Drawing Chemical Structures

Drawing Chemical Structures

Chemical nomenclature is one of those topics that is, for many, synonymous with IUPAC; and, if there is just one reference that compiles these concepts, it is "the" Principles of Chemical Nomenclature—A Guide to IUPAC Recommendations. Following the latest release of this book in December 2011, Jeffery Leigh, editor and contributing author of "the Principles," began writing a regular column for CI called "Nomenclature Notes" in which he reviews the book's coverage and content, and illustrates the intricacies of the subject.

The Nomenclature Notes in this issue is about chemical structure representation, a topic newly introduced in the 2011 edition of Principles. Leigh starts by noting that "the drawing of chemical structures is not strictly a nomenclature matter." Yet, similar to "textual" nomenclature, it is a communication tool developed and used by chemists. Oliver Sacks in his recent book The Mind's Eye reminds us that Kekule said of himself that he had "an irresistible need for visualization." This is of no surprise to chemists, and it is therefore only fitting that IUPAC set out recommendations on drawing chemical structures.

Drawing chemical structures is an alternative and supplementary tool to traditional nomenclature. Chemists, but also software, can infer chemical nomenclature from structural representations and vise versa. It is an essential communication tool used by instructors and professional chemists. The requirements for standardized drawing are not only aesthetic, but they are driven also by the feasibility (and desirability) of making electronic publications richer by way of embedded information. In chemistry, that includes chemical structure representations. Practically, recommendations for the production of chemical structure diagrams aid in the correct recognition of structural information by computer methodology, such as InChI. Simply put, the idea is to make the structures speak for themselves, not only to human eyes, but more importantly, for the computers that support and drive exchanges of information.

Such standards are a prerequisite for enriching communications about chemistry, especially through new digital media. With that said, I invite you to read Peter Atkins's feature and think about what the advent of e-books will mean for chemistry. With digital devices such as tablet computers providing a plethora of easily accessible and retrievable information, Atkins asks "How can we ensure that text books still foster imagination and creativity?"

Fabienne Meyers

fabienne@iupac.org

Page last modified 11 March 2013.

Copyright © 2003-2013 International Union of Pure and Applied Chemistry.

Questions regarding the website, please contact edit.ci@iupac.org

Drawing Chemical Structures

by Jeffery Leigh

Although the drawing of chemical structures is not strictly a nomenclature matter as usually understood, it is a way of conveying the structure of a chemical compound just as is an IUPAC systematic name, though using a visual language rather than a verbal one. Consequently, it is necessary to use certain widely-accepted conventions when drawing a chemical structure, particularly if that structure is three-dimensional and the representation of that structure as drawn on a sheet of paper is necessarily in two dimensions. IUPAC has attempted to define preferable methods for achieving this, and the new edition of Principles, unlike its predecessor, contains a summary of what is currently considered to be best practice to this end.

Certain recommendations are almost self-evident. For example, it is common, but not mandatory, to use the same font and font size in your structural diagrams as in your text. Principles uses Times New Roman, which was this editor’s choice. Some people prefer to use sans serif fonts such as Arial, though this can lead to minor confusion between symbols, such as l and 1(Times New Roman) with l and 1(Arial). Unusual abbreviations used in a diagram label should be defined somewhere in the article being written. It is not enough to assume that everyone will know what thf stands for, though this is probably acceptable for Ph. Bond lengths, thicknesses, and angles should be used consistently in all your diagrams. You should decide whether to represent aromatic rings as localized systems, as in (a) below, or as delocalized systems as in (b). Which you choose is not important, as long as your symbolism is clearly understood and is used consistently.

In the past, a variety of methods has been employed to portray a three-dimensional structure in two dimensions, for example, to show whether a bond which does not lie in the plane of the paper is pointing behind that plane or forwards towards the reader. In Principles, we have settled for conventional methods, as shown below in (i) for the tetrahedral molecule CH4.

Principles also introduces adaptations of this convention, for example, in order to represent certain ring structures, as in the representation for the ferrocene molecule shown below (ii).

More complicated polyhedral shapes than tetrahedral are frequently encountered in chemistry, and these are also discussed in Principles, which introduces the most common three-dimensional structures found in coordination chemistry and also the most common projections used to represent the three-dimensional structures of organic molecules. For the beginner, these are sometimes not easy to understand.

The octahedron is a shape very often found in coordination chemistry, but the manner in which it is represented depends upon the circumstances. In the representation (iii) below of a coordination complex formally written as [Mabcdef], the bonds between the ligands (a, b, c, etc.) to the central metal [not specifically indicated in diagrams (iii)-(v)] are represented using the formalism described above in (iii), but in (iv) the principal plane of the octahedron is drawn, but only the bonds to ligands e and f. Finally, in (v), only the octahedron is delineated and no bonds. The edges of the solid octahedron invisible to a viewer are represented by dashed lines. Yet, all three are acceptable representations of the molecule [Mabcdef], and should be equally comprehensible to the informed reader.

Organic chemists have related problems when representing organic structures in three dimensions, and they use a variety of projections to do this, the principal ones being named after their inventors: Fischer, Haworth, and Newman. These particular projections are usually applied to specific classes of molecule. In a Fischer projection, the bonds to the carbon at the center of the tetrahedron are not represented as in the drawing of Cabcd (vi), but in a plane as in (vii), the convention being that bonds drawn vertically are pointing behind the plane of the paper, and the horizontal ones in front. The central carbon atom is not specifically represented. This type of projection is used primarily for carbohydrates and amino acids.

A Newman projection is employed to represent more complex molecules, such as an ethane-type molecule C2 abcdef, where different conformations with respect to a selected carbon-carbon bond may be present. This is illustrated in (viii) and (ix) below. Finally, Haworth projections are often applied to compounds such as monosaccharides and polysaccharides.

The use of all these devices and more, including various ways to represent conformations, are discussed in the new volume of Principles, together with appropriate examples and literature references.

Jeffery Leigh is the editor and contributing author of Principles of Chemical Nomenclature—A Guide to IUPAC Recommendations, 2011 Edition (RSC 2011, ISBN 978-1-84973-007-5). Leigh is emeritus professor at the University of Sussex and has been active in IUPAC nomenclature since 1973.

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Page last modified 11 March 2013.

Copyright © 2003-2013 International Union of Pure and Applied Chemistry.

Questions regarding the website, please contact edit.ci@iupac.org