Okay, I am being imprecise again. I have been using the term “molecule” a little loosely. The technical definition of a molecule is two or more atoms chemically bonded together by covalent bonds. If two or more atoms are chemically bonded together by something other than covalent bonds (such as ionic or metallic bonds), then it is not really a molecule. This means that the smallest unit of water (two hydrogen atoms and one oxygen atom chemically bonded together by covalent bonds) is a molecule, but the smallest unit of salt (one sodium ion and one chlorine ion chemically bonded together by an ionic bond) is not.

The reason why sodium chloride is not considered a molecule is because the sodium and chlorine ions do not exist in physical pairs… they exist as separate ions held together by electrostatic attraction, and those sodium and chlorine ions are constantly changing “partners.” Consider salt in its solid state. In salt crystals, the sodium and chlorine ions are in a face-centered cubic crystal structure. Can you tell which sodium ion is paired with which chlorine ion? Distinct pairs do not exist. And when salt melts, it forms an ionic liquid. In this ionic liquid, the sodium and chlorine ions are paired, but those pairs are short-lived. Essentially, a sodium ion will ionically bond with one chlorine ion for a little while, and then switch and bond with a different chlorine ion for a little while.

While the hydrogen and oxygen atoms in a water molecule are also held together by electrostatic attraction, they also have overlapping orbitals. Two atoms that form a covalent bond are physically sharing electrons. Unlike ionic bonds, covalent bonds cannot be broken without creating new molecules and substances. The oxygen atom in a water molecule is paired with two specific hydrogen atoms, and those pairs do not change until a chemical reaction breaks the molecule apart. That is why a water molecule is a molecule and a sodium chloride ion pair is not.

We could say that ionic bonds are not chemical bonds at all, but intermolecular bonds… and that sodium chloride is a mixture and not a pure substance. However, sodium chloride has a specific chemical composition (one sodium ion for each chlorine ion) and its own distinct characteristic properties, such as density, boiling and melting points, and heats of vaporization and fusion, something that mixtures do not have. And sodium chloride does not behave anything like sodium or chlorine. Sodium is a soft, silvery metal that reacts violently in water (think explosions and poisonous gases) and chlorine is a yellow-green gas that acts as a strong bleach. Sodium chloride is a completely different substance. We use sodium chloride to salt our food. Ionic bonds are chemical bonds because they form new substances; intermolecular bonds do not.

Pure substances can typically be classified as either elements or compounds. A pure substance is classified as an element when it consists of a single type of atom. Some textbooks define an atom as the smallest unit of an element, but that is not accurate. Oxygen atoms (O), diatomic oxygen gas (O2), and ozone (O3) are all elements since they consist only of oxygen atoms. However, the oxygen atom is not the smallest unit of diatomic oxygen gas or ozone… the O2 and O3 molecules are, and all three of those pure substances have very different characteristic properties.

A pure substance is classified as a compound when it consists of two or more different types of atoms (or elements). Water (H2O) is a compound because it is a pure substance that consists of hydrogen and oxygen atoms. Sodium chloride (NaCl) is also a compound because it is a pure substance that consists of sodium and chlorine atoms. For water, and any other pure substance formed by covalent bonds, the smallest unit of the substance is a molecule. However, sodium chloride, and any other pure substance formed by ionic or metallic bonds, does not have a name for its smallest unit. Maybe that is okay since those smallest units are not permanent and constantly in flux, but it is inconvenient. Some people define the smallest unit of sodium chloride as the sodium chloride compound, but a compound is a substance, not a cluster of atoms.

In this unit, I have chosen to call the smallest unit of a pure substance a molecule, regardless of whether that substance is an element or a compound, or if its chemical bonds are ionic or covalent. When the distinction between “the smallest unit of a pure substance” and the technical definition of a molecule is important, I will make sure to point that out.

There are many ways to represent molecules. Two of the most common are chemical and structural formulas. A chemical formula identifies the type and number of atoms that make up a molecule. For example, the chemical formula for isopropyl alcohol is C3H8O. The chemical symbols identify the types of atoms. In this case, carbon (C), hydrogen (H), and oxygen (O). The subscripts identify the number of those atoms. If a chemical symbol does not have a subscript, then the number is one. This tells us that an isopropyl alcohol molecule is made up of three carbon atoms, eight hydrogen atoms, and one oxygen atom covalently bonded together. Brackets are often used to represent atoms held together by ionic bonds. So the chemical formula for magnesium chloride would be [Mg+]2[Cl2-]. However, it is not uncommon to see Mg2Cl used as shorthand. A person familiar with the chemical properties of magnesium and chloride would know that the chemical bonds are ionic and not covalent.

