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Allicin is a compound that is created when garlic is chopped or crushed. It's often used in making garlic supplements, though it actually works as an insecticide and protective measure for garlic in nature. Though he compound has been found to possess both antibacterial and antifungal properties, studies are divided on how effective it is for treating medical conditions in humans. It is also not a stable compound, and will have a relatively short shelf life.
Garlic in its natural state is not a good source of allicin. However, when the garlic bulb is cut or bruised in some manner, enzymes in the garlic begin to react and create the compound. This compound is also deactivated by acidic environments like the stomach, and is damaged by heat. Thus, cooking with crushed or minced garlic will not allow the user to receive any health benefits of these types from the allicin content of the cooked garlic. It is also not very shelf-stable, even in liquid form, and short shelf-life.
Despite its short shelf life, allicin is used to make many health supplements. It is said to be able to be able to help cure colds, boost immunity, and reduce a person's risk of strokes. It also has been shown to have antibacterial and antifungal properties in lab conditions. Studies on the effectiveness of allicin supplements are split, with some showing that garlic supplements are actually very helpful, and others showing that claims are overstated. Many studies done on this compound are done on animals, so the results may not be able to be replicated in humans.
One aspect of allicin production that is important to the preparation of cuisine is the strong flavor that is activated when the garlic is chopped or crushed. The familiar flavor is the result of the conversion of the enzyme allicinaise by the interaction of the chemical allicin in the process. While the medicinal properties of allicin do not hold up to cooking, the flavor created by this chemical reaction in the garlic compound does remain.