Molecule Basics

Atoms are made of three subatomic particles protons, neutrons, and electrons. These atoms form bonds with other atoms to create molecules. Molecules bond with other molecules to form the world around us. Let’s take a look at how we can represent the building blocks of our world.

Formulae and Representations

Just like bonds we have a lot of different ways of representing molecules. Arguably the most useful and certainly the most annoying is the Lewis Dot Structure. In these representations, all valence electrons are shown and bonds are indicated using dot notation. We can generate these drawings by counting valence electrons on the periodic table and following the octet rule. We will go through step by step how to do this in the next topic.

To illustrate the different ways of representing the same molecule let’s take a look at 1,2-Ethanediol.

Another way of representing molecules is by their structural formula. With this type of formula, the individual atoms are shown and the connections between atoms are represented using lines for bonds.

Since drawing all of those bonds is tedious and at times unnecessary chemists, especially organic chemists will use skeletal formulae. In this representation, carbon atoms are implied at every intersection of different lines, and C-H bonds aren’t shown.

All of the drawing based formulae are further simplified into a condensed formula, which retains the order and connection but transforms a picture into a list of the atoms themselves.

A molecular formula like condensed formula is a list of the elements themselves, but here the order isn’t retained. Instead, all of the like elements are combined and listed one after the other.

Lastly, an empirical formula simplifies a molecular formula further by factor out any common factors the subscripts share. As a result, the empirical formula represents the ratio of one element to the next in a molecule.

[latexpage]
For instance, our model molecule 1,2 Ethanediol has a factor of 2 in all of its subscripts. Therefore to transform this into the empirical formula we divide all of the subscripts by 2.
\[ C_2H_6O_2 \to CH_3O\]

This can be interpreted as a ratio of the atoms to one another. For example 1:3:1 ratio of carbon to hydrogen to oxygen. For larger organic molecules determining the ratios of C to O can help in determining a molecule’s overall polarity as we will see later.

Multiple different molecules might share the same empirical formula or molecular formula but they would have unique Lewis Dot, structural, and skeletal formula.

Molar Mass

In addition to representing a molecule’s shape and identity, we need to be able to determine its molar mass. Molar mass is the weight in grams of a molecule per one mole of that molecule. It gives us a standardized way of comparing molecules together and is super important for stoichiometry and chemical reactions.

If you forgot:

A mole is a somewhat arbitrary unit that describes 6 x 10²³ things, be it molecules, atoms, bats, or cats. In the case of g/mol for carbon, it tells us the weight in grams for 6 x 10²³ carbons atoms. In most cases, it will be used as a conversion factor anytime questions ask for the quantities of atoms, molecules, photons, or other subatomic particles.

Calculating the molar mass of a molecule is fairly straightforward and involves summing the average atomic mass of all involved atoms. For example, 1,2 Ethanediol has a molecular formula of C₂H₆O₂.

[latexpage]
Therefore it has two carbons each with an atomic mass of 12g/mol,
\[2 \times 12\frac{g}{mol} = 24\frac{g}{mol}\; of\; carbon\]

six hydrogens each with an atomic mass of 1g/mol,
\[6 \times 1\frac{g}{mol} = 6\frac{g}{mol}\; of\; hydrogen\]

and two oxygens each with an atomic mass of 16g/mol.
\[2 \times 16\frac{g}{mol} = 32\frac{g}{mol}\; of\; oxygen\]

Now that we have the overall weight of each individual component it is time to sum them all up to get our overall molar mass.

\[24\frac{g}{mol} of\; carbon\;+\;6\frac{g}{mol} of\; hydrogen\;+\;32\frac{g}{mol}\; of\; oxygen=62\frac{g}{mol} \; of \; C_2H_6O_2\]

Need for Speed

We have to be fast on the MCAT (okay, I probably didn’t have to tell you that.) With this in mind, it is helpful to have a couple of common atomic masses memorized so we can quickly calculate a molar mass. Since we are often, but not always focused on biological molecules in the MCAT it is helpful to memorize the atomic masses of hydrogen (1g/mol), carbon (12g/mol), nitrogen (14g/mol), and oxygen (16g/mol).