A chemical formula may tell you the type and number of atoms in a molecule, but it does not tell you how those atoms are bonded together. In chemistry, the geometry and structure of a molecule plays a significant role in how a molecule behaves and interacts with other molecules. The structural formula of an isopropyl alcohol molecule can be given as a Lewis structure. Covalent bonds can also be represented by lines. One line represents a single bond. Two lines represent a double bond. Three or more lines represent higher order bonds.

More than one molecule may share the same chemical formula, so a chemical formula is not enough to identify a pure substance. Isopropyl alcohol, n-propyl alcohol, and methoxyethane all have the same chemical formula: C3H8O. Isopropyl alcohol and n-propyl alcohol are both alcohols and have similar chemical properties. However, methoxyethane is an ether, and it has very different chemical properties compared to the other two molecules.

Some molecular representations combine features from both the chemical and structural formulas. Here is isopropyl alcohol again in two other formats:

All of these formats are easy to interpret if you are experienced at reading them and understand the geometry of molecules. But molecules are three-dimensional, and these two-dimensional representations are difficult to interpret if you have not visualized molecules before. I strongly recommend that students spend some time building three-dimensional models of molecules to gain familiarity with the shape of molecules. The easiest way to do this is with ball-and-stick models. Colored balls represent different atoms and are connected by rods representing covalent bonds. Ball-and-stick models are available from many science and educational supply stores.

When two atoms form a single covalent bond, they each contribute one electron, and those two electrons are then shared between them. In an ideal covalent bond, this sharing is equal, and the shared electrons will spend 50% of their time with one atom and 50% of their time with the other atom. However, not all atoms share electrons equally. Electronegativity is a chemical property that describes the tendency of an atom to pull electrons towards itself.

Electronegativity correlates strongly with ionization energy. In general, the more energy it takes to remove an atom’s outermost electron, the more the atom tends to attract electrons towards it. Oxygen has an electronegativity of 3.44 and hydrogen has an electronegativity of 2.20. So, when an oxygen atom and a hydrogen atom form a covalent bond, the shared electrons will be more strongly attracted to the oxygen atom, and they will spend more time with the oxygen atom and less time with the hydrogen atom. This is what gives the oxygen atom in a water molecule its slightly negative charge and the hydrogen atoms in a water molecule their slightly positive charge.

Overall, water is an electrically neutral molecule. It does not have a positive or negative charge. However, because the electron cloud is distributed unequally across the molecule (the electron cloud is denser around the oxygen atom than around the two hydrogen atoms), the hydrogen end of the molecule is slightly positive and the oxygen end is slightly negative. This separation of positive and negative charges is called an electric dipole, and it is why water molecules behave like small magnets. Molecules that behave like small magnets are called polar molecules.

Molecules that do not behave like small magnets are called nonpolar molecules. Molecules are nonpolar because either the atoms share electrons equally, or because of the symmetrical arrangement of polar bonds. When two oxygen atoms form a covalent bond, both atoms have the same electronegativity. So while the two oxygen atoms are each strongly attracting the shared electrons toward themselves, the electrons end up being shared equally and a diatomic oxygen (O2) molecule is nonpolar. On the other hand, the electronegativity of carbon is 2.55, which is lower than the electronegativity of oxygen. So, when a carbon atom and an oxygen atom form a covalent bond, the shared electrons will be more attracted to the oxygen atom, and the covalent bond will be polar. But a carbon dioxide (CO2) molecule is actually nonpolar.

The reason why carbon dioxide is nonpolar, even though its covalent bonds are polar, is because of the geometry of the molecule itself. The two oxygen atoms are on opposite sides of the carbon atom. This means that the center of the molecule is slightly positive (δ+ represents a positive dipole), and the two ends of the molecule are slightly negative (δ- represents a negative dipole). This symmetry means that, at least from a distance, carbon dioxide behaves like a nonpolar molecule. (To see why the chemical bonds in a water molecule are at an angle and not symmetrical like the chemical bonds in the carbon dioxide molecule, you would have to understand the three-dimensional geometry of molecules. It has to do with the maximum separation of electron pairs. You can see the respective shapes of a water and carbon dioxide molecule if you construct ball-and-stick models.)

Although we talk about polar and nonpolar molecules, the reality is not so clear. It is more accurate to describe a molecule as either more polar or less polar than another molecule. A substance cannot enter a liquid or solid state unless the molecules (or atoms) in the substance are attracted to each other. Water, oxygen, carbon dioxide, and helium can all enter a liquid state. This means that their molecules (or atoms) are attracted to each other, and that attraction can only be caused by the existence of electric dipoles.

