Organic Chemistry

Life, as we know, is a beautiful thing. We exist in a world of colors and shapes, in a world of growth and decay, in a world of beauty and sadness. All of this and much more is collectively defined as life. However, to understand life, one must first understand organic chemistry.

Compounds (combinations of elements) can be divided into two categories: organic and inorganic depending upon the presence or absence of carbon-hyrdogen bonds. These bonds are the backbone of life, and indeed, carbon alone is an amazing atom which enables life to a large degree through its ability to form numerous bonds with itself. Much like water is unique among liquids, carbon is unique among elements.

Ca rbon is the twelfth element in the periodic table. Elements are arranged on the periodic table according to their atomic number which is the number of protons and therefore electrons in a given atom. If we divide our total number of electrons into their orbitals, we see that carbon has four electrons in its outermost (orbitals are specific volumes in space where a given electron can be found 90% of the time. These volumes have specific shapes given by the energy function which governs the movements of electrons). Like most nonmetals (all elements in the periodic table are divided into metals and nonmetals by the stair step line), carbon requires eight electrons for a stable outer electron shell (eight is the special number given by atomic energy equations and the orbitals both occupied and unoccupied). Since all naturally occurring elements progress to their lowest energy state which is also the most stable, carbon will look to borrow or take four electrons from other elements. In more specific terms, "borrow" is known as covalent bonding where atoms share electrons filling both their needs, and "take" is known as ionic bonding where electrons are stripped or added to atoms creating ions (atoms with an absence or presence of electrons which affects the overall charge of the atom). Since carbon needs four electrons (a large number on the atomic scale), it cannot strip them from another atom and instead must bond covalently. These bonds will form at the apexes of a tetrahedron or pyramid as in the figure below due to the electrostatic repulsions between similar electrical charges.

Carbon's available bonds.
(visionlearning.com)

The second types of hydrocarbon is the alkenes and consists of molecules that contain at least one double bonded carbon-carbon bond. These molecules follow the same naming convention as alkanes with the exception that "ene" is added instead of "ane". Thus, whereas ethane was a alkane containing two carbons with a single bond between them and three hydrogens on each carbon, ethene is an alkene containing two carbons with a double bond between them and two hydrogens on each carbon atom. The chemical formula is subsequently C_nH_2n.

Alkynes are the third class of hydrocarbons with at least one triple bonded carbon-carbon bond. The naming convention for these molecules follows the familiar pattern of combining a prefix and ending. The ending for alkynes is "yne". The general chemical formula for an alkyne is given by C_nH_2n-2.

Because so many different bonds are possible with carbon, there is not necessarily a bonding geometry with precedence over another. That is to say, the shape of a given molecule is not necessarily an absolute but can exist in a number of ways. Molecules which exist in different geometries but have identical chemical formula are known as isomers. To make matters even more interesting, shape is a highly distinctive and functionalizing quality. For example, in our bodies most chemical reactions take place on the surface of enzymes. These enzymes are shaped only to bond to other specifically shaped molecules. Thus, not all isomers are created equal.

In addition to carbon and hydrogen, organic molecules often contain other elements or groups of elements. These groups are known as functional groups, and their addition again can change the behavior and chemical properties of a hydrocarbon. A good example is a hydroxl functional group. A hydroxl group is simply a hydroxide polyatomic ion or an oxygen bonded to a hydrogen and possessing a single net negative charge. The group of hydrocarbons that contains this functional group is known collectively as alcohols and is named in a fashion similar to the simply hydrocarbons. A carbon determining prefix is attached to "anol" which designate the molecule as an alcohol. For example, ethane is an alkane molecule composed of two carbon atoms with single bonds between them. If we remove one of the six hydrogens present in ethane and replace it with a hydroxl functional group, we form ethanol the active ingredient in most alcoholic beverages. Again and again we see the addition of components changes the properties of organic compounds and functionalized hydrocarbons are no different. Methane (the alkane composed of one carbon atom and four hydrogen atoms) is a gas at room temperature, but with the addition of a hydroxl group becomes methanol (a single carbon atom attached to three hydrogen atoms and a hydroxl functional group) which is a liquid at room temperature.

Organic chemistry is a complex science full of molecules and compounds with names that can contain twenty or more prefixes. It is often daunting and confusing to the casual observer. However, life could never depend upon a simple science. It instead relies upon an incredible inventory of organic chemicals, carbon and its unique properties, shape and its functional role, component construction, and many more subtleties of organic chemistry. Life is amazing, and organic chemistry is its science.