Unit 5: Molecules

Ways of Representing Molecules

Introduction

Have you ever wondered what molecules look like on a microscopic scale? Or how many
atoms of each element are present in a compound? Compounds can be represented by just the
ratio of atoms or the exact number of atoms found in each unit. This is important in figuring out the
identity of the compound, or what products may form if it reacts. For more complicated molecules,
details on how each atom is connected and how they are positioned, are important in
understanding their chemistry as well. In this lesson, you will learn how molecules are represented,
from the simple ratios or formulas to the complex structural representations.

Learn about It!

Chemical Formula
To understand the chemistry of a compound, you have to know which atoms are present
and what structures are formed. The degree of information needed depends on what information
is needed. For some, the ratio of elements present in a compound is sufficient, while others need
to see how atoms are connected to form the molecular structure. Chemical formulas are ways to
represent molecules to convey information about its composition or structure.

How important are chemical formulas for knowing

the composition and structure of a compound?

Molecular Formula
 In writing molecular formulas, the number of each atom in a molecule is indicated. The
symbols of each element are written down with a subscript indicating how many atoms are in the
compound. It is the most common way to represent molecules, especially in general chemistry.
For example, a compound containing two atoms of hydrogen and one atom of oxygen is
represented as H2O. It is the chemical formula of water. For another example, a compound
containing one atom of carbon and two atoms of oxygen is represented by CO2, which is the
chemical formula of carbon dioxide. If there is no subscript before the atomic symbol, then it means
there is just one atom present in the formula.

Empirical Formula
In some cases, only the ratio of atoms that are in a compound is given or is needed. In this
case, the empirical formula is used, which gives the simplest whole-number ratio of each element
in a compound. For example, the molecular formula of glucose is C 6H12O6. For every six carbon
atoms, there are 12 hydrogen atoms and six oxygen atoms. The empirical formula of glucose is
CH2O, wherein for every carbon atom, there are two two hydrogen atoms and an oxygen atom.
The actual molecular formula is a multiple of this ratio, meaning there can be six times that amount
for every molecule.

To get what to write as subscripts, divide each amount of atoms in the formula by the
largest number that can give the lowest whole number ratio. In mathematics, this is called the
greatest common factor. For example, the molecular formula H 2C2O4 has two atoms of hydrogen,
two atoms of carbon, and four atoms of oxygen. The greatest common factor will be 2. Divide each
number by 2; you will get a ratio of one hydrogen, one carbon, and two oxygens. The empirical
formula of the compound will be HCO2.

There may be instances where the molecular formula is already the lowest number ratio.
In this case, the empirical formula is the same as the molecular formula. For example, C 5H12 is
both the molecular and empirical formula of the compound, since it is already the lowest whole
number ratio possible.

Structural Formula
As molecules become complex, more details are needed to show the structure of the
compound. This is especially true for organic compounds, which are compounds that contain
carbon bonds. Compounds that lack these are called inorganic compounds. Recall that in your
warm-up activity, the first structure had carbon-carbon bonds. What you constructed was an
organic molecule. In this particular case, what you created was a molecule made up entirely of
carbons and hydrogens. This is part of a family of organic compounds called hydrocarbons. The
majority of organic compounds have hydrocarbons as part of its structure.
 In a complete structural formula, all bonds and atoms are shown. Carbon atom makes
four bonds with other atoms, while hydrogen can only bond with one. If there are five carbons
connected in a straight line, i.e., pentane, hydrogens would be attached in this way:

Fig. 5.2.2. The complete structural formula of n-pentane

 In a condensed structural formula, atoms that are connected to a specific carbon are
represented like molecular formulas, where more than one atom is represented by a subscript
attached to a specific carbon. The positions of carbon atoms are still written in detail, but the other
atoms, like hydrogens, are written after each carbon with a subscript. If you convert the structure
above to a condensed structural formula,

CH3CH 2CH2CH 2CH 3

Fig. 5.2.3. The condensed structural formula of n-pentane

The most simple form in representing organic compounds with hydrocarbons in its structure
would be to draw it using the skeletal or line-angle formula. The structure is drawn with lines
drawn at an angle where each corner represents a carbon. The hydrogens attached to each carbon
will not be drawn. These are called implicit hydrogens that can be deduced based on the fact
that carbon forms four bonds with other atoms. If the bonds shown in the line-angle formula are
less than 4, then it is implied that the remaining bonds are with hydrogen.

Fig. 5.2.4. The line-angle formula of n-pentane

Let’s Practice!
Example 1
What is the empirical formula of a compound having a molecular formula of C 4H8O2?

