MA00944 - Chemical Bottles (2) Click to enlarge image
MA00944 - Chemical Bottles (2) Image: Amy Butterfield
© Australian Museum

Atomic structure

Atoms are the smallest divisible components of matter that have the same properties (e.g. size, shape, mass) which differ from the properties of other elements. They are the fundamental units of each mineral's crystal structure. Each atom consists of a tiny nucleus that contains equal numbers of positively-charged protons and electrically neutral neutrons. This nucleus is surrounded by one or more shells of negatively-charged electrons. The actual radius of each atom is different and depends upon the nature of the atom, its state of ionisation, and the way that it is linked to other atoms and/or ions. A neutral atom has the same number of protons and electrons.

  • Anions: atoms or groups of atoms that have gained electrons and are negatively charged (e.g. 02-).
  • Cations: atoms or groups of atoms that have lost electrons and are positively charged (e.g. Ca2+).
  • Atomic Number: is the number of protons or electrons present in an atom.
  • Atomic weight: is the number of protons+neutrons in an atom. The effective size of an individual atom (called an angstrom) is about 10-10 m.
  • Ion: an electrically charged atom formed by the loss or gain of one or more electrons.

Valence: the number of lost or gained electrons. It can be negative or positive, e.g. 02- has a negative valence of 2 whereas Ca2+ has a positive valence of 2.

Elements and compounds

An element is the simplest form of matter that can exist under conditions that we find in a chemical laboratory. Although there are now over 112 different elements, those after Plutonium (atomic number 94) have a very short half-life, and last for only a few hours or seconds.

In geological terms, we can subdivide the elements into four main groups according to their reactivity (i.e. what elements they commonly combine with) and where they occur in the Earth:

  • Lithophile elements: those that commonly occur with oxygen within the Earth's crust.
  • Chalcophile elements: those that commonly occur with sulfur in the Earth's crust and mantle.
  • Siderophile elements: Those that commonly occur with iron in the Earth's mantle and core.
  • Atmophile elements: Those that commonly occur in the Earth's atmosphere.

The most common elements that we encounter within minerals are: aluminium, barium, carbon, calcium, chlorine, copper, fluorine, iron, hydrogen, potassium, magnesium, manganese, sodium, oxygen, phosphorous, lead, sulfur, silicon, titanium and zinc.

A compound is a group of atoms of a fixed ratio bound so tightly together that they behave as a single particle. A stoichiometric compound is one in which all the charges are balanced.


  • Empirical or simplest formula: simply gives the relative number of atoms of each element present (e.g. ethylene: CH2)
  • Molecular formula: gives the actual number of each atom found in a molecule (e.g. ethylene: C2H4)
  • Isotopes: can be formed by either the radioactive decay of unstable nuclides ( radiogenic isotopes - e.g. U, Pb, Sr, Ar, Nd) or by exchange or kinetic reactions in nonradiogenic elements (commonly referred to as stable isotopes - e.g. O, H, C, S). Isotopes of an element have the same atomic number but different atomic weights
  • Mixture: a combination of elements or compounds in no fixed ratios (can usually be broken-down into their constituent compounds and/or elements by physical processes)
  • Phase: any part of a system that has uniform composition and properties


Bonds are forces that hold atoms in their places. Within minerals, there are four main types of bonds called metallic bonds, covalent bonds, ionic bonds and van der Waals bonds.

  • Metallic bonds: are the most common type within native metals. Metallic bonding occurs when electrons can move freely from one ion to another.
  • Covalent bonds: are rarely the predominant type in minerals. In the diamond structure, a central carbon atom is surrounded by four other carbon atoms each of which shares an electron with the central carbon atom.
  • Ionic bonds: are the most important in 90% of all minerals. Each ion is surrounded by ions of opposite charge, with the number of ions being dependant upon their ionic radii and charges.
  • van der Waals bonds: are weak dipolar bonds between molecules, such as those that are responsible for the cohesion of water molecules.

The way in which the atoms are linked together is extremely important in determining the mineral's properties, e.g. carbon atoms can be linked in such a way that they form sheets (the mineral graphite). Although the sheets themselves are very strong, they are held together by very weak bonds. Carbon atoms can also be linked together into three-dimensional frameworks (the mineral diamond) with very strong links between the carbon atoms.