Structure of an Atom | Covalent, Ionic and Hydrogen Bonding |

All life is made up of matter; from the air that you’re breathing, the screen you’re looking at, the water you’re drinking, and the granola bar you may be munching on. Matter is something that has a mass and occupies space…which includes everything on this planet.

All matter is made up of elements. Elements are substances that can’t be broken down or chemically changed into another substance. The periodic table lists all the known elements; both naturally occurring and man-made. Each element in the Periodic table has a symbol; either one upper-case letter or two letters where the first one is upper-case and the second is lower-case.

Structure of an atom

An atom is the smallest component of an element. If we were to get down to the tiniest piece of an element that we could, we would get to the element’s atom. Atoms have a particular structure that we will talk about below.

Atoms contain three sub-atomic particles called protons, neutrons, and electrons. Protons are positively charged, neutrons are neutral, and electrons are negatively charged. Protons and neutrons live in the nucleus of the atom. (An atom’s nucleus is not like the cell’s nucleus where DNA lives, an atom’s nucleus is simply the space where protons and neutrons exist). Around the nucleus, electrons hover and zoom about. Electrons are in constant motion. Although we say that electrons orbit the nucleus the truth is they are like bees around a beehive, they’re buzzing around in a path we call a “shell”. 

Atomic Number and Mass Number

In the periodic table, we see the chemical symbols of elements and we also see numbers on the top and bottom of elements. The number on the top is the atomic number and is the smaller number of the two. It represents the number of protons in the atom. For example, the atomic number of N is 7 which means that N has 7 protons.

The mass number (also sometimes called the atomic mass) is the larger number and is found on the bottom of the chemical symbol. The mass number is the sum of the protons and the neutrons. For example, the mass number of N is 14.007. We know that N has 7 protons, and now we know that it has 7 neutrons as well. If we know the atomic number and mass number we know the number of protons and neutrons an atom has. 


Some elements have isotopes. Isotopes are different forms of the same element; they have the same number of protons but will have different numbers of neutrons. Carbon has three isotopes or three forms. Carbon exists as ¹²C, ¹³C, ¹⁴C. All three isotopes have an atomic number of 6 which means they all have 6 protons. Their mass numbers are 12, 13, and 14 which means that ¹²C has 6 neutrons, ¹³C has 7 neutrons, and ¹⁴C has 8 neutrons. 

Octet Rule

As we mentioned, electrons move around the nucleus in a shell (or orbital). The first shell is closest to the nucleus and can hold two electrons. The second shell can hold 8, the third can hold 8 electrons as well. The more electrons the atom has the more shells it will have. However, most of the time in science classes we only deal with atoms that have 2 to 3 shells.

C has 6 electrons and so it will have 2 shells; the first one will have 2 electrons and the second one will have 4. O has 8 electrons and so it will also have 2 shells: 2 electrons in the first shell and 6 in the second one. 

The outermost shell of the atom is called the valence shell. The number of electrons within it are called valence electrons. The goal of every atom is to have 8 valence electrons (or 2 valence electrons in the case of H and He); this is called the Octet Rule. Octet means “8”.

Only the elements in Group 8 (the last row) of the periodic table have their valence shell filled. They are called inert gases because they’re happy with their outermost shell and don’t react with other elements. Other elements are not that lucky, they will always have an incomplete valence shell. This makes them want to bond with other elements; they either share electrons (covalent bonding) or exchange electrons (ionic bonding).

Covalent Bonding

A covalent bond forms when two or more atoms come close to each other and share their electrons. All atoms then have a complete octet of 8 electrons.

For example, C has 4 electrons and H has 1 electron. C wants 4 more electrons and H wants 1 more electron. 4 H atoms come to a C atom, and they begin to share their electrons such that C now has 8 electrons and each H has 2.

Ionic Bonding

Ionic bonds form when there is an exchange of electrons.
Again, atoms are trying to gain an octet with 8 valence electrons. Table salt, NaCl, is an ionic bond. Na has 1 valence electron and Cl has 7 valence electron. Na donates its 1 valence electron to Cl making Cl an anion. An anion is a negatively charged ion. Cl gained an extra electron making it negatively charged. By the same token Na became positively charged because it lost an election. A positively charged ion is called a cation. Opposite charges are attracted to each other and so the Na cation and Cl anion will be attracted to each other forming an ionic bond. It should be noted that Na has 3 shells of electrons around it, the first one has 2 electrons, the second has 8 and the third had 1. When Na donates it’s 1 valence electron it’s left with the second shell that has a complete octet of 8 electrons.
Helpful hint: to remember that an anion is negatively charged think of anion as “an onion” which is strongly flavored and makes you cry. An onion is a negative thing! Like an anion, also a negative thing! To remember a cation think of a cat. A cat is warm and purs and makes you feel good and positive…just like a cation!

There are 3 ways to know if the bond will be covalent or ionic:

  1. Covalent bonds form between non-metals: you can look at the periodic table to see where non-metals are. They are to the right.
    Ionic bonds form between metals and non-metals. Metals are on the left side of the periodic table.
  2. Covalent bonds will form is the electronegativity difference is between two atoms is less than 2.1. If it’s greater than 2.1 then an ionic bond will form. 

Hydrogen Bonding

A hydrogen bond results when hydrogen is bonded to an electronegative atom like O, N, F. Since the atom is electronegative it will pull the shared electron pair closer to itself than to H. This will give the molecule polarity such that H will have a slight positive charge and the other atom will have a slightly negative charge. Now this polar molecule will be attracted to the other polar molecules around it. This attraction is called hydrogen bonding. This is how water molecules form hydrogen bonds. The positively charged H of one water molecule is attracted to the negatively charged O of another water molecule and in turn all water molecules are bonded to each other. 

Amna Qureshi