Chapter 11: Organic Nitrogen-containing molecules

Amines

Amines are derivatives of ammonia.

Amines

Aliphatic amines are those without aromatic rings present. Primary aliphatic amines can be prepared by reacting ammonia with a halogenoalkane. X = an electronegative species e.g. Cl, Br

Primary aliphatic amines can also be made by the reduction of nitriles using a nickel catalyst and hydrogen gas:

R-C≡N + 2H2 → R-CH2NH2

A reducing agent such as LiAlH4, can be used instead of hydrogen gas:

R-C≡N + 4[H] → R-CH2NH2

Aromatic amines are made by reducing nitroarenes such as nitrobenzene, refluxed at 100°C using a reducing agent of tin and concentrated HCl. The tin and concentrated HCl react to form hydrogen.

Aromatic amines are used in the production of dyes as they’re brightly colored.

Nucleophilic Properties

The lone pair of electrons on the nitrogen atom in amines allows them to act as nucleophiles. Haloalkanes undergo nucleophilic substitution with an ammoninucleophile to form amines. This reaction can also happen with primary amines acting as the nucleophile, using the same mechanism as ammonia, to form secondary amines.

Quaternary ammonium salt

Quaternary ammonium salts are formed when all the hydrogen atoms in an ammonium ion are replaced by alkyl group. Quaternary ammonium salts containing a large alkyl group are often used as cationic surfactants. This is because they have one long non-polar hydrocarbon chain and a charged end.

Amides

Amides can be prepared by reacting ammonia or an amine with an acid chloride. Reacting acid chloride with ammonia gives primary amide. With a primary amine, a secondary amide is formed.

Paracetamol- a useful amide

Paracetamol is a widely used and successful analgesic (painkiller) and has antipyretic properties.

Amino Acids

Proteins are very essential part of our body.

Proteins are sequences of amino acids joined by peptide links. Peptide linkages are formed from condensation reactions.

Hydrolysis of the peptide link produces the constituent amino acids

There are three levels of protein structure: primary, secondary and tertiary

    • Primary structure is the sequence of amino acids in the polypeptide chain.
    • Secondary structure is the way the chains of amino acids interact with each other to form either α-helix or a b-pleated sheet.

Tertiary structure is the three-dimensional shape into which the a-helix or b-pleated sheet is folded.

The secondary and tertiary structures are a consequence of various types of intermolecular forces

    • Hydrogen bonds – these stabilize both the secondary and tertiary structures
    • London and dipole-dipole forces – these stabilize the tertiary structure
    • Disulphide bonds – these are only important when the amino acid cysteine is part of the protein in the tertiary structure

Deoxyribonucleic Acid (DNA)

DNA is made up of nucleotide monomers: a phosphate group, 2-deoxyribose pentose sugar and a base. The base can be adenine, cytosine, guanine or thymine.

A strand of DNA is a polymer of nucleotides linked by phosphodiester bonds between the phosphate group of one nucleotide and the 2-deoxyribose of another nucleotide. Resulting in a sugar-phosphate backbone. 

The DNA double helix is composed of two complementary DNA strands held together by hydrogen bonds between complementary base pairs.