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X ray crystallography

This is all about X-ray introduction, types , instrumentation.

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X-ray Crystallography
Presented By:
Biswash Sapkota
1st M-PHARM
Dept. of
Pharmacology
8/14/2018 1X-ray Crystallography
Presented To:
Dr. Jaishree V
H.O.D
Department of Pharmaceutical
Analysis
Overview
•X-rays are electromagnetic waves with
wavelengths in the range of 0.01 to 10
nanometers and energies in the range of
100 eV to 100 keV.
•X-rays have shorter wavelengths
(higher energy ) than UV waves and,
generally, longer wavelengths (lower
energy) than gamma rays.
•Sometimes X-rays are called Röntgen
radiation, after Wilhelm Röntgen, who
is usually credited as their discoverer.
Fig: Electromagnetic Spectrum
8/14/2018 2X-ray Crystallography
Introduction
• X-ray crystallography is a technique used for determining the atomic
and molecular structure of a crystal
• The crystalline atoms cause a beam of incident X-rays to diffract into
many specific directions.
• By measuring the angles and intensities of these diffracted beams, a
crystallographer can produce a three-dimensional picture of the density
of electrons within the crystal.
• From this electron density, the mean positions of the atoms in the crystal
can be determined, as well as their chemical bonds, their disorder, and
various other information.
8/14/2018 3X-ray Crystallography
Different X-rays methods
• X-ray Absorption
• Auger Emission Spectroscopy
• X-ray Fluorescence
• X-ray Diffraction
8/14/2018 4X-ray Crystallography
X-ray Absorption
•The intensity of X-ray is diminished as they
pass through material
•Wavelength at which a sudden change in
absorption occurs is used to identify an
element present in a sample, and the
magnitude of the change determines the
amount of particular element present.
•Used in elemental analysis of barium and
iodine in body
8/14/2018 5X-ray Crystallography
Fig: X-ray Absorption
Auger Emission Spectroscopy (AES)
+
𝑒−
𝑒−
𝑒−
•The primary X-rays eject
electrons from inner energy
levels.
•Just outer level electrons fall
into vacant inner levels by non
radiative processes.
•Excess energy ejects
electrons from outer levels
8/14/2018 6X-ray Crystallography
Fig: Auger Emission Spectroscopy
Ad

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X ray crystallography

  • 1. X-ray Crystallography Presented By: Biswash Sapkota 1st M-PHARM Dept. of Pharmacology 8/14/2018 1X-ray Crystallography Presented To: Dr. Jaishree V H.O.D Department of Pharmaceutical Analysis
  • 2. Overview •X-rays are electromagnetic waves with wavelengths in the range of 0.01 to 10 nanometers and energies in the range of 100 eV to 100 keV. •X-rays have shorter wavelengths (higher energy ) than UV waves and, generally, longer wavelengths (lower energy) than gamma rays. •Sometimes X-rays are called Röntgen radiation, after Wilhelm Röntgen, who is usually credited as their discoverer. Fig: Electromagnetic Spectrum 8/14/2018 2X-ray Crystallography
  • 3. Introduction • X-ray crystallography is a technique used for determining the atomic and molecular structure of a crystal • The crystalline atoms cause a beam of incident X-rays to diffract into many specific directions. • By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. • From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their disorder, and various other information. 8/14/2018 3X-ray Crystallography
  • 4. Different X-rays methods • X-ray Absorption • Auger Emission Spectroscopy • X-ray Fluorescence • X-ray Diffraction 8/14/2018 4X-ray Crystallography
  • 5. X-ray Absorption •The intensity of X-ray is diminished as they pass through material •Wavelength at which a sudden change in absorption occurs is used to identify an element present in a sample, and the magnitude of the change determines the amount of particular element present. •Used in elemental analysis of barium and iodine in body 8/14/2018 5X-ray Crystallography Fig: X-ray Absorption
  • 6. Auger Emission Spectroscopy (AES) + 𝑒− 𝑒− 𝑒− •The primary X-rays eject electrons from inner energy levels. •Just outer level electrons fall into vacant inner levels by non radiative processes. •Excess energy ejects electrons from outer levels 8/14/2018 6X-ray Crystallography Fig: Auger Emission Spectroscopy
  • 7. X-ray Fluorescence + 𝑒− 𝑒− 𝑒− •The primary X-ray ejects electron from inner energy levels where the wavelength is equal to absorption edge. •But when the wavelength is shorter than absorption edge it emits secondary X-ray when electrons fall into inner vacant levels. 8/14/2018 7X-ray Crystallography Fig: X-ray Fluorescence
