Isomeric Forms Of Molecules

Type of physical science: Chemistry

Field of study: Chemistry of molecules; Types of molecules

A molecule is constructed from atoms sharing pairs of electrons and possessing a particular arrangement in space. It is possible for the same set of atoms to be arranged in different sequences. These unique structures are called isomers.

Overview

Matter has the property of occupying space, and only one bit of matter can occupy a particular space at a particular time. It is evident, for example, that both feet cannot fit into one shoe; moreover, the left foot does not feel comfortable in the right shoe. These familiar human observations offer a method useful for exploring one of the most fundamental of all relationships in the natural world.

It is often observed that more than one substance have exactly the same chemical composition but very different properties. For example, a common material obtained from sugar is called grain alcohol. It has well-known properties in wines and spirits, is often used as a cleaning fluid, dissolves the iodine in a traditional disinfectant solution, and serves as the fluid in thermometers. These and many other uses are dependent on ethyl alcohol's properties of taste, volatility, freezing temperature, solubility, and so on. The chemical properties--that is, what kinds of other materials it can be made into--are equally characteristic of the substance.

The chemist knows that ethyl alcohol, the common technical name of grain alcohol, is made up of two carbon atoms, six hydrogen atoms, and one oxygen atom. Through analytical methods, it has been determined that methyl ether has exactly the same chemical composition. While methyl ether has some similarities to ethyl alcohol, in other ways the two are different. For example, both are quite soluble in water, but while ethyl alcohol boils at a temperature of 78 degrees Celsius, methyl ether boils at -24 degrees Celsius. Thus, the former is a liquid and the latter a gas at room temperature. Methyl ether is little used because of its great volatility and flammability. It is related to the old-fashioned anesthetic ethyl ether, and like it shows very little tendency to react and be changed to other materials. Ethyl alcohol is made in huge quantities because it can be transformed chemically into a host of useful products.

The immediate question is, How can two substances be composed of exactly the same material yet have such different properties? The answer, acquired over many years, is that these two compounds have their atoms arranged in a different order. If two molecules are different in any detail, they will show that difference in their properties. The world "isomers" is used to designate molecules with the same chemical composition but different structures. Like feet, two isomers are composed of the same units, and, also like feet, these isomers will not fit into the same-shaped space. This apparently simplistic truth is the most generally useful method for distinguishing between isomers and different models of the same compound. To appreciate the value of this tool, another general property of molecules must first be discussed.

All matter is alive with energy. The molecules are moving in space in both the gas and the liquid states. Even in solids, in which movement is much more restricted, there is a constant vibration, especially in the bonds that hold the molecule together. In the molecule in solution, where its chemistry is most often studied, atoms sharing single pairs of electrons are generally able to turn, twist, and stretch rather freely.

The result of this freedom of movement is that a given molecule can assume a large number of shapes at very little cost in energy. Some of these conformations are more favorable and will occur more frequently, but none of them constitutes isomeric forms. In general, changes in structure caused by physical changes represent conformers, and structures resulting from chemical changes are isomers. Keep in mind that both cases demand that the molecular or chemical formula be the same in each model under consideration.

Much laboratory experience over the past two hundred years has shown that these atoms have very regular bonding capacities, or valences. In neutral, stable molecules, the carbon atom forms only four bonds. The oxygen atom forms two bonds, and the hydrogen forms one bond. These linkages, which make molecules possible and give them their character, are made from pairs of electrons, one of the most fundamental units of energy and matter in the universe.

Bringing all these observations together in a simple, logical picture, one concludes that either the two carbon atoms are attached to each other and then to oxygen, or the oxygen resides between the two carbon atoms. In either case, just the right number of hydrogens are present to fill the available bonds completely.

Several different types of isomers may be clearly distinguished. The examples of an alcohol and an ether are opposites in that the structural differences are easy to see and the changes of properties dramatic. Looking closely at the two structures reveals that while the same atoms are present, the subgroups they form are quite different in the two structures. Ethyl alcohol has a single CH₃-, or methyl group, while methyl ether has two such groups. On the other hand, ethyl alcohol has one CH₂-, or methylene group, while methyl ether has none. In a similar fashion, the disposition of the oxygen atom's bonds is hardly the same in the two formulas.

