Atoms, isotopes, ions and molecules


Everything is made of matter, people, animals, the Earth itself. By matter we understand a physical substance that occupies a space, has volume and mass.

If we take a piece of matter and start splitting it to smaller pieces we eventually are going to end up to the smallest possible piece which can not be anymore split, the atom.

The atom is the smallest, finite constituent of matter. The atom can not be devised in smaller constituents.

Raw solid gold nuggets

Image: Raw solid gold nuggets

Microscopic view of gold surface showing individual atoms

Image: Microscopic view of gold surface showing individual atoms

By zooming into the surface of a gold piece (with a very powerful microscope) we can see the individual gold atoms linked together.

An element is made of only one type of atoms. A macroscopic sample of particular type of element is made of a very large number of atoms, all of the same type, with identical chemical properties.

For example, copper is an element. If we look at a small copper coin, it’s made of approximately 3 · 1022 copper atoms.

An atom is made of 3 subatomic constituents:

  • protons
  • neutrons
  • electrons
Components of an Lithium atom: nucleus, protons, neutrons and electrons

Image: Components of an lithium atom: nucleus, protons, neutrons and electrons

The protons and neutrons are contained in the nucleus of the atom. The protons and neutrons are kept together in the nucleus by a nuclear force.

The electrons are moving around the nucleus in an electron cloud.

The protons have positive electric charge, while the electrons have negative charge. The neutrons are neutral from the electric charge point of view, they don’t have any charge. Therefore, the nucleus is positively charged and the electrons are negatively charged. The electrons are attracted to the protons within the nucleus through a electromagnetic force.

The number of protons and neutrons within the nucleus are similar, without big differences.

The nucleus contains more than 99 % of the atom’s mass. The mass of the electron is negligible in comparison with the mass of the nucleus.

In the image above we can see an lithium atom. It has 3 protons, 3 neutrons and 3 electrons. The number of protons gives the atomic number of the element. In the case of lithium, the atomic number is 3.

View of an Helium atom with electron cloud (zoom-in: Helium nucleus)

Image: View of an helium atom with electron cloud (zoom-in: helium nucleus), 1 Å (angstrom) = 10-10 m

In the image above we can see an helium atom, with it’s nucleus, containing 2 protons (atomic number = 2) and 2 neutrons, and the surrounding electron cloud. There are also 2 electrons which can be found anywhere in the electron cloud, the darker the area the higher the probability to be found there.


For a particular chemical element, what we find in nature are isotopes. An isotope is a variant of the same chemical element with a different number of neutrons. For a given chemical element all isotopes have the same number of protons and electrons but different number of neutrons.

For example, the most common isotopes of hydrogen are:

  • protium (1H)
  • deuterium (2H)
  • tritium (3H)

Protium has 1 proton, 1 electron and no neutron. It’s the most abundant form of hydrogen that can be found in nature. Almost 99.9895 % of the occurring hydrogen is protium.

Deuterium has 1 proton, 1 electron and 1 neutron.  It’s also found in nature but very scarce, about 0.0105 % of the hydrogen isotopes is deuterium.

Tritium has 1 proton, 1 electron and 2 neutrons. It’s radioactive, decaying in time, with a half-life of around 12 year. Occurs naturally but in limited amounts (traces).

Hydrogen isotopes - Protium, Deuterium and Tritium

Image: Hydrogen isotopes – Protium, Deuterium and Tritium

There are also other hydrogen isotopes, with higher numbers of neutron. These don’t occur in nature but are synthesized in the laboratory and have a very short life duration.


When we join together two or more atoms we get a molecule. The atoms which form a molecule can be of the same element (homonuclear) or a combination of different elements (heteronuclear).

Examples of molecules:

  • oxigen (O2): homonuclear, made of 2 atoms of oxigen
  • hydrogen (H2): homonuclear, made of 2 atoms of hydrogen
  • water (H2O): heteronuclear
A water (H2O) molecule

Image: A water (H2O) molecule

The water molecule consists of one atom of oxigen and two atoms of hydrogen. From the electrical point of view molecules are neutral, they don’t have any charge.


Given any atom or molecule, if the number of electrons is equal to the number of protons, the atom/molecule is neutral, doesn’t have any positive or negative charge.

An ion is an atom or molecule for which the total number of electrons is not equal with the total number of protons.

If the atom/molecule loses one or more electrons, it will end up with a positive charge. The name for an ion with positive charge is cation.

If the atom/molecule gains one or more electrons, it will end up with a negative charge. The name for an ion with negative charge is cation.

Hydrogen ions: cation and anion

Image: Hydrogen ions: cation and anion

Atoms, isotopes, molecules and ions are the basic blocks of chemistry. Gain a good understanding about them will in order to be able to understand more complicated topics in chemistry.

Test your knowledge regarding Atoms, isotopes, ions and molecules by taking the quiz below:

QUIZ! (click to open)

For any questions or observations regarding this tutorial please use the comment form below.

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