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

An Introduction to Carbonyls

• we have seen the properties and chemistry of the alcohols. Hydroxyl containing groups are much more water soluble and have higher boiling points than their hydrocarbon counterparts. This is because of the hydrogen bonds that exist between molecules in the pure state (effect on boiling point) and with water molecules (effect on solubility in water).
• can we extend these observations to thiols and sulfides? To explore this we have to consider the electronegativity of sulfur, 2.5, the same as carbon.
• thus, we cannot really consider the S-H bond to be appreaciable polarized. Thus hydrogen bonding does not occur for thiols.
• this is reflected in their boiling points (compare 6 degrees for methanethiol to 65 degrees for methanol)
• similarly, the dulfides have similar boiling points to the thiols which are constitutional isomers. For instance ethanethiol, b.p. 35 degrees, dimethyl sulfide, b.p. 37 degrees.
• they are however stronger acids than the alcohols. While ethanol has a pK_a of 15.9, ethanethiol has a pK_a of 8.5
• this is important biologically because there is a free S-H group in one of the amino acids that make up proteins, cysteine. As we will see in biochemistry, this group is important for enzyme catalysis.
• another important aspect of thiols is their ability to oxidized to higher oxidation levels. This occurs when a disulfide is formed. The disulfide is also very important biologically because it is necessary for maintaining the structures of proteins. Two cysteine amino acids in proteins can come together to form a disulfide which forms a covalent bridge between the two amino acids.

2. Reactions of Ethers:

• in general ethers are rather unreactive. This is why they are frequently used as solvents for reactions to take place in (they don't tend to react themselves).
• there is one notable exception however, the cyclic ethers where oxygen is one member of a three membered ring. This group is called an epoxide.
• although technically speaking the epoxides are ethers, they are exceptionally reactive compared to other ethers
• this is so because of the angle strain of the three membered ring (remember cyclopropane?). Although the carbons and the oxygen are sp³ hybridized, they are forced to have 60 degree bond angles
• the epoxides undergo ring opening reactions
• in the presence of an acid catalyst, the oxygen atom can be protonated to give a bridged oxonium ion. This can be attacked by water on the opposite face, thus this is anti stereochemistry. The product is a vicinal diol or a glycol (hydroxyl on adjacent carbons).
• such reactions occur spontaneously in biological systems. The hydrocarbon chains of membrane lipids can be converted to epoxides (both unintentionally following oxidative damage and intentionally, for example in leukotrienes). These epoxides break down to diols.

3. Structure and Nomenclature of Aldehydes and Ketones:

• we start now on a very important functional group, the carbonyl group. This group is immensely important to biology.
• the simplest carbonyl caontaining molecules are the aldehydes and ketones.
• the carbonyl group consists of an sp² hybridized carbon doubly bonded to an sp² hybridized oxygen atom. Because of the hybridization state of these atoms, the group is planar. The oxygen has two pairs of unshared electrons in the other two sp² orbitals.
• aldehydes are carbonyl containing compounds where the carbonyl carbon is bonded to at least one hydrogen atom. Thus they are terminal carbonyls.
• ketones are carbonyl containing compounds where the carbonyl carbon is bonded to two other carbon atoms.
• an important common feature of these compounds is that they all lack a good leaving group on their carbonyl carbon. This dictates the chemistry they have.
• how do we name them? For aldehydes, we use the longest chain containing the carbonyl as the root name. We drop the "-e" ending and replace it with "-al"
• numbering begins by definition at the carbonyl carbon. Other substituents such as alkyl groups or halides are numbered accordingly.
• if the aldehyde contains a double bond, the infix "en" is used in place of "an"
• if a cyclic molecule has a CHO group attached to it, the suffix "-carbaldehyde" is added. This is considered position 1
• to name ketones, the ending "e" is dropped from the parent name (must contain the carbonyl group) and the suffix "-one" is added. This chain is numbered such that the carbonyl group gets the lowest possible number.
• what about molecules that contain multiple functional groups? IUPAC has an order of precedence. Let's look at the six most common functional groups. The group of highest priority is at the top of the list and the order of precedence goes down the list: