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Transmission Electron Microscopy

Part III: Diffraction

Christoph T. Koch
Max Planck Institut fr Metallforschung Heisenbergstr. 3, 70569 Stuttgart Raum 5N8, Tel: 0711/689-3647 Email: koch@mf.mpg.de
Max-Planck Institut fr Metallforschung Universitt Stuttgart

Background literature
Book: (excellent introduction to reciprocal space and crystallography) Marc de Graef, Introduction to Conventional Transmission Electron Microscopy Cambridge University Press, Cambridge (2003)

Websites: Website for the book by M. de Graef: http://ctem.web.cmu.edu/ More online diffraction simulations: http://emaps.mrl.uiuc.edu/emaps.asp

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Important physical constants and relations


Rest mass: Charge: Rest energy: Kinetic energy: Total energy: Momentum: Velocity: Wavelength: m0= 9.109110-31kg q = -e = -1.60210-19C E0= m0c2 = 511keV Ekin = eV0 (V0 = accelerating voltage) E = mc2 = p2/(2m) = E0 + Ekin p = h/ v = p/m = h/(m) = h/(m0) = c [1-1/(1+E/E0)2] = (hc/e) / [V0*(2*E0+V0)]

Planck constant: Speed of light: Rel. corr. factor: Relativistic velocity:


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h = 6.525610-34Nms c = 2.9979108m/s hc/e=12.3984244103/eV = m/m0 = 1/ [1-v2/c2] = v/c


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Wavelength and electron speed


Wavelength Relativistic velocity

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FT of crystal potential: 1 unit cell

Top right: plot of a single top hat aperture function f(x) Bottom right: modulus of FFT of f(x)
http://hrem.mpi-stuttgart.mpg.de/koch/Vorlesung/MatlabScripts/test_XtalFFT.m Max-Planck Institut fr Metallforschung Universitt Stuttgart

FT of crystal potential: 2 unit cells

Top right: plot of the potential f(x) of small 1D crystal Bottom left: modulus of FFT of f(x)
http://hrem.mpi-stuttgart.mpg.de/koch/Vorlesung/MatlabScripts/test_XtalFFT.m Max-Planck Institut fr Metallforschung Universitt Stuttgart

FT of crystal potential: many unit cells

Top right: plot of the potential f(x) of small 1D crystal Bottom left: modulus of FFT of f(x)
http://hrem.mpi-stuttgart.mpg.de/koch/Vorlesung/MatlabScripts/test_XtalFFT.m Max-Planck Institut fr Metallforschung Universitt Stuttgart

Convolution

f ( x) g ( x) =

f ( x' ) g ( x x' )dx'

Convolution theorem
FT [ f ( x) g ( x)] = FT [ f ( x)] FT [g ( x)] = F (k ) G (k )
The convolution of two functions may be computed by the inverse Fourier transform of the product of their Fourier transforms.
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Convolution = Multiplication in reciprocal space


Real space:

x
Unit cell potential Reciprocal space: x finite sized lattice

=
= crystal potential

x
Structure factor x crystal shape transform

=
= FT of crystal potential

(Note that the rec. space plots show |F(k)|, which is almost what is seen in diffr. patterns) Max-Planck Institut fr Metallforschung Universitt Stuttgart

Fourier Transform of a 1-dimensional box


Top hat aperture

0, if x < a f ( x) = 1, if a x b 0, if x > b
F (k ) = = 1 2 1 2

FT[f(x)]:

f ( x)e 2ikx
2ikx

e
a

1 e 2ikb e 2ika 2ik 2

k=

1 ba

If a=-b:

F (k ) =

2 sin(2ka) 2k

k=
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3/ 2 ba
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Example: Diffraction from an interface


HRTEM

Electron beam Diffraction spots from grains

Shape transform of interface layer Amorphous interface layer, about 1nm thick

Diffraction pattern

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Changing the projected interface width

(animated tilt series of diffraction patterns, experiment: S. Bhattacharyya)


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Finite lattice and shape transform

x
Infinite lattice x

w shape of crystal

=
= finite sized lattice

x
Reciprocal space lattice x shape transform

=
= continuously sampled reciprocal space
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FT of a 1-dimensional finite sized lattice


1/a

k in nm-1 This plot shows the modulus of the Fourier transform of different size arrays of delta functions. For large enough crystals the shape transform vanishes between reciprocal lattice points.
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Reciprocal space lattice


1D: a periodic structure with a repeat distance a produces a 1D reciprocal lattice with discrete reciprocal lattice points 1/a apart. 2D: a 2-dimensional periodic structure has 2 lattice vectors (a and b) associated with it. These define the unit cell. The reciprocal lattice is spanned by the reciprocal lattice vectors a* and b* Real space: Reciprocal space:

b*

r a a = 1 a 2

r b b = 1 b 2

r 1 a b* = 2 A a1 b2 r 1 a* = A b1

a*
Unit cell area:

* =

r r A = a b sin( )
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3-dimensional reciprocal lattice


r r r b c a* = r r r c a b* = r r r a b c* = r r r Unit cell volume: = a (b c ) r r r r g hkl = ha * + kb * +lc *
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c b a

The FT of the potential of an infinite crystal may only be non-zero, if h,k, and l are integers.
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3-dimensional crystal structure

c b a

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A little more complex: Proteine crystals

Isopotential surface of Lyzozyme at 2 resolution

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Bravais Lattices
7 crystal systems: {a,b,c,,,} abc; : triclinic or anorthic (a)

{a,b,c,/2,,/2} abc; /2: monoclinic (m) {a,a,c,/2,/2,2/3} a=bc; {a,a,a,,,} a=b=c; /2: {a,b,c,/2,/2,/2} abc: {a,a,c,/2,/2,/2} a=bc: {a,a,a,/2,/2,/2} a=b=c: hexagonal(h) rhombohedral (R) orthorhombic (o) tetragonal (t) cubic (c)

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Miller indices of a plane

1. If the plane intersects the origin, shift it, so that it does not. 2. Determine the points at which the plane intersects each of the unit cell vectors. 3. The Miller indices are the inverse of these values, reduced to the smallest possible integers. 4. Notation: (hkl) Determination of Miller indices (1,2,3) of a plane in real space.

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^ Reciprocal space point = Set of real space planes

A plane may be characterized by a single 3D reciprocal space vector, the 3 Miller indices. Since this vector starts at the origin (k=0,0,0), it defines a single point in reciprocal space. The length of the Miller-vector defines the distance between a parallel set of planes in the lattice.

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Higher order Miller indices


The lattice plane described by Miller indices do NOT all need to be inhabited by atoms! Contribution of higher index planes just increase the resolution.

Visualization of the effect of including higher order Fourier coefficients


http://hrem.mpi-stuttgart.mpg.de/koch/Vorlesung/MatlabScripts/test_FFTbandwidth.m Max-Planck Institut fr Metallforschung Universitt Stuttgart

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Bragg and Laue condition


Bragg reflection Electrons exit the specimen on the same surface at which they entered it. Laue diffraction Electrons transmit the specimen.

Constructive interference

Destructive interference

Constructive interference

Destructive interference specimen surface

n = 2d sin( )
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n = d sin( )
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Structure factor
Superposition of the scattering at each individual atom i Consists of the phase shifts caused by the different positions ri=(xi, yi, zi) of the atom the scattering factor fi() of the atoms

F ( g ) = f j (| g |)e
j

rr 2ig r j

F(q) is called the structure factor and is important to calculate the scattering amplitude at different angles (diffraction pattern) Destructive interference can lead to zero intensity in the diffraction pattern

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Real space lattice of a thin TEM specimen

c b a

Unit cell potential defined on an infinite lattice

Envelope with specimen dimensions

=
Potential of crystalline specimen

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Shape transform: FT of specimen shape


Real space Reciprocal space

sample thickness t Fourier Transform

k=

1 t

Relrods are 1-dimensional objects for specimen that are infinitely large in x- and y-diections. Reciprocal Lattice Rod (relrod)
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Reciprocal space lattice of a thin TEM specimen

Reciprocal lattice rods (relrods) Reciprocal lattice is convoluted with the specimen shape transform. Thin specimen produce extended crystal truncation rods in the direction normal to the specimen surface
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Conservation of momentum: Ewald construction


kz Electron with momentum p=hk (|k|=1/) Ewald sphere: defines all possible elastic scattering vectors which preserve the momentum of the electron k

k=k+q q

kx Reciprocal lattice
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Inelastic scattering: momentum is lost


Ewald sphere for elastic scattering Ewald sphere for inelastic scattering events

|k|-|kinel|h-1(2mE)1/2
Energy lost in inelastic scattering event

k q kinel

Reciprocal lattice
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Kinematic Diffraction
A kinematic diffraction pattern is the modulus squared of the crystal potential in reciprocal-space at its intersection with the Ewald sphere. If the reciprocal space plane normal to the momentum vector of the incident electron is called zone axis. First order Laue zone (FOLZ)

-k

Zero order Laue zone (ZOLZ)

K=(0,0,0)

kx

-kz

FT of potential of a thin specimen

Diffraction spots may appear, even if the Laue condition is only roughly satisfied. For infinitely thick crystals no ZOLZ reflection appears under exact zone axis conditions.
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Tilted illumination = tilted specimen


If the momentum vector of the incident electron is slightly inclined with respect to a reciprocal-space plane densely populated with lattice points, this condition is called tilted off zone axis.

kz

K=(0,0,0)

kx

Relative tilting between Ewald sphere and reciprocal lattice may position certain reciprocal lattice points on the Ewald sphere (in diffracting condition).
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FT of pote thin specim

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Example: Graphite

Modulus of the scattering potential U(gx,0,kz) for a 2-dimensional Graphite crystal (a=2.46A, c=6.7A) which has a thickness of one unit cell, i.e. two graphene sheets. (Note: the kz-axis is on a much finer scale than the kx-axis)
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Experimental observation of reciprocal lattice rods

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Images are Interfering Diffracted Electrons


Understanding images formed in a TEM requires a complete understanding of the how electrons are diffracted, since images are just an interference pattern produced by the diffracted electrons.
Electron gun Condensor lens system

Object Objective lens Back-focal plane of objective lens

Diffraction plane

Image plane Image detector


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Effective Crystal potential U(r)


Energy-dependent effective Crystal potential U(r)

U (r ) =

2me 2m0 e V (r ) = V (r ) 2 h h2
In reciprocal space:

Ug =

rr 2m0 e 2m0 e N atom 2me 2ig r j Fg = Fg = f ( g )e h2 h2 h 2 j =1

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Excitation error (or deviation parameter sg)

Ewald sphere

sg
Shape transform at distance sg away from g
2

Structure factor at reciprocal lattice position Diffracted intensity at reflection g:

Excitation error sg:


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s r rg 2 r r 2 2 g + 2g k k (k + g ) sg = = 2k 2k

Ig = Ug

sin 2 (ts g )

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Mott-Bethe Formula
The Mott-Bethe formula relates electron scattering factors to X-ray scattering factors:

f e (q) =

|e| 16 2 0 q
2

[Z f X (q)]

Note, that fe(q) is proportional to q-2. This means that for low scattering angles (small q) electron scattering factors are much stronger than X-ray scattering factors.

These charge density maps of CuO2 were obtained by combining (low-resolution) electron diffraction and (high resolution) X-ray diffraction data.

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Thermal vibrations: The Debye-Waller factor


Phonon scattering produces diffuse scattering. This redistributes the diffracted intensity in the diffraction pattern, reducing intensity in the diffraction spots. Vibrating atoms have a time-varying potential

V (r , t ) = V (r + u (t )) = V (r ) + u (t ) dV (r ) u (t ) 2 d 2V (r ) + + ... dx u =0 dx 2 u =0 2!

The expectation value of the potential is then

V (r , t ) = V (r ) +

u 2 d 2V (r ) + ... 2! dx 2 u =0

This leads to an attenuation of the atomic scattering factor fe(q) by the Debye-Waller factor B:

f e (q) = f e (q) e

2 2 u 2 q 2

= f e (q ) e 0.25 Bq

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Notation
Coordinates in square brackets such as [100] denote a direction (in real space). Coordinates in angle brackets or chevrons such as <100> denote a family of directions which are equivalent due to symmetry operations (e.g. in a cubic system this could mean [100], [010], [001] or the negative of any of those directions). Miller indices in parentheses such as (100) denote a plane, in a cubic system the normal to the (hkl) plane is the direction [hkl]. Indices in curly brackets or braces such as {100} denote a family of plane normals which are equivalent due to symmetry operations. Negative indices are denoted by a horizontal line above _ them (e.g. [1-10] = [110]).
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Homework: Kinematic diffraction


Using WEBEMAPS*, simulate kinematic diffraction patterns of Si in the following zone axes: (001) (011) (111)

[001]
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[111]

[011]
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(*WEBEMAPS: http://emaps.mrl.uiuc.edu/emaps.asp)

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Homework: Kinematic diffraction patterns of Si


Model of Si ([001] projection) Unit cell indicated by red square. Space group: Fd-3m (227-2) [diamond structure] (001) Kinematic diffraction pattern. All odd diffraction spots are missing.

(110) kinematic diffraction pattern

(111) kinematic diffraction pattern

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Kinematic diffraction pattern of tilted Si (001)


Kikuchi lines

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animation of a Si (001) pattern tilted from zone axis up to 5 about the y-axis

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Definition: zone axis (u,v,w)


The zone axis of a given diffraction pattern is the reciprocal space vector normal 2 any of the reciprocal lattice vectors (or diffraction planes) in the pattern. Miller indices of the zone axis can be computed from the Miller indices of any two non co-linear reciprocal lattice vectors g*1=(h1,k1,l1) and g*2=(h2,k2,l2) represented in the diffraction pattern: u=k1l2-k2l1; v=l1h2-l2h1; w=h1k2-h2k1 ((uvw) must then be normalized, of course) Each reciprocal lattice vector in the pattern is normal to the zone axis and obeys the zone equation: hu+kv+lw = 0

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Kikuchi lines (and bands)


Kikuchi lines/bands help to determine the Laue center (exact zone axis center), and diffraction pattern symmetry when orienting a crystal and/or determining its symmetry. Kikuchi lines are caused by multiple scattering and require somewhat thicker specimen.

Laue center

Si (001) diffraction pattern


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Tilted 2 away from (001) zone axis


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Atomic vibrations: Phonons


Phonon modes (Eigenmodes of atomic vibrations) have wavelengths that are larger than a single unit cell (their wave numbers lie within the Brillouin Zone). Therefore they produce scattering also between Bragg spots. This diffuse (non-Bragg) scattering is called thermal diffuse scattering (TDS).

Atomic vibrations may be decomposed into phonon modes with characteristic wavelengths.
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Animation of phonon modes in a 1D lattice.

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Origin of Kikuchi lines


Diffusely scattered electrons (thermal diffuse or as a result of inelastic scattering) may have arbitrary transverse momentum (not limited to reciprocal lattice vectors, as Laue/Bragg-diffracted electrons). They therefore form a continuous background to a diffraction pattern. If any of these diffuse electrons Bragg-scatters elastically at a set of lattice planes, the scattered electrons are missing in the original direction of propagation as defiency lines and appear in the scattered direction as excess lines. Kikuchi bands may be simulated quantitatively by the frozen phonon approximation. Lattice planes Cone of directions that satisfy the Bragg condition