This kind of substantial difference in the constituent parts of a molecule often leads to isomerism, but it is not necessary. Furthermore, isomers can occur without the presence of the oxygen atom. Consider the structures that might be realized from the formula C₆H₁₄ : There are five isomers possible for this collection of atoms. In two of them, five carbon atoms are linked consecutively, and the remaining carbon is attached at either the second or the third atom of the chain.

Multiple line equation(s) cannot be represented in ASCII text; please see PDF of this article if available.

Filling in the hydrogen atoms shows that fourteen are required by each structure, and that each model has three methyl groups, two methylene groups, and one methine (-CH=) group--exactly the same set of constituent parts. Yet, the two molecules are clearly different in their structure. One way of seeing this is to look at the center carbon of the five-carbon chain, the one with the methyl group branch, or side chain. The structure on the left has a methyl group and a three-carbon fragment (a propyl group) attached, while the right-hand model has two groups, each with two carbons (ethyl groups). These molecules are isomeric because the set of identical single-carbon groups are arranged in such a way as to make up different, larger subunits. In other words, the sum of methyl group (CH₃-) and a propyl group (CH₃CH₂CH₂-) is isomeric with two ethyl groups (CH₃CH₂-).

As in every decision concerning isomerism, the fundamental test is superimposibility. If the two models cannot be made to fit the same cavity in space without chemical changes, they are isomers.

The requirements for isomerism can be met with even more subtle differences. Carbon atoms not only have an extraordinary ability to form strong bonds with other carbon atoms but also form bonds in which more than one pair of electrons are shared. The double bond, two pairs of electrons shared by adjacent carbon atoms, is formed, in a formal sense, by the loss of two hydrogen atoms. Such an arrangement is isomeric, with a single shared pair between nonadjacent carbon atoms, that is, with a cyclic, or ring, compound.

Both these compounds involve ten hydrogens and are not superimposible; thus, they are isomers.

It is not surprising that such a great difference in structure leads to isomerism, but a close look at the structure containing a double bond reveals an entirely new example of this fascinating natural puzzle. Laboratory work reveals that two different compounds having all the structural units found in the left-hand structure above exist. This statement is true even to the position of the double bond.

In the early years of the twentieth century, it became apparent that the free rotation found in single carbon-carbon bonds does not exist in double bonds. If one wishes to turn the second and third carbons in this structure, it is necessary to break one of the two bonds. With this information, one can appreciate that the methyl and ethyl groups attached to the double-bond system can lie on the same or on opposite sides of the carbon-carbon double bond. Models reveal the impossibility of superimposing these geometric isomers.

Applications

Isomerism exists because of spatial, or stereo, differences, but this term is reserved exclusively for those isomers that exist only by virtue of differences in the exact arrangement of atoms in space.

The relationship between ethyl alcohol and methyl ether is referred to as "function group isomerism." The name comes from the presence of an arrangement of atoms other than carbon and hydrogen that controls the chemical characteristics of that molecule. By contrast, the hydrocarbon portion of a molecule is relatively unreactive and serves largely to hold the chemically active functional groups. In the often rather large molecules important in nature, it is the balance between the functional groups and the carbon skeleton that makes for optimum utility.

A natural question for one beginning to learn about isomers relates to their significance. There are many examples of such isomerism in the materials that nourish bodies and maintain health. Common table sugar is actually two simpler sugars: glucose, often used in hospitals, and fructose, found in fruit. These two molecules are functional group isomers of one another. There are several differences present, but the one most characteristic is the presence of a carbon atom sharing two electron pairs with an oxygen atom. In glucose, this arrangement is similar to that in the common, tissue-preserving formaldehyde, while in fructose, it is more like that in a number of expensive perfume odors.

Stereochemical isomerism involving the carbon-carbon double bond plays an important role in the chemical difference between fats, such as lard, and oils, such as peanut oil. These materials, essential components of nutrition, have similar chemical structures, but generally the fats are solids, while the oils are liquids. Their chief difference lies in the oils having more unsaturations, or multiple bonds. The solid shortenings, such as Crisco, are produced by hardening an oil with hydrogen, which adds to the carbon-carbon double bond, making it saturated.

Essentially, all the double bonds in the oils have the two carbon atoms on one side and two hydrogens on the other. The geometry of such an arrangement is different from the chain of carbon atoms sharing only single electron pairs in the fats. While the fat molecules can have their chains closely packed together, the oils are much more randomly arranged. This difference in the way carbon chains can arrange themselves accounts for the difference in physical state. The same stereochemistry plays an important role in the formation of cell walls in the human body.

Isomerism, then, is important to the way nature arranges life's molecules. A still more impressive illustration can be seen in the stereochemistry of a single carbon atom. A single carbon atom can impart isomerism to a molecule in which it resides. The most commonly observed is called a chiral molecule. A lack of symmetry in two molecular structures means that the molecules are not superimposible. One could say that feet are stereoisomers, since they have exactly the same set of parts arranged in the same general sequence. Yet, feet do not possess the same-side, opposite-side arrangement discussed for the carbon-carbon double bond. The French scientist Louis Pasteur recognized that molecules can be isomeric by virtue of the object-mirror image relationship. Hands as well as feet show this stereoisomeric character, and from the Greek word for "hand" comes the term "chiral."

Right- and left-handed isomers result when a carbon atom is attached to four different atoms or groups of atoms. For example, a simple alcohol made from four carbon atoms contains such a chiral carbon atom.

The sugars, the starches, the steroids, the proteins, and many pharmaceuticals all contain chiral carbon atoms. Once again, it is clear that nature has placed a great emphasis on the exact arrangement of atoms in molecules of significance to birth, growth, and health.

Context

In the early years of the nineteenth century, chemists despaired of being able to imitate nature's ability to synthesize the diverse array of materials found in living matter. This limitation was explained by the existence of a "vital force" essential to the preparation of the molecules associated with life.

In 1828, the German chemist Friedrich Wohler published the results of his attempt to prepare the salt ammonium cyanate. He sought this clearly mineral compound in a perfectly reasonable manner, but he obtained the completely unexpected compound urea. At that time, urea was well known as the by-product of human chemistry and was clearly related to the natural material strychnine. The material sought and the material obtained were isomers. Thus, the very beginning of modern synthetic organic chemistry provided an excellent example of the central importance of this structural diversity. Soon Wohler had prepared the desired ammonium cyanate and shown that it had the same formula as urea, but entirely different properties.

The nineteenth century saw the preparation of huge numbers of carbon compounds, a practice that continues. It became clear that carbon forms an enormous array of structural types, including many never encountered in nature. In nearly every instance in which more than one or two carbon atoms are present, there are isomers, and these compounds differ in demonstrable ways from one another. It also became clear that nature greatly favors one isomer over another in carrying out the complex chemistry associated with living systems.

The central role of enzymes in controlling biochemical reactions can be appreciated. These large molecules involve proteins, which are formed from the combining of amino acids. With only one exception, the approximately twenty-three amino acids found in proteins have a chiral atom, and most have the left-handed arrangement. It follows logically that the enzymes formed from hundreds of chiral amino acids will also be forced into a particular arrangement in space.

Actually, there are other important forces at work, as well, in forming the exact geometry of an active enzyme; but these complement the stereochemistry and add to its effectiveness. These effects are demonstrated most emphatically by the observation that the enzymes catalyze chemical reactions with great efficiency; that is, they are capable of speeding up the conversion of one chemical to another to such an extent that it is the only chemical change that will occur. Usually, an enzyme will catalyze one particular molecule in one particular chemical reaction. One well-substantiated explanation of this selectivity is that the exact shape of the enzyme will allow only one molecule to fit in the spacial cavity provided. Once the molecule under consideration, the substrate, is associated with the enzyme, it is held in exactly the right position for rapid, efficient reaction to take place.

