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

Nomenclature and Properties of Alcohols

• we will start to examine a group of molecules which are of immense importance biologically. The structures of these molecules are similar, in that they all involve an sp³ hybridized carbon attached to an sp³ hybridized oxygen or sulfur atom.
• in the simplest example, the alcohols, the oxygen atom has two lone pairs and a covalent bond to a hydrogen in addition to the C-O bond. A thiol is the sulfur analog of an alcohol with an sp³ hybridized sulfur atom attached to carbon.
• an ether has another carbon atom in place of a hydrogen atom.
• it is important to remember that all of the molecules have two unshared electron pairs on the electronegative atom (oxygen or sulfur)
• the sp³ hybridized state of the carbon atoms means that bond angles of nearly 109.5 degrees are predicted and in fact observed. Try to remember this, it is more correct to write an OH group with a bend in it.
• let's look at the ground state electronic configuration of oxygen and sulfur. Both are in the VIA (or VIB depending on which periodic table you look in) family. Oxygen, atomic number 8, has a ground state electronic configuration of 2 1s, 2 2s, 2 2p_x, 1 2p_y, and 1 2p_z. Obviously these can be hybridized differently.
• similarly, sulfur, atomic number 16, has a ground state electronic configuration of 2 1s, 2 2s, 2 2p_x, 2 2p_y, 2 2p_z, 2 3s, 2 3p_x, 1 3p_y, and 1 3p_z.
• both elements have the same number of outer shell valence electrons, but they are in different shells. This can change the geometry considerably. Look for instance at the electronegativity values of these molecules. Oxygen is 3.5, sulfur is 2.5, essentially the same as carbon. Why?

2. Nomenclature:

• let's learn how to name these beasts, so you know what I mean when I am discussing them.
• for the alcohols, we identify the longest chain of carbon atoms conaining the OH group as the parent alkane. To indicate that the molecule is an alcohol, the ending "-e" is removed and replaced with "-ol". A number is added to indicate the location of the hydroxyl group.
• the OH group takes precedence over alkyl groups and halogens in the numbering of the parent chain
• let's try a few examples. A 2-carbon alcohol is called ethanol, that is what you drink to excess, killing your brain cells.
• let's look for a moment at 4-carbon alcohols. There are many of these. 1-butanol is a straight chain alcohol with the hydroxyl group on the terminal carbon. This is an example of a primary alcohol. It is called primary, because the carbon that the hydroxyl group is attached to is a primary carbon. Are there any other primary 4-carbon alcohols?
• the other straight chain 4-carbon alcohol is 2-butanol. This is considered a secondary alcohol, for the same reason as above.
• other 4-carbon alcohols exist, including what is commonly known as tert-butyl alcohol, or 2-methyl-2-propanol. This is considered a tertiary alcohol.
• all of the above 4-carbon alcohols are constitutional isomers of each other.
• if more than one hydroxyl is present, the prefixes di-, tri-, tetra-... are used. For example, the IUPAC name for glycerol is 1,2,3-propanetriol. Note that the terminal "e" is retained on the parent alkane name.
• what if unsaturated hydrocarbons are the parent chain? These are collectively reffered to as unsaturated alcohols. The parent chain is numbered to give the hydroxyl group the lowest possible number. This means that the OH takes precedence over the double bond in numbering.
• to name these compounds, the "an" of the parent is changed to "en", and a number corresponding to the location of the hydroxyl group is inserted before the "-ol" ending.
• for example, look at the structure of cis-3-hexen-2-ol.
• let's move on to the ethers. There are two ways you can name ethers, both are accepted by the IUPAC convention. There is the correct way, and the way everybody uses. Briefly, the longer alkyl chain is the parent alkane and the shorter chain is referred to as an alkoxy group. Examples include methoxyethane, or 2-methoxy-2-methylpropane.
• chemists almost always use the old fashioned nomenclature for ethers (bunch of old buggers aren't they?). In this system, the alkyl groups are listed in alphabetical order followed by the word ether.
• for example, diethyl ether, or ethyl methyl ether.
• cyclic ethers have silly names.
• finally, what about thiols? One selects the longest carbon chain containing the sulfhydryl group as the parent name. The full alkane name is retained and the suffix "-thiol" is added. For example, ethanethiol.
• to make life infinitely trickier, if other functional groups are present, the sulfhydryl group is referred to using the prefix "mercapto-". According to IUPAC, the hydroxyl group takes precedence over the sulfhydryl group in numbering and naming.
• for example, 2-mercaptoethanol.
• thiols have ether analogs called sulfides. Name these as you would ethers, but replace the word ether with the word "sulfide".
• for example: dimethyl sulfide.

