1 - Introduction XRD

Course Goals
To develop an understanding of basic crystallographic concepts

- Helpful if you ever need to determine a crystal structure yourself
To be able to interpret the crystallographic data in publications

- What do the data mean?
- Does the interpretation make sense?
To gain an appreciation of the steps involved in a crystal structure

determination
- Enables you to interact with the “black box” if default settings don’t lead
to a solution
Crystallography - what and why?
What?
- Determination of the atomic structure of crystalline solids
- Location and type of atoms, bond distances/local environment
- Absolute structure
Why?
- Materials’ properties are intimately related to their structures
Understanding certain properties requires knowledge of atomic
arrangement, e.g. piezoelectrics
- Structural studies of enzyme active sites can allow the rational selection
of inhibitors
- Impact of crystallography can be seen in the large number of Nobel
Prizes for work related to crystallography or diffraction
Historical development
X-rays were discovered by Wilhelm Conrad Röntgen in 1895
- “Interested in the effects of ultra-violet radiation, he covered a cathode-
ray discharge tube with black paper and darkened the room. With the
glow from the tube hidden, Röntgen was surprised to see a fluorescent
screen two metres away light up. For several weeks, Röntgen hid in his
laboratory, finding out more about the mysterious penetrating 'X' rays,
produced when the cathode rays hit the end of the discharge tube.”
(IUCr history page)
In 1914, Max von Laue discovered that X-rays are diffracted by
crystals
- Copper sulfate, recorded on film
In 1915, Sir William Henry and William Lawrence Bragg
formulated their famous Bragg law
- Birth of “crystallography”
Some Nobel Prizes for Crystallography or Diffraction
190 1 - W ilhelm C on rad Ro entg en fo r his dis co ve ry of X-rays
191 4 - M ax von La ue fo r his dis co ve ry of the diffrac tion o f X-ray s by crystals

191 5 - S ir W illiam H. Brag g,
fo r their servic es in the a nalys is of crys tal structure by m ea ns of X-rays
W illiam L. B ragg
192 7 - A . H. Com pt on fo r his dis co ve ry of sc atterin g o f X-rays by electro ns
192 9 - Lo uis-Victor d e B rogli e fo r his dis co ve ry of the wa ve n ature o f the elec tron
fo r his contributi ons to our k n owl ed ge o f m olec ular structu re throug h his in ves tigatio ns
193 6 - P eter J. De by e
on dip ole mom ents an d on the diffraction o f X-rays and el ectrons in g ases
193 7 - Cli nton J. D a visson,
fo r their ex p erim ental disc o ve ry of the diffr action o f electrons by cry stals
Geo rge P . Tho m son
194 6 - J am es B . Sumne r fo r his dis co ve ry that enz ym es can be crystallized
fo r his resea rch into the natu re o f the chem ical b on d an d its application to the el ucidatio n
195 4 - Lin us C. P aulin g
of the struc tu re o f com pl ex s ubs tances
196 2 - M ax F. P erutz,
fo r their studi es of the struc tures of glob ula r pr oteins
Jo hn C. K en drew
196 2 - Francis H.C. Crick, fo r their dis co ve ries c onc ernin g the m olec ular structu re o f nucleic ac id a nd its signific a nc e
Jam es D. W atson, M aurice H.F. W ilk ins fo r inform ation tr ans fer in li ving m ateri al (d oubl e helix)
fo r he r dete rm in ations by X-ray techni qu es of the s tructu res o f im po rtant bioc h em ical
196 4 - D orot hy C. Hod gkin
subs tances
fo r his studies on the struc tur e o f bo ran es illum inatin g probl em s of c he m ical bo ndin g
197 6 - W illiam N. Lipscom b
by X-ray diffrac tion
fo r his de velo pm e nt of cry stallog ra phic electro n m ic roscopy a nd his s tructural el ucidatio n
198 2 - S ir Aaron K lu g
of bi ologic ally im p orta nt nucleic acid-protein com pl ex es
198 2 - K en neth G. W ils on fo r his theory o f c ritic al phe nom en a in c onn ection with p hase transitions
198 5 - H erb ert A . Hau ptm a n, fo r their o utstandin g achi e vem e nts in the de velo pm e nt of di rec t metho ds fo r the
Je rom e K arle determ inatio n o f crystal struc tures
1988 - Johann Deisenhofer,
for the determination of the 3-dim ensional structure of a photosynthetic reaction center
Robert Huber, Harm ut Michel
for his application of methods for discovering order in simple systems to polymers and
1991 - Pierre-Gilles de Gennes
liquid crystals
1992 - Georges Charpak for his discovery of the m ulti wire proportional chamber
1994 - Clifford G. Shull,

