Naming Organic Molecules
Naming organic molecules involves a systematic approach established by the International Union of Pure and Applied Chemistry (IUPAC). This nomenclature is crucial due to the vast diversity of organic compounds, which can number in the millions. Each organic molecule is primarily constructed from carbon atoms, and their naming is derived from the longest continuous chain of carbon atoms, known as the parent chain. The complexity of these molecules is compounded by the presence of functional groups and heteroatoms—elements other than carbon, such as oxygen or nitrogen—that can alter the chemical behavior of the molecule.
The IUPAC system addresses potential confusion arising from the historical use of common names, which were often subjective and varied. For instance, while some compounds like acetone maintain their common names, others are systematically named based on their structure—such as 2-propanone for acetone. The method for naming includes identifying the parent chain and any side chains, numbering the carbon atoms to indicate the positions of these groups, and specifying the orientation of any substituents for more complex structures.
Overall, understanding the naming of organic molecules not only streamlines communication within the scientific community but also allows for clarity in the study and application of chemistry across various fields.
Naming Organic Molecules
FIELDS OF STUDY: Organic Chemistry
ABSTRACT
The method of naming organic molecules, as standardized by the International Union of Pure and Applied Chemistry (IUPAC), is described. The method is based on parent hydrocarbon molecular structures and the functional groups contained in their derivative compounds.
Understanding the Naming of Organic Molecules
The principal structural component of an organic molecule is a framework of carbon atoms. The various different organic molecules number well into the millions, and identifying each one with a given familiar name would be difficult and inefficient. As such, a system of standardized nomenclature based on chemical formulas has been developed instead.
Chemical and molecular formulas can be thought of as the words of the language of chemistry, spelled out with the symbols of the elements of the periodic table, which serve as the letters of the chemical alphabet. For organic compounds, the chemical alphabet is very limited, consisting almost entirely of the symbols C (carbon), H (hydrogen), O (oxygen), N (nitrogen), F (fluorine), Cl (chlorine), Br (bromine), I (iodine), S (sulfur), and P (phosphorus). Other element symbols may at times appear in chemical formulas, but such occurrences are relatively rare. Yet despite being generally limited to these few elements, organic chemistry encompasses what amounts to an infinite series of molecules of increasing complexity, ranging from those with just a single carbon atom to giant molecules containing millions of carbon atoms. Each series of organic molecules increases in complexity just one carbon atom at a time, however, which enabled the development of an equally systematic method of naming organic molecules.
Historically, molecules were given whatever name the person who discovered the molecule deemed appropriate at the time, and many names were derived from such sources as the substance from which the material was isolated, the alchemical name of the material, and even the name of the discoverer’s love interest. Since relatively few molecules were known, it was not overly difficult to keep track of chemical identities. Indeed, some of the best-known common names survived into the twenty-first century: acetone and acetic acid, for example, are most commonly referred to by those names instead of the proper names 2-propanone and ethanoic acid.
As more and more organic molecules were discovered, however, the system quickly became chaotic and confusing. In order to standardize the language of chemistry and end this confusion, the International Union of Pure and Applied Chemistry (IUPAC) developed a systematic method of nomenclature for organic compounds, based on the structures of the simplest class of organic compounds, a hydrocarbon series called alkanes. In many cases, particularly for very complex molecular structures, the common name of the compound was adopted as the official base name for all of its related compounds within the systematic method of nomenclature.
Nomenclature and Hydrocarbons
The hydrocarbons, as the name suggests, consist of only hydrogen atoms and carbon atoms. The series begins with the simplest hydrocarbon, which is methane (CH4), and progresses through C2H6 (ethane), C3H8 (propane), and so on. Beginning with C4H10, the same chemical formula can represent different molecular structures that contain exactly the same numbers and types of atoms. These are known as isomers, and without an unequivocal means of identifying the exact molecular structure in a systematic name, nomenclature would become as chaotic as the old common-name methods. In the IUPAC system of nomenclature, the name of a compound is based on the longest single chain of carbon atoms in its structure, known as the parent chain. C4H10 has two isomers, n-butane and 2-methylpropane (commonly known as isobutane). n-Butane contains of a chain of four carbon atoms, while the longest chain of carbon atoms in 2-methylpropane consists of just three carbon atoms, with the fourth bonded to the middle carbon atom as a side chain. The two structures can be represented through simple diagrams, often called skeletal formulas:
Each straight line segment begins and ends with a carbon atom, and each carbon atom is assumed to be bonded to (4 – x) hydrogen atoms, where x is the number of other carbon atoms the atom in question is bonded to.
