Within a larger molecule, it is often the functional groups that give the specific properties of that molecule. Even the reactivity with other substances is significantly influenced by them. By knowing the properties of the functional groups present, the characteristic properties of a compound can be easily deduced. In biochemistry, this knowledge is particularly helpful. This article describes the important functional groups and their properties.
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Image: ” Vintage Chemistry Sets 36″ by Windell Oskay. License: CC BY 2.0

The Hydroxyl Group – A Water Derivative: R-C-OH

Hydroxy Group Structural Formula

Image: “Hydroxy Group Structural Formula” by Jü. License: Public Domain CC BY 2.0

Organic compounds with a hydroxyl group are called alcohols. Their names often end with ol. In enols, the carbon atom with the hydroxyl group is connected to the neighboring carbon atom with a double bond. Phenols are benzene rings with an -OH group.

Differentiation between primary and secondary alcohols is based on the number of organic molecules which are attached to the hydroxyl group. Compounds with one, two or several hydroxyl groups are known as monovalent, divalent or polyvalent alcohols. They can have names ending in -diol, -triol etc.

The hydroxyl group has hydrophilic properties. As the oxygen atom has higher electronegativity, the electron pair from the water hydrogen atom is attracted to it, creating a negative charge. This is also a polar group. It’s due to this that the organic compound as well as hydrogen bonding is made enhanced.

Alcohols are therefore normally in liquid state and have high boiling points. The extra electrons on the oxygen atom also make the hydroxyl group nucleophilic, i.e. “nucleus loving”. As a result of this, reactions with electron deficient molecules can occur more easily. This group can not only donate protons, but also accept protons – it is amphoteric, meaning it can simultaneously be a weak base and a weak acid.

For this reason, the hydrogen atom can be donated easily. In such a reaction, which is an oxidation reaction, an aldehyde is formed (if a secondary alcohol reacts). If the hydrogen atom is not only donated, but also replaced, an ether is formed: R1-O-R2. The loss of the whole hydroxyl group is called a dehydration reaction. The products of this are an alkene and water.

Ether: R1-O-R2

Ethers are hydrophobic, unlike alcohols and they can only be proton acceptors. They do not form hydrogen bonds. At room temperature and pressure, they are therefore gases and they have a low boiling point. Due to the existence of two lone pairs of oxygen atoms in ethers, they are able to dissolve in cold concentrated acids to form oxonium salts which are stable. Moreover, ethers are known to form coordinate as a result of reactions with acids such as aluminium chloride to form compounds referred to as etherates. Equally important is the fact that the alkyl group is responsible for the significant action of air and light on ethers which results in the formation of peroxides.

Thiols: -SH

Where a sulfur atom takes the place of oxygen in a hydroxyl group, this is called a thiol or mercaptans. They are more acidic than alcohols as the hydrogen atom is donated much more easily. The reason for this is the higher stability of the resultant thiolate ions compared to the alcoholate. The sulfur atom is larger meaning the negative charge has less influence. The challenge experienced during the preparation of thiols is the fact that a second react may occur between with an additional alkyl halide thus resulting in the formation of a sulfide by-product. Nonetheless, this setback may be corrected through the use of thiourea (NH2)2C=S as a nucleophile. In this regard, the first reaction will lead to the formation of an alkyl isothiourea salt and an intermediate compound. The salt is then hydrolysed through a reaction with an aqueous base.

Hydrogen bonds which are formed between thiols are somewhat weaker than those of the alcohols, meaning that their boiling points are comparatively lower.

In a substitution reaction, after which a new R Group replaces the hydrogen atom, an ether – which is analogous to the alcohol – is formed, in this case it is called a thioether.

In medical practice, thiols are particularly relevant in the treatment of heavy metal poisoning. As they form complexes with these metals, they are often used for detoxification.

Amines: -NH2

The amino group is derived from the simple ammonia (NH3) molecule. When using the term enamines, we are describing (again, analogous to the alcohols) compounds with C-C double bonds, where one of the carbon atoms is attached to an amino group. A benzene ring with an amino group attached is called aniline or aminobenzine.

Amines also use the naming convention of primary, secondary and tertiary, though the name is not based on the carbon atom in this case, but on the number of R groups which are directly connected to the Nitrogen atom.

The amino group is defined by its alkalinity: it is a good proton receptor as the nitrogen atom contains a free electron pair.

