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Download the zipped version of the first installments of this series, originally published in the Sci-Tech Translation Journal, of the American Translators Association. The file is approximately 87 KB.

Previous installments of this series appeared in the July 1997, October 1997, January 1998, April 1998, July 1998, and October 1998 issues of the Translation Journal.

VII. Alicyclic Compounds (continued)

Conformation

It was pointed out earlier that carbon atoms joined by a single bond can rotate freely with respect to one another, carrying their substituents with them. In the case of ethane (H₃C-CH₃), for example, the hydrogen atoms on the two carbon atoms can be “staggered,” “eclipsed,” or “skewed” (any conformation between the other two), when the molecule is viewed from one end of the C-C bond. The staggered conformation is shown below:

All possible conformations coexist in ethane, but the staggered conformation, with the hydrogen atoms as far apart as possible, has the lowest energy and therefore predominates.
   The conformation of a molecule, the three-dimensional form it assumes when left to its own devices, becomes extremely important in biochemistry. For example, it determines whether antibody-antigen interactions or enzyme-substrate interactions can take place at all; these interactions require the partners to fit together like a lock and key. Our very lives depend on the conformations of our own chemical constituents. The Nobel Prize in chemistry was awarded in 1969 to Derek Barton for elucidating the part played by conformation in organic chemical reactions. Conformational analysis has become an important tool in the search for new drugs and new therapies.
   In the alicyclic series, only cyclopropane is planar. Cyclobutane and cyclopentane are slightly puckered to minimize the strain on their bonds, which would prefer to be separated by the tetrahedral angle of 109°28' but are restricted by the cyclic geometry of the molecules. Cyclohexane, in its attempt to achieve tetrahedral orientation of its bonds, assumes two major conformations called the “chair” and “boat” conformations:

chair	boat

The chair conformation has the least bond strain and therefore predominates.


Configuration and Stereoisomerism

While conformation relates to the spatial form of a given molecule, configuration relates to the geometric way in which the atoms of a molecule are bonded to one another. A given molecule has only a single configuration, but can be contorted into various conformations. An illustration is the simplest way to convey the meanings of these two concepts. Let’s look at 1,2-dichlorocyclopentane:

At first glance, this seems to be a simple molecule. However, there are actually three different configurations of 1,2-dichlorocyclopentane, each of which is an equilibrium mixture of its possible conformations.

(R,S)-cis-	(S,S)-trans-	(R,R)-trans-
1,2-dichlorocyclopentane

We’ve spoken of the cis,trans isomerism of alkenes, in which two substituents are either on the same side of a double bond, or on opposite sides. In the case of cycloalkanes, substituents can be either above or below the “plane” of the rings as shown above, giving rise to a different form of cis,trans isomerism.
   It might seem that there should be a fourth isomer with both chlorine atoms extending above the plane of the ring. However, it takes only minor mental gymnastics to flip the cis-isomer over and to discover that the two cis-isomers would be identical and superimposable. On the other hand, no amount of mental activity can superimpose the two trans-isomers. They are in fact mirror images of one another, like a left hand and a right hand. Their boiling points, spectra, densities, and many other physical properties are identical, but they are different compounds. They are said to be enantiomers (mirror images) of one another. The cis-isomer is a meso-isomer (superimposable on its mirror image), and is a diastereomer (geometrical isomer) of the other two.

Chirality

By definition, a chiral compound is one with a non-superimposable mirror image. An achiral compound can be superimposed on its mirror image. trans-1,2-Dichlorocyclopentane is a chiral structure; the cis-isomer is achiral. In general, a carbon atom with four different substituents is a chiral center with two possible configurations; each of the substituted carbon atoms in our example has the following four substituents:

1. -H
2. -Cl
3. -CH₂-
4. -CHCl-

1,2-Dichlorocyclopentane therefore has two chiral centers, each of which has two possible configurations, (R) or (S), standing for rectus and sinister. A chiral compound may therefore have up to 2ⁿ stereoisomeric forms (n = number of chiral centers); there will be fewer stereoisomers if some of them are superimposable.
   The method of assigning (R) or (S) configurations to a given structure need not concern a translator; only their significance needs to be grasped.
   Chiral compounds (but never achiral compounds) have the ability to rotate the plane of polarization of light. Enantiomers rotate the plane by equal amounts in opposite directions. This property is easily detected and measured in a polarimeter and is used to determine the enantiomeric purity or enantiomeric excess of a given enantiomer in a mixture. If both enantiomers are present in equal amounts, which is the normal outcome of a synthesis using achiral reactants, the mixture is called a racemic mixture and does not rotate the plane of polarized light at all. It is a major program of many drug companies at the present time to offer enantiomerically pure drugs instead of racemic mixtures. In most cases, only one enantiomer is physiologically effective, and the other may be inert or even harmful.

There are other methods of denoting chirality both in text and graphically; Part XV will describe some of them.

Readers are urged to e-mail questions, comments, or suggestions for further topics in the field of organic nomenclature to the author at: 74654.1335@compuserve.com.