Structure of Organic Molecules

Features of Organic Molecule Structures

Here we will cover some commonly recurring features within the structures of organic molecules.

Most commonly, the most recurring features that come up in organic molecules are the functional groups. Here, we will cover and go through a couple of functional groups and how their structure influences the shape of the organic molecules.

The most common types of organic functional groups that you will come across are alcohols and carbonyl groups. These groups rely on the incorporation of oxygen into organic molecules.

Alcohols are a group of compounds which have a hydroxyl group (-OH) at the end of the organic chain. They have a suffix of -ol at the end of the IUPAC name of the longest chain of the organic compound.

On the other hand, carbonyl functional groups are found in carboxylic acids, ketones and aldehydes. Carboxylic acids have a double bond between carbon and oxygen and a hydroxyl group at the end of the carbon chain (-COOH). This distinguishes them from aldehydes, which just have a carbon-oxygen double bond at the end of the carbon chains, and ketones, which have a carbon-oxygen double bond in the middle of the carbon chain.

Additionally, there are structural functional groups. These relate to the actual carbon backbone structure, and include alkanes, alkenes, and alkynes. Alkanes are the simplest, as they are comprised of the backbone having just single bonds between the carbon atoms. Alkenes have, at least one double bond between the carbon atoms, whilst alkynes have a triple bond in their structure.

For more information on functional groups, especially regarding their structures, please take a look at our article on Functional Groups!

Structure of Organic Molecules and Compounds

The structure of organic molecules relies on the overall composition of the molecule, which includes putting together all the different models of the structure together. This includes the electronic structure, Lewis dot electron structures, and skeletal structure to understand the shape organic molecules can take.

Below, we will go through each of these ways of looking at the structure of organic molecules and compounds to elucidate their shape.

Electronic Structure of Organic Molecules

The electronic structure within organic molecules to the arrangement of electrons inside atoms. The electronic arrangement of atoms will determine the number of valence electrons present, which will be very crucial for the determination of structure, such as through Lewis structures and bonding.

The electronic arrangement of organic molecules is rather simple, as organic chemistry relies on elements present at the beginning of the periodic table. These include elements which go up to atomic number 22. The arrangement of electrons between the shells of these atoms is very structured and periodical, that is to say, there are no outliers in the overall trend of filling electron shells.

The key rules for the electronic arrangement of elements involved in organic molecules are:

maximum of 2 electrons in the first shell

maximum of 8 electrons in the second shell

maximum of 8 electrons in the third shell

Using those rules, you can work out the electronic arrangement of elements involved in organic molecules by knowing the atomic number.

After determining the electronic arrangement, you will know the number of valence electrons.

With this information, you can create electronic diagrams for the elements involved in organic molecules. More importantly, you can put different electronic structures together to form Lewis structures and determine the shape of organic molecules.

Lewis Structure of Organic Molecules

Here we will cover what Lewis structures are and how you can create Lewis structures of molecules to interpret the shape of organic molecules.

Lewis structures are structures which build off of the electronic structure of organic molecules. They depict the arrangement of the electrons in bonded molecules, specifically how electrons are shared between atoms to create specific bonds.

Drawing Lewis Structures

So how do you go about drawing a Lewis structure of an organic molecule?

Some basic rules that apply to drawing Lewis structures are that electrons, usually valence electrons, are depicted as dots or crosses. They are arranged around the atom, represented by the elemental symbol of the atom in the periodic table. Then, lone pairs of electrons can also be depicted as lines instead of two dots. These lines go along the shape of the atom rather than stick out away from the centre of the atom.

First, you start off with your central atom and determine the number of valence electrons present. Depict the valence electrons as dots around the symbol for the atom.

Secondly, determine the other atoms involved in the organic molecule you are trying to represent, and determine their valence electrons. More importantly, you can have a guess at how electrons are shared between two atoms when you have all valence electrons depicted. Join different atoms by showing that they share electrons.

Lastly, where there is a pair of electrons, be it a bonded pair or a lone pair of electrons, depict it with a line. A line sticking from one element to another is representative of a bond. If more than just one pair of electrons is shared between two atoms, such as two pairs or three, draw two or three lines to show a double or triple bond. Where there is a lone pair of electrons, these arew drawn as two dots next to each other.

Take a look at the graphic below to better understand how to draw Lewis structures.

Uses of Lewis Structures

So, why are Lewis structures useful? They are very helpful to determine the shape of organic molecules.

Lewis structures most importantly can show two things clearly: the amount of bonded electron pairs and lone pairs of electrons. These can determine how many electron domains are present around each atom involved in the organic structure, and therefore determine the structure of the whole molecule. This can be done by interpreting the structure through VSEPR theory or skeletal structures.

Skeletal Structure of Organic Molecules

Here we will cover how the skeletal structure of organic molecules is a representation of the shape of organic molecules.

So the shape of organic molecules in 3D is often hard to represent within a 2D space. This is how skeletal structures can help.

Skeletal structures of organic molecules rely on stick arrangements of compounds. Every line in a skeletal diagram represents a bond, so a single bond is represented with one line, a double bond with two lines, and a triple bond with three lines.

These bonds can come together to form complex structures which rely on more than just carbon-to-carbon interactions. Even though life is based on the chemistry of carbon, it includes many more elements than just carbon. Carbon atoms are represented as the vertices in skeletal structures, meaning they are the point where two lines meet to form an angle.

Bonds in Skeletal Structures

In skeletal structures, you will come across three types of bonds, or representation of bonds. These will be a straight line, a dashed wedge or a solid (filled) wedge.

Below are the meanings of these bonds:

Solid lines: a bond within the plane of the 2D representation

Dashed wedge: the bond extends below the plane (away from the viewer)

Solid wedge: the bond extends above the place (closer to the viewer)

Here is an example to demonstrate:

Ethanol Skeletal Structure. Source: Wikimedia Commons / Public Domain

Do you notice how the two hydrogens which each have either a dashed or solid wedge go above or below the plane of the 2D representation? This is a way of showing the tetrahedral shape of the carbon bonds, as carbon is hybridised in such a way.

The solid wedge in the structure above shows the bond coming out of the paper, towards the reader, whilst the dashed wedge represents the bond behind the paper and so pointing away from the reader.

Other atoms, such as hydrogen, nitrogen, sulphur, and phosphorus, as well as any other elements which appear in organic chemistry and molecules of life are depicted by having the elemental symbol at the end of a line or at the corner where two lines meet. This way we can include complexity in our structures and use skeletal diagrams to depict any organic molecule for chemistry purposes.