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X-Ray Diffraction

X-Ray Diffraction. (X-Ray Crystallography). I. X-Ray Diffraction. Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline solid Quantitative and qualitative . Ooi , L. Principles of X-ray Crystallography (2010). A. X-Rays. 0.1 – 100 Angstroms ( Å)

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X-Ray Diffraction

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  1. X-Ray Diffraction (X-Ray Crystallography)

  2. I. X-Ray Diffraction • Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline solid • Quantitative and qualitative Ooi, L. Principles of X-ray Crystallography (2010)

  3. A. X-Rays • 0.1 – 100 Angstroms (Å) • Useful Range: 0.5 – 2.5 Å

  4. B. Amorphous Substances 1. Gases and Liquids • Extremely difficult 2. Non-crystalline Solids • Atoms are not regularly arranged or regularly shaped • Interference • Fiber Diffraction

  5. C. Crystalline Solids • Atoms are regularly arranged • “The Unit Cell” – a cookie cutter Rhodes, G. Crystallography Made Crystal Clear, 3rd ed. (2006)

  6. II. X-Ray Crystallography A. Small-molecule crystallography • Up to ~100 atoms • Organic molecules, catalysts, newly synthesized drugs, etc. • Identify each atom B. Macromolecular (protein) crystallography • Large biological molecules– nucleic acids and proteins • Identify 2° structure Note: must show that the crystal structure (asymmetric unit) is comparable to structure in solution (biological unit)

  7. III. X-Ray Diffractometer Ooi, L. Principles of X-ray Crystallography (2010)

  8. A. X-Ray Source 1. X-Ray Tube (a) 2. Rotating Anode (b) Rhodes, G. Crystallography Made Crystal Clear, 3rd ed. (2006)

  9. 3. Particle Storage Ring (Synchrotron Radiation) • Particle Accelerator Ooi, L. Principles of X-ray Crystallography (2010)

  10. National Synchrotron Light Source at Brookhaven National Lab (Long Island) Rhodes, G. Crystallography Made Crystal Clear, 3rd ed. (2006)

  11. B. Collimator • Narrow metal tube that selects and reflects the X-Rays into parallel paths Ooi, L. Principles of X-ray Crystallography (2010)

  12. C. Crystal (Sample) 1. Growth – Screens • Crystal vs. useless blob 2. Optimization • Quantity 3. Crystal Quality • Purity 4. Mount for Data Collection • Cryocrystallography Note: Diffracted in “mother liquor” Rhodes, G. Crystallography Made Crystal Clear, 3rd ed. (2006)

  13. D. Camera • Goniometer • Goniostat Rhodes, G. Crystallography Made Crystal Clear, 3rd ed. (2006)

  14. Rhodes, G. Crystallography Made Crystal Clear, 3rd ed. (2006)

  15. E. Detector 1. Charged Couple Device (CCD) 2. Image Plate (IP) Rhodes, G. Crystallography Made Crystal Clear, 3rd ed. (2006)

  16. IV. Data Analysis • Measure intensity and position of diffracted X-Rays • Intensity: strength of diffracted beam • Position: direction in which beam was diffracted by the crystal Rhodes, G. Crystallography Made Crystal Clear, 3rd ed. (2006)

  17. Computer calculates this data from the diffraction pattern Ooi, L. Principles of X-ray Crystallography (2010)

  18. A. Fournier Sum • Based on simple waves • f(x) = Fcos2π(hx+α) • F = f0 + f1 + f2 + … Rhodes, G. Crystallography Made Crystal Clear, 3rd ed. (2006)

  19. B. Bragg’s Law • States: diffraction spots occur when 2dsinθ = nλ Rhodes, G. Crystallography Made Crystal Clear, 3rd ed. (2006)

  20. Benefits Downfalls • Molecular structure in solid crystalline state with extreme certainty • Direct inference of data • Provides limitless info. • Crystals • Slow • Hydrogen • Still just a model

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