HS Chemistry - Introduction to Organic Chemistry

Introducing Organic Compounds

Overview of The Page

This page will cover:

• What are organic molecules?
• What is the naming system for organic molecules?
• What are the different ways of writing the formula for an organic molecule?

Organic chemistry pertains to the study of organic compounds, compounds found in living organisms that are necessary to their function. They form important substances, such as carbohydrates, proteins, and even DNA. While there are many different types of organic compounds, they all contain Carbon $C$ and Hydrogen $H$ atoms. Some, called hydrocarbons, are even made entirely of C and H atoms.

Organic compounds can be very short $like methane$, or very long $like starch$, but they all contain functional groups, different groups of atoms in an organic compound responsible for its physical and chemical properties. Some organic molecules, like methane, only contain one functional group. Others contain multiple functional groups, and inherit the physical and chemical properties of their different functional groups. Organic compounds of a certain functional group are not just restricted to containing the atoms of that functional group - they can also contain other atoms as well.

There are many different kinds of functional groups. The most basic functional group is an alkane. It can be thought of as the default value of a functional group - if no other functional group is present in the molecule, the molecule is a type of alkane. Alkanes are also a type of hydrocarbon - that is, they only consist of Hydrogen and Carbon atoms.

Functional groups are not only determined by their atoms, but also by the bonds between those atoms. For example, an alkane functional group is present when the organic molecule contains two Carbon atoms bonded to each other and Hydrogen atoms with single bonds, and an alkene functional group is present when the organic molecule contains two Carbon atoms bonded to each other with double bonds, and bonded to Hydrogen or other Carbon atoms with single bonds. A large organic molecule can contain both alkene and alkane functional groups.

Organic compounds that are made up of the same atoms can have different structures, and sometimes even different functional groups. Therefore, when naming organic compounds, it's necessary to denote their main functional group - the functional group of the main chain $covered more in depth [on the next page](3-Branched-Organic-Molecules.md)$. The IUPAC $International Union of Pure and Applied Chemistry$ has developed a standard naming system for organic molecules: Prefix$es$-parent-suffix

The suffix of an organic molecule is determined by its main functional group. Generally, the last few letters of the functional group's name are used as the suffix $for alkanes, the suffix is \-ane; for alkenes, the suffix is \-ene; etc.$.

The prefix is often present in the name but not always - prefix naming conventions will be covered on the next page. For simplicity, the molecules covered in this page won't have prefixes in their name.

The parent part of the name denotes the number of Carbon atoms in the main chain of the molecule - that is, the longest chain in the molecule. While this will also be covered more in depth on the next page, for now we'll stick to straight-chained molecules $organic molecules with a single chain$.

Let's take the alkane CH₄:

It's the simplest alkane we can get. It has one Carbon atom, with 4 Hydrogen atoms bonded to the Carbon atom. It's an alkane, so the suffix is -ane.

And the alkane C₂H₆:

It's a slightly more complex alkane. It has two Carbon atoms, with 3 Hydrogen atoms bonded to each Carbon atom, for a total of 6 Hydrogen atoms. It's also an alkane, so the suffix for this molecule's name is also -ane.

And the alkane C₃H₈:

It has three Carbon atoms, with 3 Hydrogen atoms bonded to the first Carbon atom, 3 bonded to the last Carbon atom, and 2 bonded to the middle Carbon atom, for a total of 8 Hydrogen atoms. It's also an alkane.

And the alkane C₄H₁₀:

Which has four Carbon atoms, with 3 Hydrogen atoms bonded to the first Carbon atom, 3 bonded to the last Carbon atom, and 2 bonded to each of the Carbon atoms in the middle. It's also an alkane.

You can see where this is going. All these alkanes are very similar, except for the fact that each one has one more Carbon atom and two more Hydrogen atoms than the last one.

The parent part of the name distinguishes these molecules apart from each other by noting how many Carbon atoms are in the main chain $the longest chain$. In straight-chained molecules, there's only one chain, so that automatically becomes the main chain.

The following table can be used to determine the parent part of the molecule's name:

Number of Carbon atoms in the main chain	Parent part of the molecule's name
1	Meth-
2	Eth-
3	Prop-
4	But-
5	Pent-
6	Hex-
7	Hept-
8	Oct-
9	Non-
10	Dec-

Taking these rules into account, the alkane CH₄:

Has one Carbon atom in its main chain. The parent part of it's name would be meth-. The molecule's name would be composed of its parent part $meth\-$ and its suffix $\-ane$. It's name would be methane.

Similarly, the name of the alkane C₂H₆:

Which has two Carbon atoms in its main chain, would be composed of its parent part $eth\-$ and its suffix $\-ane$. It's name would be ethane.

One more thing that must be noted is that since all the compounds shown above are similar to each other $they are all straight-chained alkanes$, they are all members of a homologous series, which means they have the same functional group$s$. Members of a homologous series display similar chemical properties, and trends in their physical properties.

Members of a homologous series also have the same general formula, which is an algebraic representation of the molecular formula of molecules in that homologous series. The general formula for the homologous series of alkanes is C_nH_2n+2 - that is, an alkane with n Carbon atoms will have 2n + 2 Hydrogen atoms.

