The chemistry of nitrogen containing organic compounds is mostly governed by the basicity and nucleophilicity of the electron lone pair on nitrogen except when there is more electronegative atom than nitrogen that is attached to nitrogen such as occurs in nitrosylchloride. In this case nitrogen atom behaves more like an electrophile which can accept a nucleophile.
The most important group of compounds with C-N- single bonds is the amine group. Amines differ than alcohols by being more reactive. This is so due to the more electronegative atom of oxygen. Amines can behave as nucleophiles as well as bases. They are weak bases except when they are negatively charged such as occurs with NH2- in which case this ion is extremely basic and has great affinity for a proton.
Amines react with ketones to form imines or shiff bases. Shiff bases are important clinically due to mutagenic effect. In the case of diabetes ketone bodies can form in which case if they are in high concentration can react with amines in DNA bases forming imines or shiff bases. This is a mutagenic transformation that causes cancer.
Another group of C-N- single bonds is the amino acids group. Amino acids are important due to their presence in the structure of proteins. The body can synthesize certain types of amino acids which are called non-essential amino acids. Other amino acids that the body cannot synthesize must be given in the diet. These are called essential amino acids.
Amino acids are metabolized in the liver by a deamination process of the amine group which forms as a product ammonia. Ammonia is a toxic compound in high concentrations. It is metabolized in the liver to the less toxic compound urea which is excreted in the urine.
Another compound in the body and which incorporates nitrogen in its structure are DNA and RNA bases. Nitrogen mustard is another class of organic compounds bearing nitrogen. It is an alkylating agent that are used clinically to treat cancer. In addition it has applications in chemical warfare due to its resemblance to sulfur mustard.
An example of a nitrogen mustard is 2-chloro-ethylamine. This compound does not exist as it is written because the nitrogen can displace the chlorine atom intramolecularly forming a cyclic intemediate which can react with DNA bases through the amine group in cancer cells.
Nitrogen containing organic compounds can also be cyclic such as the three membered ring of aziridine. Pyrrole and pyridine are two other heterocyclic compound containing nitrogen. Pyrrole being an aromatic compound which uses the lone pair on the nitrogen to complete the aromaticity. Pyridine is also aromatic but does not use the lone pair on nitrogen to complete the aromaticity. Therefore pyridine is more basic than pyrrole for the above mentioned reasons.
Pyridine and other amines such as triethylamine are often used in the chemical laboratory as a base which functions to trap a hydrogen ion.