Deficiancy line
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Excess line
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Crystal systems: Pearson Symbol xYi


x: Abbreviation for crystal system a - anorthic (=triclinic) c - cubic h - hexagonal m - monoclinic o - orthorhombic t - tetragonal Y: Abbreviation for Bravais Lattice P - primitive lattice S - basal face centered lattice F - face centered lattice I - body centered lattice R - rhombohedral lattice i: Number of atoms per unit cell
Examples: Silicon: cF8 (face centered cubic, 8 atoms per unit cell)
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4-index Miller-Bravais indices (h,k,i,l)


The Hexagonal system: (a=bc, =90, =90, =120) Is commonly represented by 4 unit cell vectors: a1(=a), a2(=b), a3(=-[a1+a2]), and c Reciprocal lattice vectors are then: g=ha1+ka2+ia3+lc (i=-[h+k]) The third index (i) is often also omitted and given a .as place holder, as in g*=(hk.l) __ Example: [100] = [2110] MillerBravaisMiller MillerMiller-Bravais

h' = h i k'= k i l' = l


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1 h = (2h'k ' ) 3 1 k = (2k 'h' ) 3 1 i = (h'+ k ' ) 3 l = l'


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Stereographic projection

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Stereographic projection
The stereographic projection, as used in crystallography, projects the point of intersection of a given crystallographic direction (relative to the direction defining the pole of the projection) with the unit sphere on its equatorial plane. Directions in the northern (southern) hemisphere are projected towards the south pole and are represented by solid (empty) circles.

S
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Stereographic Projection: silicon (111)

3-fold symmetry Of {111} planes 4-fold symmetry of {100} zone axes

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Stereographic projection silicon (001)

4-fold symmetry of {100} zone axes

Tilting the (001) crystallographic direction to the north pole shows its fourfold symmetry

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Symmetry
Most crystal structures have symmetry. This means that if one performs certain mathematical operations (e.g. flipping, rotating, shifting) on any of the atomic positions within the unit cell, one obtains the atomic coordinates of another atom (of the same kind) in the same unit cell. A crystal structure has a given symmetry, if this symmetry operations is valid for all atoms of the unit cell simultaneously. Henn-egg white lyzozyme (PDB entry: 5LYZ) Space group: P43212
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2D point symmetries (10 2D point groups)


No symmetry 2-fold 3-fold 4-fold 6-fold

m = mirror axis mm = 2 mirror axes


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2D Point group identified from zone axis pattern

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Symmetry operations and Group theory


Mathematical definition: A group (G,*) is defined as a set G and a binary operation "*" such that 1. (Closure) for all a and b in G, a * b belong to G. 2. (Associativity) for all a, b and c in G, (a * b) * c = a * (b * c). 3. (Identity element) there is an element e in G such that for all a in G, e * a = a = a * e. 4. (Inverse element) for all a in G there is a b in G such that a * b = e = b * a. (Example: All integer numbers for a group (Z,+), since a+b=c is again an integer.) Crystallography: An object is said to have a certain symmetry, if the symmetry operation leaves the object invariant. Symmetry operations define a group. They may be applied in any sequence and will always produce a structure that is again part of the same symmetry group. Example: A cube may be rotated by 90 in any direction and as many times as one likes it will always look the same. This means that all rotations by 90 form a group of symmetry operations under which the cube is invariant. The inverse of a rotation is a rotation about the same angle but with opposite sign of the rotation angle.
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Symmetry operations
Operations of the first kind: Rotation (n-fold symmetry: =2/n, [n=1,2( ),3( ),4( ),6( )]) Translation Operations of the second kind: Pure reflection (about a given mirror plane) Inversion (about a given point, r -r) Combinations of above operations Rotoinversion: rotation + inversion Screw axis: rotation + translation Glide plane: reflection + translation
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International Point symmetry symbols


m: _ n (e.g. 3): _ n (e.g. 2): Rotation of order n=1,2,3,4, or 6 Reflection (about a mirror axis) Rotoinversion of order n

A given combination of all possible symmetry operations for a crystal structure also identifies the crystal system. _ Examples: - If the point symmetry is 1 or 1, the crystal system is triclinic (a). Any other crystal system would have higher symmetry. - If the point symmetry contains a rotation axis of order 6, the crystal system must be hexagonal (h).