3. Physical Properties of Alcohols, Ethers and Thiols:

• we have discussed the physical properties of hydrocarbons. They have very low melting and boiling points because the only forces holding molecules together in the solid and liquid states are dispersion forces. We have seen how the melting and boiling points increase with molecular size because of the increase in surface area available for dispersion forces to occur over.
• we will look in detailat the physical properties of alcohols, ethers and thiols because they are remarkably different from hydrocarbons.
• let's start with the alcohols. These are the most important biologically of the three. The distinguishing feature is of course the presence of the hydroxyl group.
• since oxygen is a very electronegative element it pulls electrons towards itself from carbon and more so from the hydrogen. This gives oxygen a partial negative charge and carbon and in particular hydrogen a partial positive charge. So, alcohols are polar molecules.
• this is not a charge-charge interaction, because a full charge is not involved. The general term for the attraction between the positive end of one dipole and the negative end of another dipole is a dipole-dipole interaction.
• when the positive dipole resides on a hydrogen atom bonded to an electronegative atom such as O, N (or F), the attractive interaction between the dipoles is particularly strong and is given the specific name, hydrogen bonding
• the strength of a hydrogen bond in water is about 21 kJ/mol (5 kcal/mol). This is small compared to the strength of a covalent bond (O-H bond is about 498 kJ/mol), but affects the physical properties immensely
• you only have to look at the properties of water to see the implications are hydrogen bonding. Such a small molecule would have a very low melting and boiling point if dispersion forces alone held it into the solid and liquid states. But hydrogen bonding gives water a much higher melting and boiling point.
• unlike other dipole-dipole interactions, hydrogen bonds have a given length.
• how does hydrogen bonding affect the properties of alcohols? Look at Table 7.1 on page 178 of Brown. You can see that compared to hydrocarbons of very similar molecular weights alcohols have much higher boiling points are are much more soluble in water
• the higher boiling point is a result of increased intermolecular interactions in the form of hydrogen bonding. The positive forces of interaction must be overcome for the substance to dissociate from the liquid to the gaseous state. Thus a higher temperature is required for them to boil.
• the solubility of these compounds in water is also affected by the presence of hydroxyl groups. Why? The hydroxyl groups participate in hydrogen bonds with water molecules. Alcohols are both hydrogen bond donors (the partially positively charged hydrogen) and hydrogen bond acceptors (the partially negatively charged oxygen).
• by participating in hydrogen bonds with water their solubility increases immensely.
• let's look at this for a moment. Why are alkanes not soluble in water? It is because the non-polar molecules cannot interact with water through hydrogen bonding, but the water has to surround them, thereby losing H-bonding interactions with neighbouring water molecules. So, positive interactions are lost. Furthermore, and probably more importantly, the water becomes organized around the non-polar group. This leads to a loss of entropy in the system (is this gibberish or are you with me?). This is unfavourable, therefore alkanes and other pure hydrocarbons are not soluble in water.
• the hydroxyl group on a short alcohol interacts with water through hydrogen bonding. This increases its solubility. However, as the length of the hydrocarbon part (the non-polar bit) increases, the two factors weigh against each other, and the result is decreasing solubility in water as the lenght of the alcohol increases
• when boiling points are considered, they increase with molecular size due to increased dispersion forces in the pure compound.
• let's look for a moment at the ethers. Is hydrogen bonding possible? No. There is no hydrogen attached to an electronegative atom. The two carbons attached to the oxygen atom are partially positively charged, but less so than hydrogen would be. There is therefore a possibility for dipole-dipole interactions between the oxygen of one molecule of ether and the carbon of another.
• this association is very slight because these partially positive carbons are tetrahedral and surrounded by 4 atoms, this makes approach of the oxygen atom from another molecule difficult. Since dipole-dipole interactions are very dependent on distance between atoms, the interaction is slight.
• thus, boiling points for ether are similar to similarly sized alkanes
• what about solubility in water? They have no hydrogen bond donor, but they do have a hydrogen bond acceptor. This serves to increase their solubility in water, they can form hydrogen bonds with the partially positively charged hydrogens on water.