A Physics Primer 3: How Atoms Constitute Matter

There are currently 114 recognized types of atoms, called elements, the type depending on the number of protons in the nucleus1. The first element, hydrogen, has only one proton in its nucleus. Hydrogen has two, lithium has three, and so on (the number of protons is called the atomic number of the element)1. Of these 114 elements, 91 elements make up almost all substances in the universe in various combinations2. Many familiar substances are made of just one element, substances like graphite and diamond (carbon), nitrogen gas, oxygen gas, neon, aluminum, iron, copper, silver, gold, mercury, lead, and uranium. But most substances are chemically composed of more than one element, and these substances are known as compounds3.

Atoms can combine into compounds in two ways. In the first way, the atom of one element donates electrons to an atom of another element. The donator now has less electrons than protons and becomes positively charged. The recipient ends up with more electrons than protons and becomes negatively charged. Both the donor and the recipient are known as ions (the donor is called an cation and the recipient is called a anion4). Since unlike charges attract, donor and recipient atoms will stick to each other to form a new substance, often a crystal. This is how table salt (chemical name: sodium chloride) is formed: each sodium atom donates one electron to one chlorine atom5.

In the second way, groups of atoms will share electrons among themselves resulting in what is called covalent bonding. The sharing of electrons causes the atoms in the group to stick together. Each group is called a molecule. Examples are water (hydrogen and oxygen) and carbon dioxide (carbon and oxygen)5.

Atoms of the same element can bind to each other as well. The atoms of non-metallic elements can form covalent bonds with each other. Seven such elements form diatomic (two-atom) molecules: hydrogen, nitrogen, oxygen, fluorine, chlorine, bromine, and iodine6. In metals, the atoms in the metal give up their outer electrons to a sea of electrons that bathe the atoms; the electrons are no longer tied to a particular atom and can wander throughout the metal. It is this electron sea that binds the atoms together in the metal, and this bonding is knows as metallic bonding7.

Each atomic element has its valence number, the maximum number of atoms with whom an atom of that element can bond8. Hydrogen has a valence number of 1 — it can only bond with one other atom at a time. Oxygen has a valence number of 2; it can bond with two atoms. Nitrogen has a valence number of 3, carbon has a valence number of 4. Helium does not bond with other atoms, so its valence number is 0.

Although many molecules are electrically neutral having no net charge, one end of such a molecule can have a positive charge, the other end can have a negative charge. This happens when the electrons in the molecule are spending more time in one atom than they are in another. When this happens, the molecule is called a dipole. Some dipoles are permanent because one atom is attracting electrons more strongly than the others9. Other dipoles are temporary, the result of statistical fluctuations where one atom for a split second just happens to have more electrons about it than the others10. Dipoles give rise to the intermolecular forces that bind molecules together in a solid or in a liquid11. Breaking these intermolecular forces (as occurs during melting and boiling) requires the extra energy known as latent heat. More about latent heat in coming posts12.

Molecules can exist by themselves or they can become ions (that is, have a net charge), in which case they are referred to as polyatomic ions or molecular ions13. An example of this is the fertilizer and explosive ammonium nitrate. It consists of two ions: the ammonium ion, which is the ammonia molecule with an extra hydrogen atom, and the nitrate ion, which is the nitrogen dioxide molecule with an extra oxygen atom14. Like atomic ions, molecular ions have valence numbers. Both ammonium and nitrate both have a valence number of 1. Carbonate and sulfate both have a valence number of 215.

It is interesting that some of the properties that apply to atoms apply as well to molecules. Some atoms are self-contained and electrically neutral. They have little to do with the atoms around them and do not form compounds easily. These are the atoms of the so-called noble gases: helium, neon, argon, xenon, krypton, and radon16. Likewise, some molecules are self-contained and electrically neutral. They also do not enter easily into reactions with other chemicals around them. Carbon dioxide is an example17.

At the other end of the spectrum, there are atoms that, although electrically neutral, jump at the chance to react with other atoms. Sodium, potassium, fluorine, chlorine, are good examples of such atoms, to the extent that it is impossible to find these atoms by themselves in their electrical neutral state in nature18. Likewise, there are electrically neutral molecules that are extremely reactive: the hydroxide molecule for one. These atoms and molecules are known as free radicals19.

