Organic Compounds

The molecules found in life are uniquely complex in structure and function. The element carbon presents qualities that allow for the synthesis of such molecules. Due to this element's significance in biological compounds, molecules containing carbon, and typically Hydrogen, are known as "organic compounds". The study of organic compounds, organic chemistry, is a vast field, with many of the things we use everyday falling within its bounds.

Why Carbon?

Bohr Model representation of the covalent bonds of methane (CH4)

A carbon atom's nucleus is made up of four (neutrally charged) neutrons, and four (positively charged) protons, comprising a net charge of (+4). Due to this, carbon, and other elements in its group retain four valence electrons, and therefore can share those electrons with other elements to form four covalent bonds. A total of four covalent bonds allows carbon to form more stable complex molecules than other elements due to them resulting in a "full" valence shell of eight electrons.

This, along with the prevalence of carbon on Earth, allows for the synthesis of complex macromolecules and life.

Bonding

Carbon is particularly able to form large and complex organic molecules. By sharing its four valence electrons with other atoms carbon can form four covalent bonds. Each shared pair of valence electrons between two atoms is considered an individual covalent bond.

It is possible for more than one covalent bond to be present between two atoms. By sharing four total outer shell electrons, a double bond is formed (eg. O₂). In more specific scenarios, a triple bond can be formed through the sharing of six total valence electrons (eg. N₂).

Skeleton Structure

The location and number of bonds within a molecule can be represented in multiple ways (Lewis, Stick and Ball, etc.). When studying organic molecules it is typically most convenient to utilize the "skeleton" structuring style. In molecules depicted in this way, covalent bonds are shown as straight unbroken lines, with the vertices between lines being interpreted as carbon atoms. When less than four covalent bonds are depicted on an uncharged carbon atom, the remaining unrepresented bonds are assumed to be to hydrogen atoms.

Using the skeleton method of drawing organic compound structures has several advantages and disadvantages:

Skeleton Structure
Advantages	Disadvantages
Faster	Easy to misinterpret for novices
Reduces cluttering of depicting redundant hydrogens	3D configuration of bonds not as clear as other methods
Emphasizes functional groups	Can communicate false simplicity

Nomenclature Basics

Although thoroughly covering the terminology of organic compounds is outside the scope of this book, it is important to understand the systematic nature of chemical names.

IUPAC Standards

The longest unbroken chain of carbons is used in IUPAC nomenclature to describe the position of sidechains and active groups on the carbon backbone. Numbering is sequential from the side resulting in the lowest descriptive numbers.

The International Union of Pure and Applied Chemistry (IUPAC) is considered the world authority on chemical terminology. Contrary to a compound's common name, the IUPAC naming system allows for the interpretation of a compound's structure.