Organic Compound Formulae

As always, we can represent an organic molecule with both its empirical formula and its molecular formula. For example, the molecular formula of ethane is C₂H₆, while its empirical formula is CH₃

But for larger molecules like hexane, writing its empirical formula $C~3~H~7~$ or even its molecular formula $C~6~H~14~$ doesn't give us much information about the molecule. It doesn't tell us how the atoms are bonded to each other. While for hexane we can get that information from the name of the molecule, it becomes more difficult with larger molecules. Scientists therefore use a molecule's structural formula to show how the atoms are bonded to each other.

In a molecule's structural formula, all the Carbons are written out separately, and all the atoms connected to a certain Carbon atom are written next to that Carbon atom. For example, hexane's structural formula would be:

CH₃CH₂CH₂CH₂CH₂CH₃

This gives us more information than the molecular formula. The molecular formula $C~6~H~14~$ showed us how many Carbon and Hydrogen atoms there were, but not how they were bonded to each other. The structural formula, shown above, tells us that the first and last Carbon atoms each have three Hydrogen atoms attached to it, and each of the Carbon atoms in the middle have two Hydrogen atoms attached to it.

Another thing to note about the structural formula is that atoms that have single bonds between each other are written as is, but double or triple bonds between atoms are shown. This will be covered more on the Alkenes page.

But the structural formula still doesn't show us how the atoms are spatially arranged in the molecule. We can use the displayed formula to show that. The displayed formula is essentially a drawing of all the atoms in the molecule, their positions, and the bonds connecting them. For example, hexane's displayed formula would be:

It shows how the atoms in a hexane molecule are spatially arranged, with the Carbons in a single, straight chain, and then the Hydrogen atoms bonded to the Carbon atoms.

But in reality, the Carbon atoms are not in a straight chain. When we call ethene a straight-chained molecule, we mean that it has no branches $covered more in depth [on the next page](3-Branched-Organic-Molecules.md)$. Carbon atoms have a tetrahedral electron geometry, and can bond with up to 4 other atoms. When a Carbon atom bonds with up to 4 other atoms, it assumes a tetrahedral molecular geometry, which means that not all the atoms are on the same plane. If we were to place a Carbon atom on the plane of the screen, some of the atoms bonded to that Carbon atom would be on the same plane $the plane of the screen$, but some would be above the plane of the screen, and some would be behind. Thus, in reality, an hexane molecule would look more akin to:

This is called the 3D displayed formula. The Carbons are all kept on the same plane $as much as possible \- with branched molecules, covered [on the next page](3-Branched-Organic-Molecules.md), this becomes more difficult$, and the other atoms are placed in planes front or behind the Carbon atoms. This is different from the displayed formula, which is simply:

The displayed formula simply puts all the Carbons in a chain on a straight line, rather than the zigzag line of the displayed formula, and doesn't show which planes the atoms are one. Both the displayed formula and the 3D displayed formula have their uses.

But writing these out can become tedious, especially for larger molecules. To simplify and shorten the process, we can use the skeletal formula, which is also known as line notation.

The skeletal formula looks similar to the 3D displayed formula, but since most of the atoms in an organic molecule are likely to be Hydrogen and Carbon atoms, the skeletal formula eliminates the need to write those down. This is probably best shown through an example.

The 3D displayed formula of hexane is:

The Carbon atoms are arranged in a zigzag shape. A skeletal formula uses this shape, but it doesn't write down the Carbon and Hydrogen atoms. To create the skeletal formula, first we have to identify the chain$s$ of Carbon atoms:

Now we'll remove all the Hydrogen atoms:

And now we have the basis for our skeletal formula. We can just remove the Carbon atoms and connect the lines, and we'll get the skeletal formula for hexane:

In a skeletal formula, each of the points represents a Carbon atom, and the Hydrogen atoms, while not shown, are implied. Everything else is shown like the 3D displayed formula, except all the bonds are shown as lines so we can't tell which planes the atoms are on. For example, this Carbon atom $highlighted in green$:

Is connected to only one other Carbon atom $highlighted in red$ with a single bond:

And no other atoms are shown to be connected to the Carbon atom highlighted in green. Since the Carbon atom must have 4 bonds, there must be 3 more bonds for the Carbon atom, and since there are no other atoms shown to be connected to the Carbon atom highlighted in green, it is implied that there are 3 Hydrogen atoms bonded to the green Carbon atom. By comparison, this Carbon atom $highlighted in red$:

Is connected to two other Carbon atoms $highlighted in green$ with single bonds:

Since the Carbon atom in red is bonded to two other Carbon atoms with single bonds, and no other atoms are shown, it is implied that there are two other Hydrogen atoms bonded to the red Carbon atom to complete its 4 bonds.

Practice

Which of the options contains the correct name and structural formula of the following organic molecule?

Name: Butane
Structural formula: CH₃CH₂CH₂CH₃
Name: Butane
Structural formula: CH₃CH₂CH₂CH₂CH₃
Name: Pentene
Structural formula: CH₃CH₂CH₂CH₂CH₃
Name: Pentane
Structural formula: CH₃CH₂CH₂CH₃
Name: Pentane
Structural formula: CH₃CH₂CH₂CH₂CH₃

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