_ 3
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_ 2
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Stereographic projection of different symmetries:

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International Space Group symbols


There are exactly 230 space groups, if the 32 possible point group symmetry operations (combinations of rotation, reflection, rotoinversion) are combined with screw axis and glide plane operations. nt (e.g. 21): Screw axis. The translation is along the axis of rotation, by the amount t/n unit cells. (example: two-fold rotation, followed by a translation of the lattice vector along the axis of rotation) Glide planes. A reflection and a translation of half a lattice vector parallel to the mirror plane. Diagonal glide. Glide along half the diagonal of a unit cell face or space diagonal. Diamond glide. Glide along a quarter of a unit cell face
or space diagonal (featured in the diamond structure as in silicon). Example: The Space group symbol P43212 (as in lyzozyme) means: - primitive lattice (second letter in Pearson smbol), - a 4-fold screw axis with translation vector along the screw axis, - a 2-fold srew axis with translation vector , and - a 2-fold rotation axis.
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a,b,c: n: d:

Matrix representation of symmetry operations


Any of the symmetry operations (rotation, translation, reflection, inversion and combinations thereof) may be expressed in the following equation:

x1 ' = D11 x1 + D12 x2 + D13 x3 + u1 x2 ' = D21 x1 + D22 x2 + D23 x3 + u2 x3 ' = D31 x1 + D32 x2 + D33 x3 + u3
D11 D W = 21 D 31 0 D12 D22 D32 0 D13 D23 D33 0 u1 u2 , then u3 1

If r=(x1,x2,x3,1) and

r r r ' = Wr
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Forbidden reflections

In Si (face-centered cubic): Why are only diffraction spots with even indices visible in the (001) zone axis ?

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Structure factor and symmetry operations


Structure factor computed from all atom positions:
N atoms i =1

F ( g hkl ) =

f ( g )e
i hkl

2 i ( hxi + kyi + lzi )

Translational symmetry operations may be combined into a single phase factor when computing the structure factor: Structure factor computed from atom positions in asymmetric unit + translational symmetry operations: N asym N trans 2i ( hx j + ky j + lz j ) 2i ( hxi + kyi + lzi ) hkl i hkl j =1 i =1

F (g ) =

f (g

)e

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Definition of unit cell: example Silicon


Atomic positions in silicon unit cell (in reduced coordinates): 0 0 0.5 0.5 .25 0.25 0.75 0.75 0 0.5 0 0.5 0.25 0.75 0.25 0.75 0 0.5 0.5 0 0.25 0.75 0.75 0.25 Definition of the asymmetric unit: (in reduced coordinates) 0 0.25 0 0.25 0 0.25

Definition of the fcc symmetry operations generates the remaining atomic positions: x x x+0.5 x+0.5 y y+0.5 y y+0.5 z z+0.5 z+0.5 z (no operation) (translation) (translation) (translation)

Alternatively: Define only one atom position and apply the diamond structure symmetry operations (see homework).

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Example FCC symmetry


F ( g hkl ) =
N asym i =1

f ( g )e
i hkl

2 i ( hxi + kyi + lz i )

[1 + e

i ( h + k )

+ ei ( h +l ) + ei ( k +l )

FCC symmetry operations: In the (001) Zone axis: l=0 h arbitrary k arbitrary x x x+0.5 x+0.5 y y+0.5 y y+0.5 z z+0.5 z+0.5 z

[1 + e

i ( h + k )

+ ei ( h ) + ei ( k )

4 h even, k even 0 h even, k odd = 0 h odd, k even 0 h odd, k odd


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Homework: Stereographic projection

1. Sketch the configuration (see examples to the right) used to produce the stereographic projection of the outline of the earths continents shown above. 2. What is the space group symbol of the diamond structure (as in silicon)

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