(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

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)

Useful Range: 0.5 – 2.5 Å

B. Amorphous Substances1. Gases and Liquids

Extremely difficult

2. Non-crystalline Solids

Atoms are not regularly arranged or regularly shaped

Interference

Fiber Diffraction

Atoms are regularly arranged

“The Unit Cell” – a cookie cutter

C. Crystalline Solids

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

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)

III. X-Ray Diffractometer

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

A. X-Ray Source

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

1. X-Ray Tube (a)

2. Rotating Anode (b)

3. Particle Storage Ring (Synchrotron Radiation)

Particle Accelerator

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

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

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

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

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

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”

D. Camera

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

Goniometer

Goniostat

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

E. Detector

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

1. Charged Couple Device (CCD)

2. Image Plate (IP)

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)

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

Computer calculates this data from the diffraction pattern

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)

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

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

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