in a scheme where a solid wedged bond and a hashed wedged bond -- while looking quite dissimilar -- actually represent exactly the same concept. (for a good instance, consider Figures 10a and 11b in Maehr, Hubert. Graphic Representation of Configuration in Two-Dimensional Space. Current Conventions, Clarifications, and Proposed Extensions. J. Chem. Inf. Comput. Sci. 2002, 42, 894-902.)

The responsible recommendation is to pass up a perspective-based approach, and rather to interpret the bonds as more-abstract graphical objects. To summarize, a solid wedged bond should be interpreted as projecting above the plane of the paper from the narrow cease to the broad terminate (with the broad end being nearer to the viewer), and a hashed wedged bond should exist interpreted every bit projecting below the plane of the paper, as well from the narrow end to the wide end (with the wide end being further away from the viewer).

PREFERRED

That said, it is possible to use the other bond types in ways that are unambiguous. In particular, any type of hashed bond is unambiguous when continued to an atom with no other substituents (a hydrogen cantlet, a chlorine atom), no other not-hydrogen substituents (a hydroxy group, an amino grouping), or at most one other non-hydrogen substituent (an ethyl group, an ethoxy group). In each of those cases, a viewer would have no difficulty in understanding that the hashed bond projects below the plane of the paper from the other atom to that atom. Accordingly, both the unwedged hashed bond and the hashed wedged bond with reverse directionality are adequate when used exclusively in those cases.

Yet, anyone using bonds of these types should be aware that they are non the most common bond types used to represent behind-the-airplane configuration. At best, an writer using these types may cause a moment of confusion as a reader figures out which convention was intended. In extreme cases, a reader might really interpret the construction incorrectly � for instance, past interpreting an unwedged hashed bail in the convention where it would represent relative (and not accented) configuration, as discussed in a higher place. Fortunately, such cases are rare. The hashed wedged bond (interpreted from the narrow end to the broad finish) remains preferred.

Because the unwedged hashed bond is visually not-directional, it absolutely must not be used when connecting two stereocenters. (See also ST-0.5.)

NOT Adequate

The dashed bail should exist reserved for the indication of partial bonding of various types, including hydrogen bonding. It should not be used to represent configuration.

Not ACCEPTABLE

Wavy bonds

If configuration is unknown, this can be indicated explicitly past a wavy line . The waves in such a line may exist rounded or angular, but they should be of constant amplitude. The utilize of "wedged wavy" bonds is discouraged.

In well-nigh cases, a wavy bond is conceptually identical to a evidently bail, and a plain bond should exist used instead. Wavy bonds are about ofttimes used in general usage when an author wants to identify special emphasis on the unknown nature of the configuration at a specific position; the wavy bond would usually exist accompanied by additional explanatory text in that example.

Historically, wavy bonds have oft been used to represent a mixture containing several enantiomers or diastereoisomers. That is reasonable, since the configuration of whatever arbitrary structure inside such a mixture is indeed unknown. It is preferred to use a plain bail to depict a mixture, just as it is preferred when depicting single structures. If the nature of the mixture needed further accent, a wavy bond would remain acceptable for mixtures also.

Some specific classes of compounds have farther conventions for depiction of unspecified configuration within those classes. In steroid nomenclature, for instance, atoms 8, 9, 10, 13, and xiv are always assumed to be in standard configuration unless explicitly denoted with a wavy bond. In Haworth projections of carbohydrates, the anomeric carbon is oft indicated with a wavy bond when representing a mixture of anomers. These usages of a wavy bond should not be extended to structures outside those classes.

Stereobonds between stereocenters

Stereobonds betwixt stereocenters should exist avoided at all costs. This was stated above but bears repeating considering it is so important.

In rare cases -- for instance when one stereocenter is completely surrounded by four other stereocenters -- a stereobond must be nowadays between 2 stereocenters. There is no ideal solution in such cases, as some ambiguity is unavoidable. In this case, similar the others, merely the cantlet at the narrow end of a stereobond should be considered as having a specified configuration.

Acceptable

If the cardinal atom has a specific configuration and the surrounding atoms besides have specific configurations, additional stereobonds must be added to the surrounding atoms. It is preferred to select a depiction style for the central atom that has as few stereobonds as possible, since that will eliminate completely any ambivalence regarding the intended configuration at some of the adjacent atoms.

Asterisks

Asterisks have traditionally been used in several contexts: not but to point the presence of a stereogenic center, but likewise to specify isotopic labeling or excited states. Accordingly, the utilise of an asterisk equally an indicator for whatever one of those items (including as an indicator for stereochemistry) is potentially misleading and should be avoided. Any utilize of the asterisk should be undertaken with farthermost care, and should mostly be accompanied by additional descriptive text that explains its meaning in that specific context.

CIP stereochemical indicators

Absolute stereochemical configuration tin be described using descriptors derived from the Cahn-Ingold-Prelog (CIP) priority rules. While quite powerful, the CIP rules can also be difficult for even skilled chemists to interpret correctly. CIP descriptors may certainly be present in a diagram to indicate the absolute configuration, but should never be used equally a replacement for proper stereochemical representation (hashed wedged and solid wedged bonds). Obviously, if a CIP stereodescriptor is included in a diagram, extra care should be used to ensure that it is authentic.