X-Ray is an electromagnetic radiation
By definition, X-Ray is an electromagnetic radiation which is having a short wavelength between 0.02Å to 100Å (~10-10m) emitted when electrons jump from a higher to a lower energy state. On the other hand, Crystallography is a study about crystal. The word ‘crystal’ it self is a molecule in which the atoms are arranged in the orderly manner where it consists of a periodic arrangement of the unit cell into a lattice. Thus, we can define X-Ray Crystallography (XRC) in a simple word as a technique or tool to investigate a 3-D molecular structure of a compound by using an X-Ray. In other words, XRC is a method to determine the 3-D arrangement of atoms within crystal of a particular compound which can be obtained when a beam of X-Ray strike a crystal and diffracts into many specific directions. It was found that X-Ray is very useful to explore the atoms within a crystal as the wavelength of X-Ray is similar to the size of atoms. Hence, XRC is the ultimate structural analysis of a compound. X-Rays are found to be the most important component in XRC, as without the X-Rays (light), we can’t obtain the image or 3-D internal arrangement of atoms within a crystal.
Based on the following Einstein Equation, the energy of X-Rays like other electromagnetic radiations is inversely proportional to the wavelength.
E = hv = hc/ג
where E = energy
h = Planck's constant, 6.62517 x 10-27 erg.sec
v = frequency
c = velocity of light = 2.99793 x 1010 cm/sec
ג = wavelength
Since X-Rays have smaller wavelength than the visible light, X-Rays tend to have higher energy as compared to the visible light. Therefore, other than size of the wavelength which is similar to the atom, the property of X-Rays which have higher energy will allow them to penetrate the crystal more easily than the visible light.
2.1 X-Ray Tube
Photo of an X-Ray Tube
Before we understand the detail principle on XRC, we also need to know how the X-Rays are produced. X-rays are commonly produced in a device called an X-ray tube. Based on the following illustration of an X-Ray tube, it consists of an evacuated chamber with metal target at one end; called an anode and tungsten filament at the other end called the cathode.
When electrical current is run through the tungsten filament, it will cause the tungsten filament, to glow and emit electrons. A large voltage difference (measured in kilovolts) which is placed between the anode and the cathode will cause the electrons to move at high velocity from the filament to the anode target. When the electrons bombard the atoms in the target, the electrons knock out inner shell electrons of the atoms resulting in outer shell electrons having to jump to a lower energy shell to replace the electrons that has been knocked out. These electronic transitions will result in the generation of X-rays. The X-rays that have been produced will then move through a window in the X-ray tube and it can be used to provide information on the internal arrangement of atoms in crystals. The high voltage rapidly heats up the anode, so it needs to be cooled. Efficient cooling is done by so‐called rotating anodes where the metal plate revolves during the experiment so that different parts are heated up. Rotating anode X-ray generators are the staple equipment in X‐rays labs. This phenomenon can be further illustrated based on the following Bohr Model of atoms.
Bohr Model of an atom
By using the simple Bohr model of the atom as the above, we can see that the nucleus of the atom which contains the protons and neutrons is surrounded by shells of electrons. The innermost shell is called the K- shell and it is surrounded by the L- and M - shells. When the energy of the electrons bombarded toward the target or anode becomes high enough to dislodge K- shell electrons, electrons from the L - and M – shells will move in to take over the place of those electrons that have been knocked out or to fill in the empty space. The process will continue until the outer-most shell is reached and this will result in the emission of a series of characteristic X- ray photons.
As mentioned, each of these electronic transitions will produce X-rays. Kα X-ray will be produced when there is a transition from the L - shell to the K- shell. On the other hand, Kß X-ray will be produced when there is a transition from an M - shell to the K- shell.
Kα X-rays are having higher intensity and the strongest X-Ray spectral line than Kß X-rays. The wavelength of these characteristic X-rays is different depending on the type of atom used as the anode i.e. based on atom in the periodic table, only those elements with higher atomic number will have L- and M - shell electrons that can undergo transitions to produce X-rays. Kß X-rays which contain the lower intensity is commonly be filtered out by using a filter or monochromator.
X-Rays as well as other types of electromagnetic radiation, can also be generated by other sources known as synchrotron radiation facilities. In these installation, either electrons or positrons are accelerated at relativistic velocities along closed orbit of very large radii, several meters or even hundreds of meters. These sources are very complex and expensive. Therefore, they are not generally built by single laboratories or institutions, but rather planned, built, and managed as national or international facilities.
3.0 Choice of target(ANODE) : Understand the need for Copper and Molybdenum
There are a lot of targets or sources that can be used as the anode such as Mo, Cu, Co, Fe and Cr. However, we can not simply employ all the sources in the structure analysis as the selection of the target/anode depending on the compound that we need to analyze. Currently, the most commonly used target (anode) in the X-Ray tube are made of molybdenum and copper metal. The following table summarizes the characteristics of both Mo and Cu.
Kα Wavelength (ג) Å
1.5418- Thus, Cu shows better intensity.
0.7107 – Thus, Mo has low intensity
Absorption of radiation by sample
-Used as a target source for macromolecular structural study when absolute configuration is needed.
-Useful in determination of organic molecules that do not contain atom that absorbs this radiation strongly
-Used as a target source for small molecule and single crystal structural study
-Useful in determination of a metal compound of a very small crystal with strongly absorbing material
Max angle of the reflection that will be recorded
Cu may be required to record lower order reflection
Mo may be required to record higher order reflection which are not accessible to Co radiation.
Detection efficiency to record the diffracted intensities
X-ray film, area or positron sensitive detector (PSD) based on gas ionization are optimized for copper radiation
Diffractometer counters and area detectors based on charge coupled device (CCD) or phosphor technology have a very high counting efficiency for Mo radiation.
Other types of target materials, e.g. Cr, Fe, W, or Ag, occasionally are chosen for specialized diffraction experiments. Sources with Cr or Fe targets are often chosen when anomalous differences need to be enhanced or when protein crystals are very small. On the other hand, X-ray tubes with sources such as W or Ag are usually selected when samples are very strongly absorbing or when extremely high resolution data are needed.
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