Quartz
Quartz is the most common mineral on earth; it belongs to a group of minerals known as silicates that make up much of the earth’s crust. The crystal structure of quartz is based on a framework of SiO₄ tetrahedra, although trace amounts of other elements may be present. The many varieties of quartz are produced by these trace elements and/or the crystal structure of the quartz (coarsely crystalline or microcrystalline). Quartz crystals are typically hexagonal prisms, although massive quartz is also popular in jewelry. Quartz comes in a very wide variety of colors, may be transparent to translucent and is a hard mineral on the Mohs scale at 7.

Amethyst and Citrine
Amethyst is a variety of quartz that comes in various shades of violet and purple. Citrine is a closely related variety of quartz that is light yellow in color (similar to topaz). These colors are caused by trace amounts of iron. Iron ions may be present interstitially, in other words it is not a part of the crystal lattice structure. Or iron may take the place of silicon in some of the tetrahedra within the crystal structure. If the iron is irradiated it can lose an electron; this process creates color centers in the crystal. The color centers are imperfections in the crystal that absorb specific wavelengths of light giving the gemstone a particular hue. If the iron is present as Fe⁺⁴, then the gemstone is amethyst. However, amethyst can be discolored by heat and sunlight. These elements can cause the Fe⁺⁴ to be reduced to Fe⁺³, transforming amethyst into citrine. Most commercially available citrine is heat-treated amethyst.

Aventurine
Aventurine is actually a rock, rather than a mineral. It is a type of quartzite- formed when sandstone composed almost entirely of quartz grains becomes metamorphosed. Aventurine may contain platy inclusions of fuchsite (chromium mica) producing a green colored stone, or hematite/goethite (iron oxides) producing a red/orange colored stone. In addition to producing a color, the mica and iron oxide inclusions also cause an optical effect called aventurescense that causes aventurine to exhibit a sparkly sheen.

Rose Quartz
A pink quartz variety, almost always found as massive quartz. Only very rarely is rose quartz found as well formed crystals. The color in massive quartz was once thought to be due to trace amounts of the elements titanium, iron or manganese. Recently the color has been attributed to microscopic fibrous inclusions of a pink mineral, suspected to be dumortierite or a closely related mineral containing a larger amount of iron.

Rutilated Quartz
This variety of colorless quartz contains golden needlelike inclusions of the mineral rutile (TiO₂). The rutile inclusions have a metallic sheen, and can create the appearance of golden threads running through the stone.

Chalcedony Chalcedony refers to the fibrous microcrystalline form of quartz- it is an aggregate of microscopic needlelike crystals. Chalcedony is deposited from aqueous solution, often within cavities in rocks. It can come in a wide variety of colors, is semitransparent to translucent, and may even be banded. Many these fibrous varieties of microcrystalline quartz have been given their own names.

Agate This is a banded variety of chalcedony with pronounced layers of alternating colors. The banding is likely caused by fluctuations in the chemical composition of the solution that deposits it, as well as the conditions under which it is deposited.

Carnelian A red-orange chalcedony that is colored by hematite (iron oxide).

Chrysoprase An apple green chalcedony colored by trace amounts of nickel. Due to its beautiful green translucent color, it is a highly appreciated form of quartz.

References
Klein, Cornelis 2002. Mineral Science. John Wiley and Sons, Inc., New York.
Nesse, W. D. 2000. Introduction to Mineralogy. Oxford University Press, New York.