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X-ray powder diffraction in agate research

Most minerals are crystalline even if the crystallinity is not always obvious. Collectors of agate will observe that larger quartz crystals can occasionally form between bands (Fig. 1) but is more usually found at the centre of the agate geode.  Large macrocrystalline quartz (mqz) crystals contain many well defined crystal faces and its crystallinity is obvious. The agate itself appears to be devoid of crystallinity and will fracture in a similar manner to bottle glass. Quartz has a regular arrangement of the atoms and it is this that makes it crystalline while the atoms in glass have no regular order and is amorphous. However, agate does show that it is crystalline under the polarising microscope. Agate with chert, flint, jasper and chalcedony is one of the microcrystalline quartz minerals.  
Thin section mexican agate
Fig. 1  A thin section of Mexican crazy lace agate.  The agate has a layer macrocrystalline quartz (Qz) that marks the end of a dusty-like growth of chalcedony and the start of the usual fibrous chalcedony.  (Scale bottom edge = 3 cm)
Light and X-rays are part of the electromagnetic spectrum. If you hold a thin section of agate against the light, then the light passes through the section and sometimes reveals a growth pattern. However, light cannot interfere with the agate structure because the wavelength of light is some 10 000 x greater than the distance between atoms in the crystal. X-rays have a wavelength that is similar to the atomic radii. When X-rays pass through, or are by  reflected by,  the atoms they produce an interference effect.
In a diffractometer, X-rays are produced by high energy electrons striking a metal surface. The generated X-rays are directed at the substance under study. For powder X-ray diffraction, the substance is crushed , sieved and then subjected to X-rays. A detector allows the voltage pulses to be counted so that the data can be collected and examined (Fig. 2).
A simple but very limited analogy would be to consider a mirror that has been broken into many pieces (the crushed powder). If the pieces are dropped into a bucket of sand, then the mirror fragments point in a variety of directions. A torch light (X-ray beam) is now directed at the bucket of sand but only those fragments facing the torch will be able to reflect the light. If the torch gradually moves in an arc, then fresh mirror fragments will reflect the light. In an X-ray diffractometer, the reflections are measured in counts / unit time and appear as peaks for particular exposed crystal faces. The collection, position and relative intensity of a set of peaks are as diagnostic of a particular mineral as are finger prints for a   human being.  X-ray image 4
Fig. 2  X-ray diffractogram of Brazilian macrocrystalline quartz and Brazilian agate.
Fig. 2 shows the reflections produced by Brazilian agate and Brazilian macrocrystalline quartz (mqz). The actual counts are shown on an arbitrary scale and the angle of  X-ray incidence is degrees theta although it is measured in 2 theta. The counts on the vertical axis are measured as a square root in order to minimise the peak difference between the two substances.
What do the plots show?

  • Notice how the reflections of the two substances are almost identical. This fingerprint confirms the link between agate and mqz. Although the substances are chemically the same, the reflections in the agate are broader and less intense. This is because the crystallinity of the agate is poorer.
  • The reflections at b) have partially fused together in the agate. The broad base of one has overlapped with its neighbour.
  • Agate is generally not 100% quartz. Additionally, it has an extra crystalline phase of moganite (a) ). Moganite was first discovered in the ignimbrite lava flows in Gran Canaria in 1976. The mineral is a form of silica that is not seen in the hand specimen as it develops as an intergrowth between the fibres. Together, the  moganite and quartz reflections produce  this lop-sided first reflection in agate.
  • The backgrounds (the flat runs of the diffractogram) of the mqz and agate are also different.  Notice how the mqz reflections develop sharply but have little effect on the background. In the Brazilian agate, the reflections overrun and reinforce the background. This produces a hanging effect.
  • Silicon is added to both substances. It is used as a standard to correct for increased instrument broadening.