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Chemistry 2131:
Organic Chemistry for the Life Sciences (3)

Functional Groups

• in the last couple of classes we looked at a number of molecules that had different compositions. If you sit down and think about it the possibilities for the number of different molecules is huge. To known the properties of molecules, do we have to memorize them for each molecules? Fortunately not, they fall into groups depending on which atoms are combined in which ways.
• this leads us to the concept of the functional group. By definition a functional group is an atom or group of atoms that has characteristic behaviour. The chemistry of every organic molecule, regardless of its size and complexity, is determined by the functional groups it contains. So, if we learn how to recognize the functional groups, and gain an understanding of their properties and reactivities, then we can make very good predictions on the properties and chemistry of the molecules that contain them.
• I have divided the functional groups into three general classes, those that contain carbon-carbon multiple bonds, those that involve carbon singly bonded to a more electronegative atom, and those having carbon doubly bonded to oxygen.
• before discussing these systematically, we will start with the "non-functional" group, the alkanes. The names of these end "-ane". When referred to as a group attached to a larger molecule, these groups are referred to as alkyl groups.
• so, what are they? They are groups or molecules containing only carbon and hydrogen, and having only carbon-carbon single bonds and carbon-hydrogen bonds. They are sometimes referred to as saturated hydrocarbons, because they have the maximum possible number of hydrogen atoms per carbon atom (they are saturated with hydrogen)
• all of the carbon atoms in an alkyl group or an alkane are sp³ hybridized. This means that all of the carbon atoms are tetrahedral.
• alkanes are relatively chemically inert. The important exception is that they do react with oxygen during combustion. In other words they burn. For example methane (natural gas), butane (in lighters)...
• This is the first group of compounds that we will study in detail, and we will start on that Monday.

2. Carbon-Carbon Multiple Bonds:

• we looked at examples last day of carbon-carbon double and triple bonds. We will treat these groups, ones containing these bonds as the first class of functional groups.
• the general name for a molecule containing a carbon-carbon double bond is an alkene. They are often referred to as unsaturated hydrocarbons. Compare the alkene ethene to the alkane ethane to understand this difference in hydrogen saturation. More specifically, the names for simple alkenes end in "-ene".
• the carbon atoms involved in the double bond are sp² hybridized which means that they have a trigonal planar shape. Other carbon atoms in the molecule can be tetrahedral.
• unlike the alkanes, the alkenes undergo a number addition reactions, oxidations, reductions. They can react with HX (X being the universal symbol for an unspecified halogen), water, X₂, H₂.
• we also looked at carbon-carbon triple bonds last day. These molecules are called alkynes, and the names end in '-yne". The carbon atoms involved in the triple bond are both sp hybridized, and are thus linear in shape. Like the alkenes, the alkynes undergo addition reactions with similar reagents.
• the last group in the multiple bond category, a very important group, is the arenes or aromatic compounds. I won't even try to talk about naming them now, that will wait until we get there.
• the parent compound is benzene. Benzene was discovered in 1825 as a residue in the illuminating gas lines in London. It was determined that the formula was C₆H₆. It took a long time before the structure was determined.
• all of the carbon atoms in the benzene ring are sp² hybridized. This means that the molecule is flat. The problem with benzene is that it has two equal contributing resonance structures.
• what this means is that is it not made up of alternating double and single C-C bonds, but uniform 1.5 bonds. Normal C-C single bonds are 0.154 nm and double bonds are 0.134 nm. The bonds in benzene are a uniform 0.139 nm. The electronic structure of benzene consists of a six membered ring with each carbon having 2 carbon carbon sigma bonds and a carbon hydrogen sigma bond, then there is a cloud of electrons above and below the plane of the ring from the 2p orbitals on each carbon.
• aromatic compounds are much less reactive than alkenes and alkynes. The most common reaction type is electrophilic aromatic substitution. In these reactions, one of the hydrogen atoms is replaced by something, for example a halogen, a nitro group, an alkyl group...

