The most basic materials science characterization tool is powder x-ray diffraction (XRD). The most basic information that this gives you is if your sample is crystalline (the atoms have what is called long-range order, or repetition), or amorphous (the atoms are just all jumbled up). Basically, the way XRD works is that the machine shoots x-rays at your sample over a range of angles. The crystalline planes in your sample will reflect the x-rays only at certain angles depending on what planes are present in the crystal. A detector measures the reflected x-rays and produces a graph showing the intensity over a range of angles. If your sample is amorphous, there are no crystal planes to reflect the x-rays, so you get a scan with no peaks, like this one (intensity on the y-axis, angle, or 2-theta, on the x-axis).
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The one of the bottom is a reference scan that comes from a huge database of known crystalline structures. Once you perform XRD on your sample, you can use various matching techniques to compare your sample to reference scans to determine exactly what you have made. Once you know what you have made, you can use data about the relative peak intensities, the peak width, peak symmetry, etc, to determine the size and shapes of the crystals in your sample. You can also look at the "2-theta shift" to determine crystal sizes relative to each other. If you look at the top two scans here, you can see that they have the same peaks, but the second one is shifted slightly compared to this first one. This indicates that the crystal size in the second sample is slightly smaller than in the first one. In this case, this was because I had been substituting smaller atoms into the crystal, so I used this scan to prove that I was successful in this substitution.
If you want to get an actual look at your material, you can use electron microscopy, either scanning (SEM) or transmission (TEM). In an SEM, the machine shoots a high-energy beam of electrons at your sample. Normally, these high-energy electrons are generated by heating up a tungsten filiment to a very high temperature. These electrons can interact with your sample in a variety of ways. The first is elastic scattering, in which the electrons hit the atoms in the sample and then rebound with the same amount of energy, but in a different direction. There is also some inelastic scattering, where some of the electrons' energy is dissipated in the collision. This energy has to go some where, so electromagnetic radiation is also emitted in these collisions. Most SEMs only measure the elastic scattering. Here is a random SEM picture (I seem to have lost the ones I had from my research from last summer). You can see the individual crystals, which in this case are hexagonal prisms.
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TEM is very similar to SEM, except that instead of looking at eletrons that are reflected off the sample, you are looking at electrons that have passed through the sample. For this reason, the sample must be very very thin. Here is a TEM picture that was not taken by me, but is of a material I worked with last summer:
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