We have seen that both atoms and molecules can exist as ions, carrying a net electrical charge, and that these ions are attracted to ions of the opposite charge. Carbonate, nitrate, and sulfate are examples of negative molecular ions. They combine with positive ions to form such compounds as calcium carbonate, magnesium nitrate, and potassium sulfate20.

Molecules can even form parts of larger molecules. A fine example are the numerous protein molecules in your body. Each protein is made up of smaller molecules called amino acids, strung together in an exact order to form the building blocks and the molecular engines of living cells21.

The branch of chemistry that studies carbon-based compounds is called organic chemistry. Organic molecules tend to be much larger than inorganic molecules. Most inorganic molecules do not consist of more than a dozen atoms; organic molecules can consist of thousands of atoms22. A large part of organic chemistry is the study of parts of molecules that tend to give compounds certain specific characteristics, such as alkene, alcohol, ketone, and ester, called functional groups23. Is it possible to consider a functional group to be a molecule within a molecule? In other words, a molecule that plays the role of an atom within a larger molecule?


  1. Georgia State University, Department of Physics and Astronomy, Hyperphysics website, section “Atoms and Elements”. To view, click here. There are actually 118 elements; you can see this on any up-to-date periodic table or by consulting Jefferson Lab’s It’s Elemental website. Four of 118 elements are as yet confirmed — see Wikipedia’s article Timeline of chemical elements discoveries, and scroll down to the section “Unconfirmed discoveries.” This leaves 114 elements confirmed by science. Of these 114 elements, only 91 occur naturally. 23 elements (including technetium, element 43) must be synthesized by humans and last minutes at most before disintegrating into simpler elements.
  2. The Free Dictionary website. Chemical Element. To view, click here. Note that the definition claims there are 92 naturally-occurring elements. There are only 91. They forgot that technetium (element 43) does not occur naturally.
  3. Chemicool website. Definition of Compound. To view, click here.
  4. Note on pronunciation: “Cation” does not rhyme with “nation”, it is pronounced cat-eye-on. “Anion” does not sound like “onion”, it is pronounced an-eye-on.
  5. University of California at Davis ChemWiki website. Ionic and Covalent Bonds. To view, click here.
  6. Princeton University website. Diatomic molecules. To view, click here. Examples of non-diatomic covalent bonds among non-metals include the allotropes of carbon (graphite, diamond, buckyball) and phosphorus (white, red, violet, black)
  7. University of California at Davis ChemWiki website. Metallic Bonds. To view, click here.
  8. Frostburg State University General Chemistry Online website. What is the difference between valence, and number of valence electrons? To view, click here.
  9. Utah Valley University OChemPal website. Dipole Moment. To view, click here.
  10. Master Organic Chemistry website. The Four Intermolecular Forces and How They Affect Boiling Points. To view, click here, then scroll to section 4: “Van der waals Dispersion forces (London forces)”.
  11. Master Organic Chemistry website. The Four Intermolecular Forces and How They Affect Boiling Points. To view, click here.
  12. This post is not ready yet.
  13. Frostburg State University General Chemistry Online website. Polyatomic Ions. To view, click here.
  14. Princeton University website. Ammonium Nitrate. To view, click here.
  15. Helmenstine, Anne Marie. About.com Chemistry website. List of Common Polyatomic Ions. To view, click here.
  16. University of California at Davis ChemWiki website. The Noble Gases. To view, click here.
  17. The Columbia Electronic Encyclopedia, published on the Infoplease website. Carbon Dioxide. To view, click here.
  18. Sodium and potassium are alkali metals, chlorine and fluorine are halogens. For alkali metals, see Bentor, Yinon, Periodic Table: Alkali Metals. ChemicalElements.com website. To view, click here. For halogens, see the Purdue University website Bodner Research Website, The Chemistry of the Halogens. To view, click here.
  19. Australian Research Council, ARC Centre of Excellence for Free Radical Chemistry and Biotechnology website. What Are Free Radicals? To view, click here.
  20. General Certificate of Secondary Education science website. Atomic Structure. To view, click here.
  21. Bailey, Regina, Amino Acid. About.com Biology website. To view, click here.
  22. Personal observation.
  23. Fromm, James Richard, The Concept of Functional Groups. Third Millenium Online Website. To view, click here.

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