Water is clearly a very polar molecule. It has a high boiling point and it takes a significant amount of energy to break the intermolecular forces holding water molecules together. Because of its symmetry, carbon dioxide is a much less polar molecule. It takes much less energy to break the intermolecular forces holding carbon dioxide together. Its weak polarity comes from its polar covalent bonds. However, when close together, the dipole charges on the carbon and oxygen atoms will hold carbon dioxide molecules together. Oxygen molecules do not have polar covalent bonds; the oxygen atoms share their electrons equally. But at very low temperatures, oxygen molecules will enter a liquid state. This is because, even though oxygen molecules do not have formal dipole charges, they do have different regions. The electron density will be slightly different in the regions around the atomic nuclei compared to the region between the atomic nuclei and the regions at the far ends of the molecule. Helium atoms are so nonpolar that they need to be cooled to almost 0 K (absolute zero) before entering a liquid state. Unlike oxygen molecules, helium atoms are spherical. However, if you get close enough and move slow enough, the fact that the helium atom has a positive center (the nucleus) surrounded by a negative cloud (the electrons) is enough separation between positive and negative charges to hold the atoms together.

When you are given the chemical formula of a pure substance, the first thing you should do is try to figure out the structural formula of the substance’s molecule. Visualizing the three-dimensional geometry of the molecule will give you insights into its physical and chemical properties.

The chemical formula for nitrous acid is HNO2. This tells us that a nitrous acid molecule is made up of one hydrogen atom, one nitrogen atom, and two oxygen atoms. There are two ways to figure out the structure of the nitrous acid molecule. You can pull out your ball-and-stick model kit and try to build the molecule. The nice thing about a ball-and-stick model kit (at least when you are working with simple atoms like hydrogen, nitrogen, and oxygen) is that it will guide you through the building process by forcing you to fill valence shells and maintain proper molecular geometry.

You can also identify the chemical bonds in the molecule by analyzing the Lewis structures of the four atoms and applying the octet rule. To achieve a stable electron configuration, a hydrogen atom can either lose an electron, accept an electron, or share an electron; a nitrogen atom can accept and/or share three electrons; and an oxygen atom can accept and/or share two electrons.

At first glance, it looks like there is only one way to put these four atoms together. The hydrogen atom shares one electron with the first oxygen atom. The first oxygen atom shares one electron with the hydrogen atom and one electron with the nitrogen atom. The nitrogen atom shares one electron with the first oxygen atom and two electrons with the second oxygen atom. And the second oxygen atom shares two electrons with the nitrogen atom.

However, there is a second way to put these four atoms together. Instead of the hydrogen atom forming a covalent bond with the first oxygen atom by sharing its electron, it could form an ionic bond by losing its electron. By losing its electron to the first oxygen atom, the atoms would form a positive hydrogen (H+) ion and a negative “nitrite” (NO2-) ion, and the two ions would be electrostatically attracted to each other. You should notice that the hydrogen ion does not form an ionic bond with the first oxygen atom (the atom it lost its electron to); it forms an ionic bond with the entire nitrite (NO2-) ion.

A nitrous acid molecule can have two possible molecular structures. So which structure is the “real” one? Actually, they both are. The first structure (with the hydrogen atom covalently bonded to the molecule) is the chemically stable state. This means that structure has the lowest energy and is the most stable state for those four atoms. Although the second structure (with the hydrogen atom ionically bonded to the molecule) has higher energy and is a less stable state, it is still metastable, and some molecules will have that structure.

This system is in dynamic equilibrium. Some molecules will be in the first state and some molecules will be in the second state… and molecules will be moving back-and-forth between states. The proportion of molecules in the first state will depend on the relative stability (energy levels) of the two states and the energy of the system. If the energy of the system is higher, then it will be easier for molecules to move between states and there will be a higher proportion of molecules in the second (higher energy) state. This is all based on probabilities.

There is one final complication with the nitrous acid molecule. Take a closer look at the nitrite (NO2-) ion. One oxygen atom shares a covalent bond with the nitrogen atom and has accepted one electron from a hydrogen atom. The other oxygen atom shares a double covalent bond with the nitrogen atom. One of those electron configurations is more stable than the other. I am guessing that it is the double covalent bond with four shared electrons occupying the space between two atomic nuclei. Both oxygen atoms will pull that electron density towards its own side of the molecule, and a tug-of-war ensues.

To you, both structures may be the same. But to the two oxygen atoms involved, they are very different. And neither atom can win this particular tug-of-war since they are perfectly matched. Instead of constantly flipping back-and-forth between the two states, the nitrite ion actually adopts a structure called a resonance hybrid.

The resonance hybrid is the chemically stable state for the nitrite ion because it has the lowest energy. The ion’s negative charge is distributed equally across both oxygen atoms, and the electrons in the p-orbitals are delocalized. Normally, electrons are either bound to one atomic nucleus or shared between two atomic nuclei in a covalent bond. When an electron is shared across more than two atoms, it is described as delocalized. This occurs in metals and in the nitrite ion. P-orbital electrons flow freely from one oxygen atom, to the nitrogen atom, and then to the other oxygen atom.