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(X-Ray Crystallography) X-RAY DIFFRACTION

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Page 1: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

(X-Ray Crystallography)

X-RAY DIFFRACTION

Page 2: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

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)

Page 3: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

A. X-Rays 0.1 – 100 Angstroms (Å)

Useful Range: 0.5 – 2.5 Å

Page 4: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

B. Amorphous Substances1. Gases and Liquids

Extremely difficult

2. Non-crystalline Solids

Atoms are not regularly arranged or regularly shaped

Interference

Fiber Diffraction

Page 5: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

Atoms are regularly arranged

“The Unit Cell” – a cookie cutter

C. Crystalline Solids

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

Page 6: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

II. X-Ray CrystallographyA. 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)

Page 7: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

III. X-Ray Diffractometer

Ooi, L. Principles of X-ray Crystallography (2010)

Page 8: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

A. X-Ray Source

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

1. X-Ray Tube (a)

2. Rotating Anode (b)

Page 9: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

3. Particle Storage Ring (Synchrotron Radiation)

Particle Accelerator

Ooi, L. Principles of X-ray Crystallography (2010)

Page 10: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

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

National Synchrotron Light Source at Brookhaven National Lab (Long Island)

Page 11: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

B. Collimator Narrow metal tube that selects and reflects the X-Rays into parallel paths

Ooi, L. Principles of X-ray Crystallography (2010)

Page 12: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

C. Crystal (Sample)

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

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”

Page 13: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

D. Camera

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

Goniometer

Goniostat

Page 14: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

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

Page 15: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

E. Detector

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

1. Charged Couple Device (CCD)

2. Image Plate (IP)

Page 16: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

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)

Page 17: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

Ooi, L. Principles of X-ray Crystallography (2010)

Computer calculates this data from the diffraction pattern

Page 18: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

A. Fournier Sum Based on simple waves

f(x) = F cos 2π (hx + α)

F = f0 + f1 + f2 + …

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

Page 19: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

B. Bragg’s Law States: diffraction spots occur when 2 d sin θ = n λ

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

Page 20: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline
Page 21: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline
Page 22: (X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline

Molecular structure in solid crystalline state with extreme certainty

Direct inference of data

Provides limitless info.

Crystals

Slow

Hydrogen

Still just a model

Benefits Downfalls


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