Some minerals have color because of what they do to light that passes through them or reflects from their surfaces. There are thousands of different minerals. Certain varieties of about 15 are prized as gemstones. A small percentage of those are well-formed, colorful, transparent crystals.

Atoms that make up a crystal are arrayed in a repeating three-dimensional grid. Each mineral has a particular pattern of atoms that are called the “crystal lattice,” and each has a unique composition in its pure state. Some minerals occur in only one color, while others come in multiple colors, such as with emerald and aquamarine or ruby and sapphire.

The colors of gems are a result of the interaction of light with the electromagnetic environment inside the crystal. Electrical forces hold atoms of a crystal lattice in place, and the space between atoms is high in electrical potential.

A transparent crystal’s color is a consequence of the atoms in the crystal lattice selectively absorbing some wavelengths of light while transmitting the remainder. We see the transmitted wavelengths as a single color much in the same sense as we hear the blending of musical notes as a single chord.

There are nearly 250 different crystal lattices, and there are many different kinds of atoms that can occupy sites in the lattices. The effect of all of the possible combinations and variations of 30 or so different kinds of atoms in 200-plus different lattices is that the electromagnetic environment inside each crystal is unique to each mineral variety. In addition, each is unique in the way it interacts with light.

The composition of the pure mineral determines color of some minerals: Pyrite is always golden and malachite is always green.

Others are often clear. Quartz, for example is colorless and transparent in pure form, but it also comes in colored varieties such as amethyst. The colored varieties contain extremely small amounts of impurities. The presence of minute numbers of “foreign” atoms distributed throughout the crystal lattice changes the electromagnetic environment within the crystal. It is only a slight change but enough to affect light passing through the crystal to give each mineral species a unique color signature.

The most common coloring impurities are members of a related group of metals known as transition metals, which are responsible in one way or another for almost all of the colors that we see in naturally occurring rocks and minerals. The primary transition metals are iron, chromium and manganese, with lesser contributions from cobalt, nickel, copper, vanadium and titanium.

Ruby is a form of corundum, or aluminum oxide. In the aluminum ions there are no partially filled energy levels or orbitals. However, in the chromium ion, impurities there are partially filled energy levels or orbitals. It is these electrons that light excites while passing through the crystal, causing absorption of certain wavelengths of light and resulting in the red color.

Sapphire is another form of corundum. It comes in various colors, including blue, pink blue- violet, blue-green and combinations of these colors. Blue sapphires contain iron and titanium. The cause of color in the many hues of other sapphire colors is less well researched: vanadium — grayish blue to green; iron with a missing electron — yellow; iron alone — pale yellow; chromium with a missing electron — orange.

On the other hand, the mineral beryl that contains chromium impurities appears green and is known as emerald. However, the presence of iron impurities in beryl produces the color of aquamarines.

Richard Brill is a professor of science at Honolulu Community College. His column runs on the first and third Fridays of the month. Email questions and comments to brill@hawaii.edu.