bruce c. noll, phd. senior applications scientist bruker ... · crystallography texts on...
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Basic Crystallography
26 May 2019 1
Bruce C. Noll, PhD.Senior Applications ScientistBruker Nano, Inc.
10th Canadian Chemical Crystallography Workshop
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Introduction
• Crystals and Crystallography
• Crystal Lattices and Unit Cells
• Diffraction
• Bragg's Law and Reciprocal Space
• X-ray Diffraction Patterns from Crystals
Top: JJ Harrison (https://www.jjharrison.com.au/)Bottom: http://www.sunnyray.org/Quartz.htm
26 May 2019 210th Canadian Chemical Crystallography
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What is a Crystal?
3
• Crystal: a body that is formed by the solidification of a chemical element, a compound, or a mixture and has a regularly repeating internal arrangement of its atoms and often external plane faces
• Glass: any of various amorphous materials
formed from a melt by cooling to rigidity without crystallization
26 May 201910th Canadian Chemical Crystallography
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From Merriam Webster:
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Examples of Crystals
26 May 2019 410th Canadian Chemical Crystallography
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Foundations of Crystallography
• Crystallography is the study of crystals.
• Scientists who specialize in the study of crystals are called crystallographers.
• Early studies of crystals were carried out by mineralogists who studied the symmetries and shapes (morphology) of naturally-occurring mineral specimens.
• This led to the correct idea that crystals are regular three-dimensional arrays (Bravais lattices) of atoms and molecules; a single unit cell is repeated indefinitely along three principal directions that are not necessarily perpendicular.
26 May 2019 510th Canadian Chemical Crystallography
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Making a Crystal:the asymmetric unit
26 May 2019 610th Canadian Chemical Crystallography
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D.J. MacDougall et al, doi:10.1039/b413434f
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Making a Crystal:the unit cell
26 May 2019 710th Canadian Chemical Crystallography
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Making a Crystal:the extended structure
26 May 2019 810th Canadian Chemical Crystallography
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a
b
c
Unit Cell Description in terms of Lattice Parameters
• a ,b, and c define the edge lengths and are referred to as the crystallographic axes.
• , , and give the angles between these axes.
• Lattice parameters dimensions of the unit cell.
26 May 2019 910th Canadian Chemical Crystallography
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Ralph Krätzner
26 May 2019 1010th Canadian Chemical Crystallography
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The Unit Cell Concept
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Choice of the Unit Cell
26 May 2019 1110th Canadian Chemical Crystallography
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Choice of the Unit Cell
26 May 2019 1210th Canadian Chemical Crystallography
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Choice of the Unit Cell
26 May 2019 1310th Canadian Chemical Crystallography
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Choice of the Unit Cell
26 May 2019 1410th Canadian Chemical Crystallography
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Choice of the Unit Cell
No symmetry - many possible unit cells. A primitive cell with angles close to 90º (C or D) is preferable.
C D
A
B
C
A
The conventional C-centered cell (C) has 90º angles, but one of the primitive cells (B) has two equal sides.
B
26 May 2019 1510th Canadian Chemical Crystallography
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X-ray Diffraction
26 May 2019 1610th Canadian Chemical Crystallography
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Diffraction of X-rays by Crystals
• The science of X-ray crystallography originated in 1912 with the theory by Max von Laue that crystals diffract X-rays.
• Walter Friedrich and Paul Knipping performed experiments to prove Laue’s theory
Max Theodor Felix von Laue
(1879 – 1960)
26 May 2019 1710th Canadian Chemical Crystallography
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Diffraction of X-rays by Crystals
After Von Laue's pioneering research, the field developed rapidly, most notably by physicists William Lawrence Bragg and his father William Henry Bragg.
In 1912-1913, the younger Bragg developed Bragg's law, which connects the observed scattering with reflections from evenly-spaced planes within the crystal.
William Lawrence Bragg
William Henry Bragg
26 May 2019 1810th Canadian Chemical Crystallography
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Bragg’s Law
• X-rays scattering coherently from 2 of the parallel planes separated by a distance d.
• Incident angle and reflected
(diffracted angle) are given by q.
26 May 2019 1910th Canadian Chemical Crystallography
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Bragg’s Law
• The condition for constructive interference is that the path difference leads to an integer number of wavelengths.
• Bragg condition concerted
constructive interference from periodically-arranged scatterers.
• This occurs ONLY for a very specific geometric condition.
q
sin2
d q sin2dn
26 May 2019 2010th Canadian Chemical Crystallography
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Bragg’s Law
We can think of diffraction as reflection at sets of planes running through the crystal. Only at certain angles 2θ are the waves diffracted from different planes a whole number of wavelengths apart (i.e., in phase). At other angles, the waves reflected from different planes are out of phase and cancel one another out.
n = 2d sin(q)
d
26 May 2019 2110th Canadian Chemical Crystallography
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Diffraction Geometry in 2D
26 May 2019 22
Source
X-ra
y d
ete
cto
r
Ewald
sphere
Reciprocal
lattice
λ = 2d sin(θ)
10th Canadian Chemical Crystallography Workshop
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Detection area in 3D, square detector
26 May 2019 23
• The detection area of a detector is the projection of the (square) detector onto the surface of the EWALD sphere
10th Canadian Chemical Crystallography Workshop
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26 May 2019 24
Detection area in 3D, square detector
• The size of the detection area depends on the detector’s size and its distance from the sample
• The position of detection area depends on the 2θ swing angle of the detector
10th Canadian Chemical Crystallography Workshop
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4-circle diffractometer
26 May 2019 2510th Canadian Chemical Crystallography
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Omega scans
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• omega scans are geometrically very flexible
• A combination of omega scans can cover reciprocal space very effectively
10th Canadian Chemical Crystallography Workshop
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Omega scans
26 May 2019 27
• omega scans are geometrically very flexible
• A combination of omega scans can cover reciprocal space very effectively
10th Canadian Chemical Crystallography Workshop
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Phi Scan
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• Phi scans are always oriented along the phi spindle axis
• They are most efficient if they are perpen-dicular to the beam
10th Canadian Chemical Crystallography Workshop
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Phi Scan
26 May 2019 29
• Phi scans are always oriented along the phi spindle axis
• They are most efficient if they are perpen-dicular to the beam
10th Canadian Chemical Crystallography Workshop
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Recommended reading
26 May 2019 3010th Canadian Chemical Crystallography
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• Crystal Structure Analysis: A Primer (International Union of Crystallography Texts on Crystallography Book 14) 3rd Edition, Kindle Edition
• by Jenny Pickworth Glusker, Kenneth N. Trueblood
• Crystal Structure Determination 2nd ed. 2004, Corr. 5th printing 2010 Edition
• by Werner Massa (Author), Robert O. Gould (Translator)
• Fundamentals of Crystallography (International Union of Crystallography Texts on Crystallography)
• by Carmelo Giacovazzo, Hugo Luis Monaco, et al. | Jun 4, 2011
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