Positively charged substituents can be attracted by this pair of electrons. As a result of this salt forming reaction, the whole molecule becomes positively charged. In nature there are many nitrogenous heterocycles. The following are commonly used in examples and are important to remember:

  • Pyrrole (aromatic)
  • Pyrrolidine
  • Pyridine (aromatic)
  • Pyrimidine (aromatic)
  • Purine (aromatic)

The Carbonyl Group: -CHO

In the carbonyl group, a carbon atom is connected to an oxygen atom with a double bond. Additionally, it has two R-groups and the corresponding molecule is named a ketone. If one of the R-Groups is a hydrogen atom, meaning the functional group is automatically terminal as a result, this is known as the aldehyde group. Aldehydes are more reactive than ketones. Their boiling points are higher than that of alkanes, but lower than those of the alcohols.

The carbonyl group is also a polar functional group. The carbon atom forms an electrophilic centre and can be attacked by nucleophilic molecules. The pi-complex electron pair then transfers to the oxygen atom, which in turn attracts a hydrogen atom. The carbonyl group becomes a hydroxyl group.

Conversely, the oxygen atom is a nucleophilic centre that electrophiles can attack. This unique reaction space has great significance in biochemistry.

The aldehyde and carbonyl groups are involved in many common reactions:

  • If an aldehyde results through oxidation from an alcohol, then the carbonyl group can naturally be reduced back to a hydroxyl group.
  • In an addition reaction with water, a hydrate, a germinal diol.
  • Alcohol forms a hemiacetal initially. In the following reaction with an acid, the acetal is created. In molecules that have both a hydroxyl group and a carbonyl group, this combination can result in intramolecular hemiacetal formation. The resultant molecules are heterocyclic 5 or 6 membered rings.
  • A primary amine is formed in connection with the first zwitterion, which then shifts to a hemiaminal. This is however also unstable and decomposes by the elimination of a water molecule into a Schiff base, which then eventually becomes an imine. If the reactant is a secondary amine, then enamines are formed instead.

A further special reaction of the aldehydes is the so called aldol condensation: two aldehyde molecules react with one another in a basic environment. The first step is where a proton is donated to hydroxide ions. The resultant molecule is an anion (carbanion) which has nucleophilic properties and attacks a further aldehyde. An instable aldehyde-alcohol compound (aldol) is formed. Through dehydration (condensation), an aldehyde with a C-C double bond is formed. In this manner, longer chains and macromolecules can be formed.

Tip: If you want to work out which smaller aldehydes are at the heart of a reaction, split the molecule at the double bond. On one half, add an -OH group and on the other half, complete the molecule with the addition of a -H atom.

Ketones also demonstrate a so called keto-enol tautomerism. This is different to mesomerism as it refers to two different, existing forms of one ketone which are in equilibrium with one another through the intramolecular shifting of a proton via the intermediate enolate stage. The tautomeric balance usually falls on the side of the keto form.

An exception to this is phenol, in which the balance falls of the side of the enol structure as the keto form has no aromaticity.

Examples of Ketones and Aldehydes includes propanone which is mainly used a solvent since it has the capability of dissolving both in water as well as other non-organic compounds while it is also used as a fingernail polish remover. Formaldehyde is known for its antiseptic properties and thus is widely used as a preservative for biological specimens including its application during the embalming process. Moreover, acetaldehyde is applied in the manufacture of hypnotics and sedatives through the process of polymerization.

The Carboxyl Group: -COOH

Carboxylic acid is characterized by a carboxyl group in which a carbon atom is connected to an oxygen atom by a double bond and is also bonded to a hydroxyl group. Carboxylic acids are formed by the oxidation of aldehydes. The reverse reaction is a decarboxylation, where CO2 is separated. Fatty acids, which are key nutritional components, are examples of carboxylic acids.

Salt formation occurs if a carboxylic acid reacts with a base. If the hydroxyl group is replaced by other R-groups, then carboxylic acid derivatives are formed. The following compounds are just a few of these:

  • Carboxylic acid chlorides: These are formed when the carboxylic acid reacts with an inorganic, chloride based solution. Carboxylic acid chlorides themselves are very reactive
  • Carboxylic acid anhydrides: These represent the connection between two identical carboxylic acids. They are also very reactive.
  • Carboxylic acid esters: These are formed in the reaction between a carboxylic acid or carboxylic acid derivative with an alcohol in a highly acidic environment.
  • Carboxylic acid amides: These are not created directly from carboxylic acids, but are produced in the reaction between carboxylic acid anhydrides or carboxylic acid chlorides with an amine. They are much less reactive and have mesomeric resonance structures. In the reaction of a carboxylic acid directly with an amine, a carboxylate ion is created that forms salts.
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