Until scientists have persuasive evidence of a better explanation, one can accept the understanding that allows one to ask important new questions and the hope of gaining new insight. Few single cases of scientific inquiry have provided more practical outcomes than the structural theory of carbon compounds.

Principal terms:

BIOCHEMISTRY: the study of molecules and chemistry found in living matter; chemistry applied to biological problems and vice versa

BOND: a pair of electrons providing the force for holding atoms together; especially shared pairs, or covalent bonds, in molecules

CATALYST: a substance that provides a lower energy pathway for a chemical reaction, thus speeding it up, but is not itself altered by the reaction

CONFIGURATION: the exact arrangement in space of the atoms in a stereoisomer

CONFORMATION: any one of the possible special arrangements that a molecule may assume without being chemically converted to a new substance

ENZYME: a protein that, alone or in association with other materials, acts as a catalyst for a biochemical reaction

FUNCTIONAL GROUP: a particular group of atoms in a molecule that accounts for at least some of the chemical characteristics of that substance

STRUCTURE: the sequence and exact location in space of the atoms and bonds found in a molecule

SUBSTRATE: the molecule being chemically converted to a new material; used especially with enzymes

SUPERIMPOSITION: the fundamental test for isomers; the intellectual exercise of placing every atom, electron pair, and electron bond of two molecules in exactly in the same spacial arrangement

Bibliography

Benfey, O. Theodor. FROM VITAL FORCE TO STRUCTURAL FORMULAS. Boston: Houghton Mifflin, 1964. Makes an excellent presentation of the meaning of isomers and their importance in the early development of organic chemistry. Extensive and well translated. Contains quotations from the founders of the field, along with brief biographies and suggestions for further reading.

Bettelheim, Frederick, and Jerry March. INTRODUCTION TO GENERAL, ORGANIC, AND BIOCHEMISTRY. 3d ed. Philadelphia: Saunders, 1990. A textbook for the student without a background in chemistry. Contains problems to test understanding and includes many excellent drawings of isomeric molecules, along with many practical illustrations from biochemistry.

Davies, Robert E., and Peter J. Freyd. "C167 H336 Is the Smallest Alkane with More Realizable Isomers than the Observed Universe Has `Particles.'" JOURNAL OF CHEMICAL EDUCATION 66 (April, 1989): 278-281. A brain twister for the reader who becomes fascinated by the concept of isomers. Offers some quite valid criticisms of the way in which the concept of isomerism is oversold in the typical chemistry course, thus raising interesting questions about the shapes of molecules.

Finley, K. Thomas, and James Wilson, Jr. FUNDAMENTAL ORGANIC CHEMISTRY. Englewood Cliffs, N.J.: Prentice-Hall, 1970. An attempt to present organic chemistry with a minimum of previous knowledge. Historical and biographical information is integrated with the structure of carbon compounds and examples from the field of biochemistry.

Ihde, Aaron J. THE DEVELOPMENT OF MODERN CHEMISTRY. New York: Harper & Row, 1964. Covers all chemical history, from the ancients to the modern day, in a fashion that should appeal to all readers. Places the development of organic and biochemistry in historical context, and makes the personalities involved come alive.

Morrison, Robert Thornton, and Robert Neilson Boyd. ORGANIC CHEMISTRY. 4th ed. Boston: Allyn & Bacon, 1983. The complete first-year study of organic chemistry and much more. Tough going for the nonchemist, but well worth the effort. Many excellent problems of varying difficulty.

Perkins, Robert R. "Stereochemistry of Cyclic Hydrocarbons." JOURNAL OF CHEMICAL EDUCATION 66 (February, 1989): 860. Brief, but gives excellent definitions and illustrations of a wide variety of types of isomers, along with advice for dealing with their identification.

Westheimer, Frank H. "The Structural Theory of Organic Chemistry: A Summer Short Course." 3 parts. CHEMISTRY 38 (June, July, and August): 12-18, 10-16, 18-19. The first two sections deal extensively with isomers and the structural theory, including its shortcomings.

Cyclic, or ring, compound

It is impossible to superimpose these geometric isomers

Carbon and Carbon Group Compounds

Chemical Formulas and Combinations