Site hosted by Angelfire.com: Build your free website today!

Use of perspective to indicate configuration

[Main Page]

Introduction

Most often, the three-dimensionality of chemical structures can simply be ignored when creating chemical diagrams. Thus, cyclohexane is traditionally drawn as a regular hexagon even though its prevailing chair configuration is far from planar. Sometimes, however, the precise three-dimensional configuration of a structure is critical to understanding its properties or behavior. Perspective drawings are most often used in bridged ring systems. There are many cases where perspective drawings are highly appropriate (bicyclo[2.2.1]heptane) or unavoidable without significant distortion of the parent structure (cubane, pagodane, buckminsterfullerene).

PREFERRED ACCEPTABLE ACCEPTABLE

The biggest caveat with regard to perspective drawings is straightforward: perspective is a difficult concept. The artwork of M. C. Escher famously demonstrates the ambiguities that can easily arise from the use and misuse of perspective. Even when used completely properly, perspective diagrams of chemical structures rely on subtle visual cues to impart significant changes of meaning in portions of the diagram that are far removed from those cues. In the first depiction of adamantane above, for example, the single bond crossing implies the configuration of all four bridgehead atoms.

Human researchers, for the most part, are trained to understand perspective diagrams and can usually interpret them properly. Unfortunately, computer interpretation of chemical structures is not as advanced. At the current time, few computer-based software packages will recognize perspective at all, let alone recognize it accurately and completely. For this reason, although perspective-based diagrams can be quite useful for humans, they should still be avoided in situations where accurate computer interpretation is important.

Restrictions on perspective drawings

Except where the author specifically wants to convey a three-dimensional concept, the use of perspective drawings should be limited to ring systems, and should usually be further limited to bridged ring systems.

NOT ACCEPTABLE

Perspective drawings of ring systems should always be drawn "from above and to the right", so that the nearer atoms of a mostly-horizontal ring are positioned lower in the drawing than those that are further away. As a guide to the viewer, the front-to-back ordering of crossing bonds must be indicated. That ordering is depicted with a small discontinuity in the backmost bond. In cases where the depicted front-to-back ordering (as indicated by such a discontinuity) conflicts with the notion that the lower atoms be nearer to the viewer, the depicted front-to-back ordering should take precedence and the diagram should be interpreted as being drawn "from below". These situations should be strongly avoided.

PREFERRED NOT ACCEPTABLE NOT ACCEPTABLE NOT ACCEPTABLE

The similar style drawn "from above and to the left" is acceptable, but not preferred because the "from above and to the right" style is much more prevalent in common usage.

NOT ACCEPTABLE

In cases where the depicted front-to-back ordering (as indicated by such a discontinuity) conflicts with the notion that the lower atoms be nearer to the viewer, the depicted front-to-back ordering should take precedence and the diagram should be interpreted as being drawn "from below". These situations should be strongly avoided.

NOT ACCEPTABLE

When considering perspective drawings -- as when considering all types of drawings -- the diagram must be unambiguous, and it is the author's responsibility to use whatever techniques are practical to remove ambiguity. In the specific case of perspective drawings, the proper indication of front-to-back ordering (by use of a discontinuity in the backmost bond) is especially important. Without the use of such a discontinuity, the point of intersection might reasonably be interpreted as an additional quaternary carbon in its own right. It is often possible to depict such structures with no ambiguity or overlap whatsoever if a non-perspective depiction style is used.

ACCEPTABLE NOT ACCEPTABLE ACCEPTABLE

When present, the discontinuity should always be clear and unambiguous. For printed materials, that will generally mean that the discontinuity should be at least twice as wide as the width of a single bond. In low-resolution usages (for example, in GIF or JPEG files on the web or in documents that are expected to be faxed), the discontinuity may need to be larger so that it doesn't risk disappearing due to blurring of the drawing.

Configuration in perspective drawings

At a basic level, a perspective drawing is a simple projection of a three-dimensional structure into a two-dimensional plane. Accordingly, a well-drawn projection always can be interpreted as implying the absolute configuration specified by the original three-dimensional structure. A disubstituted bicyclo[2.2.1]hept-2-ene may be depicted as shown as with a bond crossing shown explicitly.

PREFERRED

In this case, the proper interpretation of the bicyclic system implies that the hydrogens at each bridgehead must be directed outwards relative to the small cyclic system. The hydrogen connected to the lower bridgehead is projecting toward the viewer, while the hydrogen connected to the other bridgehead is projecting away from the viewer.

ACCEPTABLE

Unfortunately, there is a significant limitation in this common approach. If the original drawing -- with no hashes or wedges -- is taken to imply an absolute configuration, then there is no way to depict the similar structure where no absolution configuration is implied. Taken a step further, even the second structure with explicit bridgehead hydrogens leads to further problems. With the presence of the wedged and hashed bond, it is clear that the author intended the two bridgehead atoms to have the absolute configurations shown. However, what is intended by the bridging atom, with the A and B substituents? By perspective, the viewer must assume that it also represents an absolute configuration, but that leads to the same quandary: how would the similar structure be drawn if the absolute configuration at the bridging atom is not known?

Accordingly, perspective drawings must always be interpreted as having fully-specific absolute configuration at all asymmetric atoms (in the absence of other textual description). It is acceptable to further emphasize those stereocenters with additional solid wedged or hashed wedged bonds, but it is not necessary to do so.

PREFERRED ACCEPTABLE ACCEPTABLE

When solid wedged or hashed wedged bonds are used, however, they must be used in agreement with other configurational details implied by the perspectivity.

NOT ACCEPTABLE NOT ACCEPTABLE

If the absolute configuration of a structure is not known, a perspective drawing should not be used, and a flat depiction style should be used instead.

PREFERRED

Use of bold bonds to emphasize perspective

Since perspective diagrams imply a single absolute configuration, it is not necessary to use solid wedged or bold bonds to emphasize that configuration further. Although such bonds may in some cases make the diagram slightly easier for an inexperienced viewer to understand the perspective used, such benefits are counterbalanced by the ambiguities introduced by depictions that incorporate stereobonds that connect two stereocenters.

ACCEPTABLE ACCEPTABLE ACCEPTABLE ACCEPTABLE

Only solid wedged and bold bonds should be used for the purpose of emphasizing perspective. Hashed wedged bonds and hashed unwedged bonds should not be used, either in isolation or in combination with bold bonds.

NOT ACCEPTABLE NOT ACCEPTABLE

It is, of course, always appropriate to depict such a structure in a non-perspective form, in which case solid wedged and hashed wedged bonds would be used normally to indicate stereochemical configuration.

PREFERRED