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Structure of Organic Molecules

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Structure of Organic Molecules

In this article, you will learn how to determine and draw the shape of organic molecules using different methods. Knowing the shape of organic molecules is very important since it contributes to the physical and chemical properties of compounds. Knowing the shape helps in knowing the function and properties of different organic molecules. This is a field that is used throughout STEM, pharmaceuticals, and the food industry.

  • Here we will cover the key features of organic molecules, such as functional groups.
  • We'll then cover the electronic arrangement of elements involved in organic molecules.
  • We'll look at what Lewis structures are and how to draw them.
  • Finally, we'll cover how skeletal structures of organic molecules can help us depict 3D molecules in 2D.

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.

Functional group: a group of elements in a particular arrangement that give specific physical and chemical properties to 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.

Remember that organic molecules have a carbon backbone.

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.

Other functional groups which include oxygen include esters and ethers.

Ethers are defined by an oxygen atom in the middle of the carbon chain.

Esters are defined by oxygen in the carbon chain and a double bonded oxygen on the adjacent carbon after the oxygen.

You can imagine esters as being a combination of an ether and a ketone.

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.

Other functional groups which can act as features of organic molecules include the incorporation of other elements, such as sulphur to create thiols, or nitrogen to create amines and amides.

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.

Atomic number dictates the number of protons in the element's nucleus, which is indicative of the number of electrons in the non-ionic form of the element.

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

Valence electrons are the electrons in the outermost shell of the atom.

You can also find the valence electrons of an atom by its group number.

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.

Lewis Structure. Shape of Organic Molecules. StudySmarterBonding in fluorine, represented by its Lewis structure. Source: chem.libretexts.org

In molecules that have a charge, the charge is distributed between the whole molecule. Thus, you have to put brackets around the whole Lewis structure and indicate the charge outside the brackets accordingly.

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 are able to 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.

The skeletal structure of organic molecules is a 2D representation of organic molecules, drawn by sticks for bonds, where vertices depict atoms in a molecule.

So the shape of organic molecules in 3D is often hard to represent within a 2D space. This is how skeletal structures are able to 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 accross 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 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 demonstate:

Ethanol. Shape of Organic Molecules. StudySmarterEthanol 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.

Usually, in skeletal diagrams, the angle between two lines at carbon will be 120° to represent the 3D tetrahedral arrangement of carbon atoms.

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.

A small note regarding hydrogen in organic skeletal structures is that hydrogen is usually not depicted unless it is at the end of chains. This is because it is assumed that hydrogen is present to satisfy the bonding between carbon atoms.

Structure of Organic Molecules - Key takeaways

  • Here you learned the recurring features of organic molecules, which are the functional groups.
  • We also covered how the electronic arrangement of atoms determines the valence electrons and thus the bonding properties of elements.
  • We saw how elements join together by sharing electrons, which you can represent by Lewis structures.
  • Finally, we covered using skeletal structures to roughly show the 2D shape of complex organic molecules.

Frequently Asked Questions about Structure of Organic Molecules

Organic molecules can form long chains and be modular by using functional groups, which gives them a lot of variety. 

To determine the structure of an organic molecule, you need to know the electronic arrangement of atoms, as well as the Lewis structure of the molecule, to then be able to create a skeletal structure of the organic molecule. 

The structure of organic molecules dictates their function. From the way they interact in the body, to how they behave chemically, the structure underpins the workings of the organic molecule.

Organic molecule structure can be viewed in many ways, one of which includes the skeletal structure which can provide an insight on the details of the carbon chains and bonding within organic molecules. 

Final Structure of Organic Molecules Quiz

Question

What are the 4 key elements involved in organic molecules other than carbon?

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Answer

Hydrogen, Sulphur, Nitrogen, and Oxygen 

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Question

How many types of structural functional groups are there? Name them

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Answer

3: alkanes, alkenes, and alkynes

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Question

Which of the following functional groups have oxygen

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Answer

Thiols

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Question

What are the key parts that Lewis structures are able to represent?

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Answer

Bonded and unbonded (lone) pairs of electrons. 

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Question

Do electronic structures of elements show electrons if they are not present in the valency shell?

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Answer

No

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Question

In a skeletal structure, what is the angle created between two bonds (lines)?

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Answer

120°

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Question

Which of the following functional groups has an oxygen at the end of the carbon chain? 

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Answer

Aldehyde

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Question

Are alcohols considered carbonyls?

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Answer

No, as they do not have a carbon double bonded to oxygen. 

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Question

What is the definition of a carbonyl? 

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Answer

Oxygen double bonded to a carbon. 

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Question

In Lewis structures, how can you depict lone pairs of electrons?

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Answer

Two dots 


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Question

How many electrons can fill up the first shell of an atom?

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Answer

2

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Question

How many electrons can fill up the second shell of an atom?

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Answer

8

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Question

In skeletal structures of organic molecules, are all hydrogens depicted with bonds?

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Answer

No, only at the end of chains. 

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Question

What is another term for 'features' of organic molecule structure?

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Answer

Functional groups

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Question

How do you call an alcohol by the IUPAC rules?

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Answer

Add the suffix -ol at the end of the IUPAC name for the longest carbon chain in the molecule. 

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