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Chemistry 2131:
Organic Chemistry for the Life Sciences
An Introduction to Nomenclature and the Alkanes
1. The Structure of Alkanes:
- now we start our step by step examination of organic compounds. We start with the simplest organic compounds, those that are made up exclusively of carbon and hydrogen joined by single bonds. The group, officially called the alkanes, is also commonly referred to as saturated hydrocarbons, because the carbons are fully saturated with hydrogen atoms. Another name often used to describe these molecules is aliphatic hydrocarbons. Regardless of the name used, these are all molecules or parts of molecules made up exclusively of carbon and hydrogen.
- this composition of alkanes tells us much about their structure and properties. All of the carbon atoms in the molecule are sp3 hybridized, therefore every carbon has tetrahedral geometry and all bond angles are 109.5¡.
- all of the straight chain alkanes have a common general formula, and that is CnH2n+2. For every carbon atom there are 2 times plus 2 as many hydrogen atoms.
2. Naming of Straight Chain Alkanes:
- we will start today to learn the rules for naming organic molecules. There is a very long and complicated set of rules for naming organic compounds. We will learn the essentials as we proceed through the course. The reason that such a system exists and why we will learn it is that when a compound is named the reader must be able to know exactly what is meant, and when one wishes to write or talk about a molecule one must know precisely how to describe it.
- so we start with the naming of simple straight chain alkanes. Each name has two parts, a prefix that tells one how many carbons are in the chain and a suffix that tells one that the molecule is a saturated hydrocarbon. The latter is the suffix "-ane". The following table indicates the prefixes for 1 to 20 carbons:
Number of Carbons Prefix 1 meth- 2 eth- 3 prop- 4 but- 5 pent- 6 hex- 7 hept- 8 oct- 9 non- 10 dec- 11 undec- 12 dodec- 13 tridec- 14 tetradec- 15 pentadec- 16 hexadec- 17 heptadec- 18 octadec- 19 nonadec- 20 icos- - when the prefix refers to only a part of a molecule, or a group, we refer in general to the group as an alkyl group, and in specific to methyl, ethyl... groups
3. Constitutional Isomers:
- the naming system above is the basis of a vastly more complex naming system, IUPAC Rules. Why do so many rules have to exist? Because molecular structures are rarely as simple as straight chain, saturated hydrocarbons.
- as a first example of this complexity we will discuss branched alkanes. Methane, ethane, and propane have only one possible way of connecting carbon atoms. The complexity first appears at the four carbon alkanes. If the fourth methyl group is added directly to the end of the chain we get butane. If it is added to the middle carbon we get a different molecule. The formula of both molecules is C4H
- these molecules are called constitutional isomers. Constitutional isomers have the same molecular formulae, but different orders of attachment of the atoms. Turns out, and we'll look at this in detail later in the week, that constitutional isomers can have very different physical properties as well, all because their shapes are different.
- this brings us to the question of how to name these isomers, and branched chain alkanes in general. For this we turn to the IUPAC rules for the naming of alkanes:
- the general name for saturated hydrocarbons is an alkane
- for branched chain alkanes, the alkanes corresponding to the longest contiguous chain of carbon atoms is designated at the parent compound, and its name becomes the root name. If two chains of equal length are present, choose the one with the greatest number of branches as the parent chain
- groups attached to the parent chain are called substituents. Each of these is given a name and a number. The name is derived using the appropriate prefix (for that number of carbons) and the suffix '-yl". The number refers to the carbon number on the main chain where the group is attached
- if the same substituent occurs more than once, the number of each carbon atom in the main chain attached to a group is given and a prefix indicating the number of that groups of that type is included. These are di- for two, tri-for three, tetra- for four, penta- for five, hexa- for six...
- if there is only one substituent, number the parent chain from the end that gives it the lower number
- if there are two or more identical substituents, number the parent chain from the end that gives the lower number to the substituent encountered first
- if there are two or more different substituents, list them in alphabetical order and number the parent chain form the end that gives the lower number for the first encountered substituent. If there are different substituents in equivalent positions on the parent chain, the substituent with the beginning with the letter earliest in the alphabet is given the lower number
- the prefixes di, tri, tetra... and not included in alphabetizing
- hyphenated prefixes, such as sec- and tert- are not considered when alphabetizing. Beware of "iso" which is not hyphenated therefore counts in alphabetizing
- so how do we assemble a name from all of these rules? We figure out the root name. Then, using the rules above we figure out the groups and the numbering. Then we list the substituents in alphabetical order. For each substituent we give a number (indicating the point of attachment to the parent chain), then a hyphen and the name of the group.
- when only one group is present the name of the group is strung together with the parent name (for example 2-methylpentane)
- when multiple groups are present each set of number and name is separated by a hyphen and the last (alphabetically) is attached to the root name (for example 4-ethyl-2-methylhexane)
- when a group is present a number of times, the numbers are given separated by commas (for example 2,3-dimethylpentane)
- there are a number of common names that one is likely to run across. In such common terminology, the prefix n- indicates a straight chain unbranched hydrocarbon (it stands for normal).
- likewise the prefix iso is used very precisely to mean that an otherwise unbranched chain terminates in a Y-shape or a (CH3)2neo refers to otherwise straight chain alkanes that terminate in 3 methyl groups (CH3)3. Thus 2,2-dimethylpropane is often referred to as neopentane.
4. Classification of Carbon Atoms:
- depending on its placement in a molecule, carbon atoms can be assigned different types. If a carbon atom is bonded to one other carbon is called a primary carbon, 1o. Primary carbons are found at the ends of chains.
- a carbon bonded to two other carbons is called a secondary carbon, 2o.
- a carbon bonded to three other carbons is called a tertiary carbon, 3o.
- a carbon bonded to four other carbon atoms is called a quaternary carbon, 4o
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