  • 8. X-ray Diffraction Methods • When a beam of monochromatic X radiation is directed at a crystalline material, one observes reflection or diffraction of the X-rays at a various angle with respect to the primary beam • The relationship between the X-radiation, angle of diffraction and distance between each set of atomic planes of crystal lattice is given by Braggs condition. nλ= 2dsinθ 8/14/2018 8X-ray Crystallography
  • 9. Methods 1. Laue Photographic Method 2. Bragg X-ray Spectrometer Method 3. Rotating Crystal Method 4. Powder Crystal Method 8/14/2018 9X-ray Crystallography
  • 10. 1. Laue Photographic Method • Laue has studied the phenomenon of diffraction of crystal by two methods oTransmission method and o Back reflection method 8/14/2018 10X-ray Crystallography
  • 11. Transmission method •A is a source of X-rays. This emits beams of continuous wavelength, known as white radiation which is obtained from a tungsten target at about 60,000 volts. •B is a pinhole collimator. When X-rays obtained from A are allowed to pass through this pinhole collimator, a fine pencil of x-rays is obtained. This diameter of pinhole is of importance from the stand point of detail in diffraction pattern. The smaller is the diameter, the sharper is the interference. 8/14/2018 11X-ray Crystallography Fig: Laue Transmission Method
  • 12. Contd.. • C is a crystal whose internal structure is to be investigated. The crystal is set on a holder to adjust its orientation • D is a fine arranged on a rigid base. This film is provided with beam stop to prevent direct beam from causing excessive fogging of the film. • The x-rays are recorded on photographic plate and study of diffraction patterns helps to know the structure of crystal . 8/14/2018 12X-ray Crystallography Fig: Laue diagram of crystal
  • 13. Back Reflection Method • In the back-reflection method, the film is placed between the x-ray source and the crystal. The beams which are diffracted in a backward direction are recorded. • This method is similar to Transmission method however, black-reflection is the only method for the study of large and thick specimens • It is very simple and rapid and does not involve the calculations in solving the patterns obtained. 8/14/2018 13X-ray Crystallography Fig: Back Reflection Method
  • 14. Contd.. • The main disadvantage of Laue’s method is that a big crystal is required and furthermore there is uncertainty in significance due to unhomogenous nature of X-rays 8/14/2018 14X-ray Crystallography
  • 15. 2. Bragg X-ray Spectrometer method When x-rays are scattered from a crystal lattice, peaks of scattered intensity are observed which correspond to the following conditions: 1.The angle of incidence = angle of scattering. 2.The path length difference is equal to an integer number of wavelengths. The condition for maximum intensity contained in Bragg's law above allow us to calculate details about the crystal structure, or if the crystal structure is known, to determine the wavelength of the x-rays incident upon the crystal. 8/14/2018 15X-ray Crystallography
  • 16. Contd.. • The Braggs equation is nλ= 2dsinθ • where n is a positive integer • λ is the wavelength of incident wave • d is the path length • Θ is the incident angle 8/14/2018 16X-ray Crystallography
  • 17. 3. Rotating Crystal Method •The rotating crystal method was developed by Schielbold in 1919 •The X-ray beam passed to the crystal through collimating system •The rotating shaft hold the crystal and it also rotates • This causes the sets of planes coming successively into their reflecting positions. • Each plane will produce a spot on photographic plate. 8/14/2018 17X-ray Crystallography Fig: Rotating Crystal Method
  • 18. Contd.. • One can take photographs in two ways; Complete rotation method: In this method there occurs a series of complete revolutions. It is observed that each set of planes in crystal diffracts four times during the rotation. These four diffracted beams are distributed into a rectangular pattern about the central point of photograph. Oscillation method: In this method, the crystal is oscillated through an angle of 15O or 200. The photographic plate is also moved back and forth with a same period as that of rotation of the crystal. The position of spot on the plate indicates the orientation of crystal at which the spot was formed. 8/14/2018 18X-ray Crystallography
  • 19. 4. Powder Crystal Method 8/14/2018 19X-ray Crystallography Fig: Powder Crystal Method •X-ray powder diffraction (XRD) is a rapid analytical technique primarily used for phase identification of a crystalline material and can provide information on unit cell dimensions. •The analyzed material is finely ground and homogenized •A is a source of X-rays which can be made monochromatic by a filter. •Allow the X-ray beam to fall on the powdered specimen P through the slits S1 and S2.