As the number of carbon atoms increases, the number of possible structures for the same chemical formula also increases. The basic method of the IUPAC system is able to accommodate this.
To determine the nomenclature of the above molecular structure, first identify the longest unbroken linear chain of carbon atoms. This is easiest to see when the structure is drawn out as above. In this case, it is the horizontal nine-carbon chain.
Second, identify the various side chains that are attached to the parent chain. Here there is a two-carbon ethyl group and a three-carbon propyl group, the names of which derive from the two-carbon hydrocarbon ethane and the three-carbon hydrocarbon propane, respectively.
Third, number the carbon atoms in the parent chain. Start the numbering on whichever end would result in the side chains being attached to the carbon atoms with the lowest numbers. For this compound, the carbon atoms in the parent chain should be numbered from left to right.
This places the ethyl and propyl side chains on C-4 and C-5. Numbering the chain from right to left would place them on C-5 and C-6, which are higher numbers and therefore not allowed.
The parent chain, being nine carbons in length, is named nonane, from the Latin for "nine." The full IUPAC name of the compound specifies the name of the parent chain and the location of each side chain on the parent chain. In this case, the basic name of the compound is 4-ethyl-5-propylnonane.
There are other considerations when establishing the full, unique name of the compound. For example, the carbon atoms at C-4 and C-5 in this compound are defined as asymmetric centers, since they are each attached to four different groups of atoms; that is, even though C-4 is attached to three carbon atoms and just one hydrogen atom, each of those three carbon atoms is part of a group containing different numbers of carbon and hydrogen atoms, called a substituent group, and the same is true for C-5. Every asymmetric center exists in two isomeric forms, and the full name would also specify the order of the substituents about each asymmetric center.
The hydrocarbon series of linear compounds also includes the alkenes (characterized by the presence of double carbon, or C=C, bonds) and the alkynes (characterized by the presence of triple carbon, or C≡C, bonds). There are also corresponding series of hydrocarbons with cyclic structures rather than linear structures. The naming process for each series employs the same basic approach as described above and specifies the locations and orientations of the structural features as well as the substituents, as shown in the following examples:
Heteroatoms and Functional Groups
Heteroatoms are atoms of any element other than carbon—typically oxygen, nitrogen, sulfur, or phosphorus—that are included in the basic structure of an organic molecule. The presence of heteroatoms in a structure complicates the naming system somewhat by introducing several common names as the base structures of various classes of organic compounds. Heteroatoms are also present in certain functional groups. The alkanes are very stable compounds and do not react with many typical reagents, such as acids, bases, reducing agents, and oxidizers. The presence of a functional group in an organic molecule provides a reactive site where such reagents can function and bring about a reaction. Typical functional groups include alcohols, ethers, carboxylic acids, amines, thiols or mercaptans, ketones, aldehydes, and several others. The common feature of all functional groups is that the specific atoms that compose any functional group impart the same behavior in chemical reactions regardless of the remaining structure of the molecule. The technique for generating a unique IUPAC-standard name for such compounds is the same as for hydrocarbons, in that the name must identify the location and type of the functional group. The structures below are examples of such naming.
Naming Organic Compounds in Biochemistry
The IUPAC naming convention is appropriate for many small compounds in biochemical systems. However, the complexity of most biochemical compounds makes such a naming approach wholly inadequate. It would be exceedingly difficult to attempt to ascribe an IUPAC standard name to the deoxyribonucleic acid (DNA) molecule, for example. Even very small proteins are impossible to name by the IUPAC conventions. They are typically referred to by a biology-based reference to their role, as in the cases of aconitase and RNA polymerase.
PRINCIPAL TERMS
- functional group: a specific group of atoms with a characteristic structure and corresponding chemical behavior within a molecule.
- IUPAC: the International Union of Pure and Applied Chemistry, an organization that establishes international standards and practices for chemistry.
- nomenclature: a system of specific names or terms and the rules for devising or applying them; in chemistry, refers mainly to the system of names for chemical compounds as established by the International Union of Pure and Applied Chemistry (IUPAC).
- parent chain: the longest continuous hydrocarbon chain in an organic compound, used as the basis for its unique name identification.
- side chain: a group of atoms that branches off from the main chain, or backbone, of an organic molecule.
Bibliography
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