for their pioneering research in neutron scattering
Bertram N. Brockhouse
1996 - Robert F. Curl,
for their discovery of the fullerene form of carbon
Sir Harold W. Kroto, Richard E. Smalley
1997- P. D. Boyer, J. E. Walker, for their elucidation of the enzymatic mechanism underlying the synthesis of adenosine
J. C. Skou triphosphate (A TP) and their discovery of an ion-transporting enzyme
What is possible today?
Determination of small molecule structure is routine nowadays
- This was not true 50 years ago!
- Takes 6-12 h of data collection in most cases
Crystal structures of macromolecules can be solved from single
crystal data
Synchrotron radiation can in some cases yield single crystal
structures from crystals that are smaller than 10 µm
Powder methods are becoming more advanced and can in some
cases enable full structure determinations, too
How do we determine a structure?
Oldest methods relied on simple physical observations only
- Example: Crystal habit
- Could determine symmetry of crystal, but usually not atomic scale
structure
NMR has become one of the most powerful structural tools for
organic molecules
- Can also be used for amorphous materials
- Often less straightforward for solids and/or non-standard nuclei
Crystallographic methods
- Gives detailed time-averaged picture in 3D
- Works only for crystalline materials
Electron microscopy
Electron microscopy is a powerful tool for the visualization of

particles and/or lattices (high resolution)
Electrons can be focused using magnetic lenses
Gives structural information on a short length scale
- Provides a 2D image
- Samples are often damaged by the intense electron beams
- Only very thin samples can be measured
- Images can be difficult to interpret
Picking the appropriate probe
Light scattering can give “structural”
information on the length scale of light
waves
- Light microscopy
- Measurement of particle size distributions by
light scattering
Analysis of atomic length scale ordering
requires a probe with the appropriate
wavelength
- Typical bond distances are 1-3 Å
- X-rays have Angstrom wavelengths
How do we focus X-rays without
appropriate lenses?
How a microscope works
Light is focused
using lenses
Ways of focusing X-rays
There are no refractive lenses for X-rays, as the refractive index

in all materials is close to 1
- Between 0.99 and 0.999
X-rays can be focused using diffraction based optics

- e.g., a “peak” of X-rays is used as the source
At small incident angles, X-rays can be focused by using X-ray

mirrors
- grazing incidence
- usually <0.5° for Pt at 10 keV
X-ray cathodes
Typical setup for a diffraction experiment
Specimen C on support table H, can be rotated around axis O;

X-ray source S with line focal spot on the target T; A, B and F
are defining/focusing slit systems; counter G supported by
carriage E, which can also be rotated around O, angular
position can be read on scale K. E and H are mechanically
coupled so that E rotates twice as far.

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Course Goals

To develop an understanding of basic crystallographic concepts

To be able to interpret the crystallographic data in publications

To gain an appreciation of the steps involved in a crystal structure

191 4 - M ax von La ue fo r his dis co ve ry of the diffrac tion o f X-ray s by crystals

192 7 - A . H. Com pt on fo r his dis co ve ry of sc atterin g o f X-rays by electro ns

194 6 - J am es B . Sumne r fo r his dis co ve ry that enz ym es can be crystallized

1994 - Clifford G. Shull,

Electron microscopy is a powerful tool for the visualization of

There are no refractive lenses for X-rays, as the refractive index

X-rays can be focused using diffraction based optics

At small incident angles, X-rays can be focused by using X-ray

Specimen C on support table H, can be rotated around axis O;

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