  • 20. Contd.. • Fine powder, p, struck on a hair by means of gum is suspended vertically in the axis of a cylindrical camera. This enables sharp lines to be obtained on the photographic film which is surrounding the powder crystal in the form of a circular arc. 8/14/2018 20X-ray Crystallography
  • 21. Contd.. • Theory: When a monochromatic beam of X-rays is allowed to fall on the powder of a crystal, then following possibilities may happen:  There will be some particles out of the random orientation of small crystal in the fine powder, which lie within a given set of lattice planes for reflection to occur. While another fraction of the grains will have another set of planes in the correct position for the reflections to occur and so on. Also, reflections are also possible in the different order for each set. 8/14/2018 X-ray Crystallography 21
  • 22. Application of X-ray Diffraction • Characterization of crystalline materials • Identification of fine-grained minerals such as clays and mixed layer clays that are difficult to determine optically • Determination of unit cell dimensions measurement of sample purity • Determination of Cis- trans isomerism 8/14/2018 22X-ray Crystallography
  • 23. Instrumentation • This includes, 1. Production of X-rays 2. Collimator 3. Monochromator 4. Detectors 8/14/2018 23X-ray Crystallography
  • 24. 1. Production of X-ray • X-rays are produced inside the x-ray tube when high energy projectile electrons from the filament interact with the atoms of the anode . • Conditions necessary: Source of electrons Target (anode) High potential difference Cooling facility 8/14/2018 24X-ray Crystallography
  • 25. Production of X-rays 8/14/2018 25X-ray Crystallography Fig : Coolidge X-ray Tube
  • 26. Contd.. • There is a cathode which is a filament of tungsten metal heated by a battery to emit the thermionic electrons. • This beam of electrons moves towards anode and attain the kinetic energy and 99% of energy is converted into heat via collision and remaining 0.5-1% is converted to X-rays via strong coulomb interactions ( Bremsstrahlung process) • Generally the target gets very hot in use. This problem has been solved to some extent by cooling the tube with water. 8/14/2018 26X-ray Crystallography
  • 27. What Happens Actually? • If sufficiently energetic electrons are available, the transfer of energy from the impinging electron beam may eject an electron from one of the inner levels of the target atoms • Within each atom, the place of the ejected electron is promptly filled by an electron from an outer level whose place, in turn is taken by an electron coming from still farther out • Thus the ionized atom returns to its normal state in as series of steps, in each of which an X-ray photon of definite energy is emitted or excess energy is released by ejection of a second electron with characteristic energy 8/14/2018 X-ray Crystallography 27
  • 28. Contd .. •The k series of line is observed when an electron in the innermost K level (n=1) is dislodged and electrons drop down from the L (n=2) or M (n=3) levels into the vacancy in k level. •Corresponding vacancies in the L levels are filled by electron transitions from outer levels and give rise to L series 8/14/2018 28X-ray Crystallography Fig: K series
  • 29. Contd.. Disadvantage of most of X-ray tubes is that there is lack of focusing of electrons so that whole surface becomes a source of X-rays. 8/14/2018 29X-ray Crystallography
  • 30. 2. Collimator 8/14/2018 30X-ray Crystallography Fig: Collimator
  • 31. Contd.. • The X-rays produced by the target material are randomly directed. • They form a hemisphere with a target at the centre. In order to get a narrow beam of X-rays, the X-rays generated by the target material are allowed to pass through a collimator which consists of two sets of closely packed metal plates separated by a small gap. • The collimator absorbs all the X-rays except the narrow beam that passes between the gaps. 8/14/2018 31X-ray Crystallography
  • 32. 3. Monochromator A. Filter monochromator: • A filter is a window of material that absorbs undesirable radiation but allows the radiation of required wavelength to pass. • An interesting example is use of zirconium filter which is used for molybdenum radiation. • When X-rays emitted from molybdenum are allowed to pass through a Zirconium filter, the Zirconium strongly absorbs the radiation of molybdenum at short wavelengths but weakly absorbs the K alpha lines of molybdenum. Thus, zirconium allows the K beta lines to pass. 8/14/2018 32X-ray Crystallography
  • 33. Contd.. B. Crystal monochromator: • A crystal monochromator is made up of a suitable crystalline material positioned in the X-ray beam so that the angle of reflecting planes satisfied Bragg’s equation for the required wavelength. • The beam is split up by the crystalline material into the component wavelengths in the same way as a prism splits up the white light into rainbow. Such a crystalline substance is called an analysing crystal. • They are two types; 8/14/2018 33X-ray Crystallography
  • 34. Contd .. 8/14/2018 34X-ray Crystallography
  • 35. 4. Detectors A. Photographic methods: • In order to record the position and intensity of X-ray beam a plane or cylindrical film is used. • The film after exposing to X-rays is developed. The blackening of the developed film is expressed in terms of density units D given by • Where, I0 and I refer to the incident and transmittance intensities of X-rays. • The quantity D is related to the total X-ray energy that causes the blackening of photographic film. • The value of D is measured by densitometer. • This is used in diffraction studies since it reveals the entire diffraction pattern on single film but this method is time consuming and uses several hours 8/14/2018 35X-ray Crystallography
  • 36. Contd.. B. Counter methods: • The Geiger tube is filled with an inert gas like argon and the central wire anode is maintained at a positive potential of 800 to 2500V. • When an X-ray is entering the Geiger tube, this ray undergoes collision with the filling gas, resulting in the production of an ion pair: the electron produced moves towards the central anode while the positive ions move towards outer electrode. • The electron is accelerated by the potential gradient and causes the ionisation of large number of argon atoms, resulting production of an avalanche of electrons that are travelling towards the central anode., 8/14/2018 36X-ray Crystallography
  • 38. Contd .. • The Geiger tube is in expensive and is relatively trouble free detector. This tube gives the highest signal for given X-ray intensity. • The disadvantages are The efficiency of Geiger tube falls rapidly at wavelength below 1 A0 As the magnitude of the output pulse does not depend upon the energy of the X-ray which causes ionisation, a Geiger tube cannot be used to measure the energy of ionising radiation. 8/14/2018 38X-ray Crystallography
  • 39. References • Instrumental method of analysis- Willards, 7th edition, CBS Publishers • Instrumental method of chemical analysis- Chatwal , Himalayan Publishing House 8/14/2018 X-ray Crystallography 39