Unit 2 - Annotations

In this unit we will start to look at organic molecules. The basic core of all organic molelcule is made up of carbon and hydrogen atoms. Molecules that contain only carbon and hydrogen are called hydrocarbons. One of the characteristics of organic molecules is the vast number of molecules that are organic; literally millions of organic molecules have been isolated and characterized. Organic molecules can also display a wide range of physical and chemical properties. To help us to better understand organic molecules, chemists have found that organic molecules can conveniently catalogued into families based on easy to recognize structural characteristics, and that members of a give family share a common set of physical and chemical properties. We will look first at the families of hydrocarbons and will see why it is possible to form so many different organic molecules using a limited number of elements. We will see that many organic molelcules share the same molecular formula with other organic molecules; these different molecules that share a common molecular formula are called isomers. We will also see that there are different types of isomers. We will also begin to look at including elements other than carbon and hydrogen in organic molecule, beginning with oxygen. This discussion will introduce the concept of function group. We will see that it is functional groups that are used to define the different families of organic molecules. The objectives we will focus on include:

Familes: Alkanes
(Section 4.4)

In this section we are introduced to organic molecules, starting with the alkanes. Organic molecules are molecules that contain carbon. Alkanes are one family of organic molecules. We will see that there are many different families of organic molecules, each characterized by a type of functional group; alkanes are the special family of organic molecules that contain no functional groups. Consequently, they represent the core on which the other familes are built by adding functional groups. Alkanes are one of four families that are made up entirely of carbon and hydrogen; collectively this gourp of familis is known as the hydrocarbons.

See the Elaboration - Alkane Structure page for a pictoral description of the the structures of alkanes.

This section also describes the systematic set of rules that is used for naming organic molecules based on their structural formulas. This set of rules is called the IUPAC rules. We will be using variations of these rules to name members of nearly all the families organic molecules.

See the Elaboration - Naming Alkanes page for some step-by-step examples of naming alkanes.

Concepts: Constitutional Isomers
(Section 4.5)

As was discussed in the Elaboration - Alkane Structure and Elaboration - Naming Alkanes, more than one organic molecule can share the same molecular formula. Molelcules that have different structures but share the same molecular formula are called isomers. There are different kinds of isomers; the ones we have talked about so far are called constitutional isomers. Constitutional isomers are molecules that have the same molecular formula but different atomic connections. As the number of carbons in an alkane increases, the number of possible isomers increases dramatically. This is one of the reasons there are so many different organic molecules, i.e., there are just a lot of ways of connecting carbons and hydrogens together to form different molecules. While a structural formula can accurately describe the atomic connections in a molecules, it is possible to write these formulas in ways that can be easily confused as representing different molecules. A good way to determine if two structural formulas represent the same or different molecules is to apply the IUPAC rules to name the molecule; if the structural formulas represent the same molecule you should get the same name.

Concepts: Conformations
(Section 4.6)

When an alkane contains 4 or more carbon atoms it can exhibit multiple shapes due to rotations around the carbon-carbon single bonds. These different shapes are called conformations, should not be confused with isomers. Conformations are different shapes of the same molecule, whereas isomers are different molecules.

See the Elaboration - Conformations to view 3-dimensional models that illustrate different conformations for the molecule n-butane.

Conformations are very important in biological chemistry. For example, a functional protein molecule usually depends on the protein having a particular conformation. When some proteins have the wrong conformation, diseases can result. Examples are Alzheimer's disease and mad cow disease. The Health-Link on p.104 of Raymond describes the prion diseases, which result from aberrant conformation of a prion protein and which include mad cow disease chronic wasting disease (CWD).

Families: Cycloalkanes
(Section 4.7)

When the number of carbons in an alkane is three or larger, the two ends of the chain can be connected to form a ring. Such rings are called cycloalkanes. The 3 and 4 carbon rings are highly strained and unstable, however the 5 and 6 member rings are quite stable. For simplicity, when drawing structural formulas for cycloalkanes, skeletal structural formulas are used to represent the rings; triangles for 3-carbon rings, squares for 4-carbon rings, pentagons for 5-carbon rings and hexagons for 6-carbon rings. When naming cycloalkanes, the application of the IUPAC rules works as it does for alkanes with the addition of the cyclo- prefix to indicate a ring of carbons. When the cycloalkane is part of the parent name for a molecule the -ane ending is used, for example cyclopropane, cyclobutane, cyclopentane and cyclohexane. When the cycloalkane is a substituent group, then the -yl ending is used: cyclopropyl, cyclobutyl, cyclopentyl and cyclohexyl.

One consequence of the ring formation is that the carbon-carbon single bonds within the ring are no longer free to rotate. In some cases, this can lead to a new kind of isomer. Unlike constitutional isomers, these isomers have a the same atomic connections and the same name, however they have different three dimensional shapes, which cannot be interconverted without making and breaking covalent bonds. This is what makes them isomers. Such isomers are called stereoisomers. There are a couple of different types of stereoisomers, but those that result from restricted bond rotation, as is the case with cycloalkanes, are called geometric isomers.

See the Elaboration - Geometric Isomers for a discussion, along with 3-dimensional models, illustrating what the geometric isomers of alkanes look like.

Families: Alkenes, Alkynes and Aromatic Compounds
(Section 4.8)

In addition to the alkanes, there are three other families that are hydorcarbons, i.e., they are made only of the carbon and hydrogen atoms. Unlike the alkanes, theses families are said to be unsaturated hydrocarbons. They are said to be unsaturated because they have less than the maximum number of hydrogen atoms given the number of carbon atoms they have. This is because they contain double and triple carbon-carbon bones.