Chalcedony including flint, chert and agate is shown by infrared and X-ray study to contain (OH) in structural sites in addition to several types of non-structural water, already recognized, held in association with internal surfaces and pores. The content of structural (OH) varies zonally both in chalcedony fibers and in natural and synthetic crystals of the same spectral type as chalcedony. The (OH)-rich zones are more rapidly etched, have lower X-ray reflection angles, lower indices of refraction, and whiten on heating to 550–600°C.

Chalcedony and its varieties together with colorless quartz crystals and amethyst formed at low temperatures in association with chalcedony, and synthetic quartz crystals, have a distinctive infrared absorption spectrum in the 3200 cm−1 to 3600 cm−1 region (Type B quartz). A different spectrum in this region is afforded by natural quartz crystals formed at higher temperatures (Type A quartz). The structural (OH) is housed by different mechanisms in these two types of quartz, apparently depending on the structural role and availability of Al.

The generally fibrous nature of low-temperature natural Type B quartz appears to be a character deriving from the content of (OH) and its effect on dislocations.

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