3. Carbon Singly Bonded to an Electronegative Atom:

• the next group that we will look at involves carbon singly bonded to an atom more electronegative than it. The most common ones that we run across are oxygen, nitrogen, sulfur and the halogen.
• for starters, one key unifying feature of these functional groups is that the carbon atom in question is always in the sp³ hybridization state (therefore tetrahedral). Another common feature of these groups is that since the carbon atom is by definition bonded to a more electronegative atom, there is a polarization of the bond between these two atoms. The extent to which the bond is polarized depends on the electronegativity of the atom involved, but the direction of polarization is always such that the carbon has a partial positive charge and the electronegative atom has a partial negative charge.
• the first group are the halides. As the name suggests, the electronegative atom is a halide (F, Cl, Br, or I). The names of these compounds have the prefix "bromo-" or "chloro-"... These compounds react in nucleophilic substitution reactions, where the halogen atom is substituted with something else, and elimination reactions where the halogen atom leaves and a double bond is introduced instead.
• the next group is the alcohols. These molecules contain a carbon atom singly bonded to an oxygen atom, which itself is also bonded to a hydrogen atom. The group is called a hydroxyl group. The names usually end in "-ol". Alcohols react similarly to halides, they undergo substitution and elimination reactions. They can also be oxidized to aldehydes (see below).
• another functional group that involves carbon singly bonded to oxygen is the ether. In ethers thoughm the oxygen atom is bonded to another carbon atom instead of hydrogen. Ethers are fairly chemically inert.
• analogous to the alcohols and ethers are the thiols and sulfides, except that the "electronegative" atom is sulfur not oxygen. The thiols and sulfides are not as reactive as the alcohols and ethers because the electronegativity difference is much smaller (in fact close to zero).
• the final group in this catergory are the amines, which have carbon singly bonded to a nitrogen atom. The names of these compounds usually have the term "amino somewhere in them. Reactions of amines are a little trickier, we'll deal with them later.

4. Carbon-Oxygen Double Bonds:

• for biologists this class of functional groups are probably the most important. All of these functional groups have at the centre of them a carbonyl group. The carbonyl group is a carbon atom doubly bonded to an oxygen atom. Both the carbon and the oxygen atoms are sp² hybridized. This means that the group is trigonal planar. Another important feature of the group is that there is a strong polarization of the C-O double bond. Oxygen, being rather electronegative, is not good at sharing its electrons, it hogs them, and there are 4 electrons shared between the carbon and the oxygen, this makes the carbon rather partially positive, and the oxygen partially negative.
• if the carbonyl carbon is bonded to one other carbon atom and a hydrogen, we call this group an aldehyde. The names end in "-al". If on the other hand the carbonyl carbon is bonded to two other carbon atoms, the group is called a ketone. The names end in "-one".
• these two groups behave very similarly. They both undergo nucleophilic addition reactions. The major difference in their chemical reactivity is that the aldehydes can be oxidized, and the ketones cannot (this would involve carbon-carbon bond breakage).
• when the carbonyl carbon is bonded to a hydroxyl group, the functional group is called a carboxylic acid. These can be obtained by the oxidization of aldehydes. The carboxylic acids have names ending in "-oic acid".
• a number of carboxylic acid derivatives also exist. These all have an atom other than hydrogen bonded to the carbonyl carbon. Acid chlorides have a chlorine atom directly attached to the carbonyl carbon. These are very reactive groups, and the chloride is easily replaced. This reaction type is called nucleophilic substitution.
• there are other carboxylic acid derivatives, there are esters, which have an oxygen bonded to the carbonyl carbon which is also bonded to another carbon atom, acid anhydrides, which are like esters, but the other carbon is also a carbonyl. These are also very reactive.
• the final groups of carboxylic acid derivatives are the amides, where the carbonyl carbon is attached to a nitrogen atom.
• all of the carboxylic acid derivatives undergo nucleophilic substitution reactions.