A Translator’s Guide to Organic Chemical

Nomenclature
Part XIV

by Chester E. Claff, Jr., Ph. D.

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.

© Copyright 1998 Translation Journal and the Author

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