Solution
Step 1: Identify the given
There are four atoms of carbon, eight atoms of hydrogen, and two
atoms of oxygen in the molecular formula of the compound.

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Unit 5: Molecules

Step 2: Find the greatest common factor for the subscripts.

The greatest common factor of 4, 8, and 2 is 2.

Step 3: Divide the subscripts by 2.

For carbon:

For hydrogen:

For oxygen:

Step 4: Write the empirical formula using the lowest whole number ratio of atoms in the
molecule.

The empirical formula is C2H4O.

1
Try It!
Arginine has a molecular formula of C6H14N4O2. What is its empirical formula?

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Unit 5: Molecules

Example 2
The complete structural formula of 1-butene is shown below. Draw its condensed structural
formula.

Solution
Step 1: Count the number of hydrogens in each carbon.
From left to right, carbon-1 has two hydrogens, carbon-2 has one, carbon-3
has two, and carbon-4 has three.

Step 2: Write the hydrogens attached to each carbon with the number as subscripts.
Retain the position and number of bonds in each carbon in the structure. Take
note of the double bond connecting carbon-1 to carbon-2. The condensed
structural formula can be drawn as:

CH2=CHCH2CH3

2 Try It!
Given the complete structural formula below, what would be its condensed structural
formula?

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Unit 5: Molecules

Example 3
Given the complete structural formula of the hydrocarbon, what would be its line-angle formula?

Solution
Step 1: In the line-angle formula for hydrocarbons, hydrogens are implied based on the fact
that each carbon forms four bonds with other atoms. The first step is to remove the
hydrogens from the structure.

Step 2: Carbons should now be represented either as the end of a line if it is a terminal
carbon, or as the corners (or the vertices) of the drawn figure.
The angles should be obtuse (greater than 90 degrees). If there are other atoms aside

from carbon or hydrogen, it should be shown in the final structure. In this structure,

it is entirely a hydrocarbon; therefore, the structure would look like this.

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Unit 5: Molecules

3 Try It!
Draw the line-angle formula of the structure below.

Molecular Model
A 3D model is the best way to see how atoms are connected in a molecule. They show us geometry
and help us predict its properties and reactions. There are numerous ways in which a molecular
model is presented.

Ball-and-Stick Model
Recall the Warm Up activity at the start of the lesson. The molecules are represented using ball-
and-stick models. In this type of model, balls represent atoms, while sticks represent bonds
between the atoms. The balls included in the kit are color-coded, and these colors represent a
particular element that can form a specific number of bonds. This model shows the geometry of
the molecule and helps us predict properties.

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Fig. 5.2.5. Ball-and-stick model for n-pentane

Did You Know?

August Wilhelm von Hofmann was the first chemist to make and use
ball-and-stick molecular models. In 1865, he used these models in his
lectures at the Royal institution of Great Britain. These models have
been adapted by other companies for mass production.

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Unit 5: Molecules

Space-Filling Model
A better estimate of the actual shapes of the molecules would be seen in the space-filling model
of the molecule. In this model, bonds represented by sticks in the previous model are cut short so
that there is a better estimation of what the molecules look like if they were visible.

Fig. 5.2.6. Space-filling model of n-pentane

Why is it important that molecular models

show the correct geometry of the compound?

Key Points
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● A chemical formula is a way to represent molecules to convey information about its

composition or structure.
● A molecular formula is the most common chemical formula wherein symbols of each
element are written down with a subscript indicating how many atoms are in the
compound.
● An empirical formula is a chemical formula showing only the simplest whole-number
ratio of each element in a compound.
● Organic compounds are compounds containing carbon bonds. Compounds that lack
these bonds are called inorganic compounds. Molecules that contain only carbon and
hydrogen are part of a family of organic compounds called hydrocarbons.

● Structural formulas are detailed chemical formulas that show the structure of a

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compound.
○ A complete structural formula is a structural formula wherein all bonds and atoms
are shown.
○ A condensed structural formula is a structural formula indicating the number of
attached hydrogens to each carbon
○ A skeletal or line-angle formula is a representation of a structural formula wherein the
hydrogen and carbon atoms are implied from the shape of the structure.
● A molecular model is a 3D model showing how atoms are connected in a molecule.

○ A ball-and-stick model is a molecular model where different colored spheres represent

atoms, and sticks represent bonds.
○ A space-filling model is a model wherein bond lengths are shortened for
better estimation of its length relative to the size of the atoms.
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